Data integration from pathology slides for quantitative imaging of multiple cell types within the tumor immune cell infiltrate

Background

Immune cell infiltrates (ICI) of tumors are scored by pathologists around tumor glands. To obtain a better understanding of the immune infiltrate, individual immune cell types, their activation states and location relative to tumor cells need to be determined. This process requires precise identification of the tumor area and enumeration of immune cell subtypes separately in the stroma and inside tumor nests. Such measurements can be accomplished by a multiplex format using immunohistochemistry (IHC).

Method

We developed a pipeline that combines immunohistochemistry (IHC) and digital image analysis. One slide was stained with pan-cytokeratin and CD45 and the other slide with CD8, CD4 and CD68. The tumor mask generated through pan-cytokeratin staining was transferred from one slide to the other using affine image co-registration. Bland-Altman plots and Pearson correlation were used to investigate differences between densities and counts of immune cell underneath the transferred versus manually annotated tumor masks. One-way ANOVA was used to compare the mask transfer error for tissues with solid and glandular tumor architecture.

Results

The overlap between manual and transferred tumor masks ranged from 20%–90% across all cases. The error of transferring the mask was 2- to 4-fold greater in tumor regions with glandular compared to solid growth pattern (p < 10^?6). Analyzing data from a single slide, the Pearson correlation coefficients of cell type densities outside and inside tumor regions were highest for CD4 + T-cells (r = 0.8), CD8 + T-cells (r = 0.68) or CD68+ macrophages (r = 0.79). The correlation coefficient for CD45+ T- and B-cells was only 0.45. The transfer of the mask generated an error in the measurement of intra- and extra- tumoral CD68+, CD8+ or CD4+ counts (p < 10^?10).

Conclusions

In summary, we developed a general method to integrate data from IHC stained slides into a single dataset. Because of the transfer error between slides, we recommend applying the antibody for demarcation of the tumor on the same slide as the ICI antibodies.

     

Evaluating Potential Effects of Exotic Freshwater Fish From Incomplete Species Presence–absence Data

Many freshwater ecosystems and biotas around the world are threatened with extinction. Freshwater fishes, for example, are the most endangered vertebrates after amphibians. Exotic fish are widely recognized as a major disturbance agent for native fish. Evaluating the ecological effects of invaders presents many challenges and the problem is greatly augmented in parts of the world where the native fauna is poorly known and where exotic species are commonplace. We use the fish community of Patagonia, a small and distinct native biota dominated by exotic salmonids, as a case study to ask: what can we learn about the effects of exotic fish species from fragmentary or partial data and how do such data point the way to what needs to be learned? We review the available data and literature on the distribution and status of native and introduced fish. We compile a novel regional presence/absence species database, build fish distribution maps, describe distribution patterns of native and exotic species, and identify critical information voids. A comparative review of literature from Patagonia and Australasia, where a similar native and exotic fish fauna is found, helps us to identify research priorities and promising management strategies for the conservation of native fish fauna. We conclude that the main challenge for fish conservation in Patagonia is to identify management strategies that could preserve native species while maintaining the quality of salmonid fisheries.     

Androgen deficiency in women

Androgens are defined as the steroids having a binding affinity of the androgen receptor. In the reproduction age a daily production of testosterone is equally divided between the ovaries and adrenal and local tissue conversion of androstenedione and DHEA. After menopause the 80% of testosterone is produced in ovaries, but majority of precursors for peripheral conversion is adrenal origin. Androgen receptors are present throughout in the body; over 200 cellular actions of androgens have been described. Androgenic action is determined by quantitative level of the androgen present in the circulation, its degree of binding to proteins, the degree of interconversion to other androgens and estrogens, and the biological potency and androgen receptor binding affinity of the androgen. The most common clinical symptoms of androgen deficiency are the reduction of sex motivation, sex fantasy, sex enjoyment, sex arousal, vaginal vasocongestion, but also reduction of pubic hair, bone mass, muscle mass, worsening of quality of life (mood, affect, energy), more frequent vasomotors symptoms, insomnia, depression, headache. All these signs and symptoms can be multifactorial. Most common conditions associated with hypoandrogenism in women are hypothalamic-pituitary abnormalities, lack or insufficiency of ovaries, adrenal insufficiency, glucocorticoid therapy, exogenous estrogen administration. Besides the clinical picture the free testosterone measuring is important for diagnosis. The method of choice of this measure is equilibrium dialysis assay. Despite of clinical importance of androgen insufficiency in women, none of methods of androgen substitution is approved by FDA.     

IFN-beta 2, B cell differentiation factor 2, or hybridoma growth factor (IL-6) is expressed and released by human epidermal cells and epidermoid carcinoma cell lines

IL-6, which is also known as IFN-beta 2, hybridoma growth factor, hepatocyte-stimulating factor, and B cell differentiation factor, mediates acute phase responses including fever, has lymphocyte-stimulating capacities, and antiviral activity. IL-6 is produced by monocytes, fibroblasts, certain lymphocytes, and various tumor cells. The present study demonstrates that this multifunctional cytokine is released also by normal human epidermal cells (EC) and human epidermoid carcinoma cell lines (A431, KB). Accordingly, supernatants derived from freshly isolated EC, long term keratinocyte cultures, A431, or KB cells stimulated the proliferation of a hybridoma growth factor/IL-6-dependent plasmacytoma cell line (B9). IL-6 constitutively was produced in the presence of serum proteins. The addition of IL-1 alpha, IL-1 beta, or the tumor promoter PMA significantly enhanced the synthesis and release of EC-derived IL-6 (EC-IL 6). Like monocyte or fibroblast-derived IL-6, EC-IL-6 exhibited Mr microheterogeneity within 21 and 28 kDa. Similarly in Western blotting experiments an antiserum directed against human rIFN-beta 2/IL-6 detected the different Mr forms of EC-IL-6. Moreover, this antiserum was able to block the B9 cell growth-promoting capacity of EC-IL-6 strongly suggesting that this EC-derived mediator is closely related, if not identical with IL-6. This was further confirmed by Northern blot analysis detecting IL-6 specific mRNA both in long term cultured keratinocytes and A431 cells by hybridization with a cDNA fragment encoding for B cell differentiating factor 2/IL-6. Therefore, in addition to the production of other cytokines as previously reported, EC and in particular keratinocytes also synthesize and release IL-6. This further supports the important regulatory role of the epidermis during the pathogenesis of inflammatory, autoimmune, and neoplastic diseases.     

