Spatial heterogeneity of cancer associated protein expression in immunohistochemically stained images as an improved prognostic biomarker.

The identification of new tumor biomarkers for patient stratification before therapy, for monitoring of disease progression, and for characterization of tumor biology plays a crucial role in cancer research. The status of these biomarkers is mostly scored manually by a pathologist and such scores typically, do not consider the spatial heterogeneity of the protein's expression in the tissue. Using advanced image analysis methods, marker expression can be determined quantitatively with high accuracy and reproducibility on a per-cell level. To aggregate such per-cell marker expressions on a patient level, the expression values for single cells are usually averaged for the whole tissue. However, averaging neglects the spatial heterogeneity of the marker expression in the tissue. We present two novel approaches for quantitative scoring of spatial marker expression heterogeneity. The first approach is based on a co-occurrence analysis of the marker expression in neighboring cells. The second approach accounts for the local variability of the protein's expression by tiling the tissue with a regular grid and assigning local spatial heterogeneity phenotypes per tile. We apply our novel scores to quantify the spatial expression of four different membrane markers, i.e., HER2, CMET, CD44, and EGFR in immunohistochemically (IHC) stained tissue sections of colorectal cancer patients. We evaluate the prognostic relevance of our spatial scores in this cohort and show that the spatial heterogeneity scores clearly outperform the marker expression average as a prognostic factor (CMET: p-value=0.01 vs. p-value=0.3).

Subtyping Of Triple Negative Breast Carcinoma On The Basis Of RTK Expression.

Background: "Triple-negative breast cancers" (TNBC) comprise a heterogeneous group of about 15% of invasive BCs lacking the expression of estrogen and progesterone receptors (ER, PR) and the expression of HER2 (ERBB2) and are therefore no established candidates for targeted treatment options in BC, i.e., endocrine and anti-HER2 therapy. The aim of the present study was to use gene expression profiling and immunohistochemical (IHC) characterization to identify receptor tyrosine kinase (RTK) profiles that would allow patient stratification for the purposes of target-oriented personalized tumor therapy in TNBC. Methods: Twenty-nine cases of TNBC selected according to routine diagnostic IHC/cytogenetic criteria were examined by reverse transcription polymerase chain reaction (RT-PCR). RTK mRNA expression profiles were generated for a total of 31 tumor-relevant biomarkers, mainly belonging to the IGF- and EGF-receptor families but also including biomarkers related to downstream signaling. Protein expression of selected biomarkers was investigated by IHC. Results: Hierarchical cluster analysis revealed a dichotomous differentiation pattern amongst TNBCs. A significant difference in gene expression was observed for 16 of the 31 RTK-associated tumor relevant biomarkers between the two newly identified TNBC subgroups. The findings were verified at the posttranslational level by the IHC data. The RTKs HER4, IGF-1R and IGF-2R and the hormone receptors ER and PR below the IHC detection limit play a central role in the differentiation of the two TNBC subgroups. Observed survival was reported as Kaplan-Meier estimates and point towards an improved survival of patients with RTK-high with superior three-year survival rate of 100% compared to RTK-low gene signatures with superior three-year survival rate of 60% (log-rank test, p-value = 0.022). Conclusion: Gene-expression and IHC analysis of the EGF and IGF receptor families and biomarkers associated with downstream signaling point to the existence of two distinct TNBC subtypes. The RTKs HER4, IGF-1R, IGF-2R and the hormone receptors ER and PR appear to be of particular importance here. Based on survival analysis the differentiation of TNBC with RTK-high and RTK-low gene signatures seems to be of prognostic relevance. Additionally, correlation analysis of the relationship between RTKs and ER suggests co-regulatory mechanisms that may have potential significance in new therapeutic approaches.

Tissue Phenomics for prognostic biomarker discovery in low- and intermediate-risk prostate cancer.

Tissue Phenomics is the discipline of mining tissue images to identify patterns that are related to clinical outcome providing potential prognostic and predictive value. This involves the discovery process from assay development, image analysis, and data mining to the final interpretation and validation of the findings. Importantly, this process is not linear but allows backward steps and optimization loops over multiple sub-processes. We provide a detailed description of the Tissue Phenomics methodology while exemplifying each step on the application of prostate cancer recurrence prediction. In particular, we automatically identified tissue-based biomarkers having significant prognostic value for low- and intermediate-risk prostate cancer patients (Gleason scores 6-7b) after radical prostatectomy. We found that promising phenes were related to CD8(+) and CD68(+) cells in the microenvironment of cancerous glands in combination with the local micro-vascularization. Recurrence prediction based on the selected phenes yielded accuracies up to 83% thereby clearly outperforming prediction based on the Gleason score. Moreover, we compared different machine learning algorithms to combine the most relevant phenes resulting in increased accuracies of 88% for tumor progression prediction. These findings will be of potential use for future prognostic tests for prostate cancer patients and provide a proof-of-principle of the Tissue Phenomics approach.