Topographic determinants on cytochrome c. I. The complete antigenic structures of rabbit, mouse, and guanaco cytochromes c in rabbits and mice1.

Rabbit, mouse, and guanaco cytochromes c differ from each other by only two amino acid residues. The identification is described of all of the antigenic determinants of mouse and guanaco cytochrome c that elicit an antibody response in rabbits, and those of the rabbit and guanaco proteins that elicity antibodies in the mouse. All except one of these sites center around single amino acid residue differences between the antigen and the host cytochrome c. The corresponding antibody popylations bind only to the areas of the protein in which the substitutions occur. Such antigenic determinants manifested in rabbits by quanaco and mouse cytochromes c are centered around residues 62 and 89, and residues 44 and 89, respectively. Similarly, the mouse recognizes sites containing residues 44 and 62 in guanaco cytochrome c, and residues 44 and 89 in rabbit cytochrome c. In none of these instances has a change in sequence failed to produce an antibody response. Each of these determinants appears to elicit and bind to its antibody, independently of other determinants present on the protein. In addition, two different autoantigenic responses have been detected. The antibodies produced against the determinant formed by glutamyl residue 62 of the guanaco protein in both rabbits and mice, the cytochromes c of which carry an aspartyl residue in that position, also bind to the aspartyl-containing region but with lower affinity. However, mouse and rabbit cytochrome c also elicit antibodies to the area of residue 62 in rabbits and mice, respectively, and these antibodies still bind more strongly to the glutamyl-than to the aspartyl-containing determinant. This last response occurs only when there are residue substitutions elsewhere in the molecule, because mice and rabbits fail to respond to their own cytochrome c. Antibodies produced in mice against the change from alanyl to valyl residue 44 by rabbit and guanaco cytochromes c also bind to the alanyl-containing determinant, except less tightly than to the valyl region. Conversely, antibodies raised in rabbits against the change from valyl to alanyl residue 44 only bind to this region when it carries an alanine. It is suggested that antigenic determinants that arise as a result of amino acid residue substitutions between the immunizing and the corresponding host protein, without a change in the spatial arrangement of the polypeptide backbone, be termed topographic determinants.     

Comparison of potential protective effects of melatonin, indole-3-propionic acid, and propylthiouracil against lipid peroxidation caused by potassium bromate in the thyroid gland

Potassium bromate (KBrO3) is a prooxidant and carcinogen, inducing thyroid tumors. Melatonin and indole-3-propionic acid (IPA) are effective antioxidants. Some antioxidative effects of propylthiouracil (PTU)--a thyrostatic drug--have been found. The aim of the study was to compare protective effects of melatonin, IPA, and PTU against lipid peroxidation in the thyroids, collected from rats treated with KBrO3, and in homogenates of porcine thyroids, incubated in the presence of KBrO3. Wistar rats were administered KBrO3 (110 mg/kg b.w., i.p., on the 10th day of the experiment) and/or melatonin, or IPA (0.0645 mmol/kg b.w., i.p., twice daily, for 10 days), or PTU (0.025% solution in drinking water, for 10 days). Homogenates of porcine thyroids were incubated for 30 min in the presence of KBrO3 (5 mM) plus one of the antioxidants: melatonin (0.01, 0.1, 0.5, 1.0, 5.0, 7.5 mM), or IPA (0.01, 0.1, 0.5, 1.0, 5.0, 7.5, 10.0 mM), or PTU (0.01, 0.1, 0.5, 1.0, 5.0, 7.5, 10.0 mM). The level of lipid peroxidation products (MDA + 4-HDA) was measured spectrophotometrically in thyroid homogenates. In vivo pretreatment with either melatonin or with IPA or with PTU decreased lipid peroxidation caused by KBrO3--injections in rat thyroid gland. Under in vitro conditions, PTU (5.0, 7.5, and 10.0 mM), but neither melatonin nor IPA, reduced KBrO3-related lipid peroxidation in the homogenates of porcine thyroids. In conclusion, melatonin and IPA may be of great value as protective agents under conditions of exposure to KBrO3.     

The many faces of protease-protein inhibitor interaction

Proteases and their natural protein inhibitors are among the most intensively studied protein-protein complexes. There are about 30 structurally distinct inhibitor families that are able to block serine, cysteine, metallo- and aspartyl proteases. The mechanisms of inhibition can be related to the catalytic mechanism of protease action or include a mechanism-unrelated steric blockage of the active site or its neighborhood. The structural elements that are responsible for the inhibition most often include the N- or the C-terminus or exposed loop(s) either separately or in combination of several such elements. During complex formation, no major conformational changes are usually observed, but sometimes structural transitions of the inhibitor and enzyme occur. In many cases, convergent evolution, with respect to the inhibitors' parts that are responsible for the inhibition, can be inferred from comparisons of their structures or sequences, strongly suggesting that there are only limited ways to inhibit proteases by proteins.