KRAS, BRAF genotyping reveals genetic heterogeneity of ovarian borderline tumors and associated implants.

BACKGROUND: Patients diagnosed for a serous ovarian borderline tumor (s-BOT) typically present with an excellent clinical outcome. However there have been controversies concerning the prognostic impact of so-called implants, an extra ovarian spread occurring alongside the s-BOT in certain cases. It remains obscure whether these implants actually resemble metastasis owning the same genetic pattern as the ovarian primary or whether they develop independently. METHODS: The current study, in the aim of further clarifying the genetic origin of implants, assessed BRAF/KRAS hot spot mutations and the p53/p16INK4a immunophenotype of s-BOTs and corresponding implants (n=49) of 15 patients by pyro-sequencing and immunostaining, respectively. RESULTS: A significant proportion of both s-BOTs and implants showed KRAS or BRAF mutation and though p16INK4a was found to be abundantly expressed, p53 immunoreactivity was rather low. When genotypes of BRAF/KRAS mutated s-BOTs and corresponding implants were compared no patient presented with a fully matching mutation profile of s-BOTs and all corresponding implants. CONCLUSIONS: The current study reveals genetic heterogeneity of s-BOTs and implants, as none of the markers examined showed constant reciprocity. Hence, our findings may assist to explain the different clinical presentation of s-BOTs and implants and might encourage to applying more individualized follow up protocols.

Aberrant expression of CD30 in neoplastic mast cells in high-grade mastocytosis.

Systemic mastocytosis either presents as aggressive neoplasm with short survival time or indolent systemic mastocytosis with normal life expectancy. In both instances, neoplastic mast cells usually harbor the D816V-mutated variant of KIT. Phenotypically, mast cells in systemic mastocytosis usually express CD25. However, no robust marker that discriminates between aggressive and indolent variants of systemic mastocytosis has been identified yet. We here report that CD30, also known as Ki-1 antigen, is expressed in neoplastic mast cells in a majority of patients with advanced systemic mastocytosis (11/13, 85%), whereas in most patients with indolent systemic mastocytosis (12/45, 27%; P<0.001), only a few if any mast cells stained positive for CD30. These results could be confirmed by TissueFAXS analysis in subsets of patients with indolent systemic mastocytosis (n=7) and advanced systemic mastocytosis (n=4; P=0.008). The mast cell leukemia cell line HMC-1, derived from a patient with aggressive systemic mastocytosis also expressed the CD30 protein. In addition, we were able to detect CD30 mRNA in HMC-1 cells as well as in bone marrow biopsy samples in patients with systemic mastocytosis. In contrast, CD30 transcripts could not be detected in bone marrow biopsies in cases of reactive mast cell hyperplasia and in various other myeloid neoplasms. In conclusion, CD30 is preferentially expressed in neoplastic mast cells in advanced mast cell neoplasms. Upregulated expression of CD30 in advanced systemic mastocytosis may thus be employed as a potential marker for grading systemic mastocytosis in hematopathology.

Broad, ectopic expression of the sperm protein PLCZ1 induces parthenogenesis and ovarian tumours in mice.

Mammalian metaphase II (mII) exit and embryogenesis are induced at fertilisation by a signal thought to come from the sperm protein, phospholipase C-zeta (PLCZ1). Meiotic progression can also be triggered without sperm, as in parthenogenesis, although the classic mouse in vivo parthenogenetic model, LT/Sv, fails in meiosis I owing to an unknown molecular etiology. Here, we dissect PLCZ1 specificity and function in vivo and address its ability to interfere with maternal meiotic exit. Wild-type mouse Plcz1 expression was restricted to post-pubertal testes and the brains of both sexes, with region-specifying elements mapping to a 4.1 kb Plcz1 promoter fragment. When broad ectopic PLCZ1 expression was forced in independent transgenic lines, they initially appeared healthy. Their oocytes underwent unperturbed meiotic maturation to mII but subsequently exhibited autonomous intracellular free calcium oscillations, second polar body extrusion, pronucleus formation and parthenogenetic development. Transfer of transgenic cumulus cell nuclei into wild-type oocytes induced activation and development, demonstrating a direct effect of PLCZ1 analogous to fertilisation. Whereas Plcz1 transgenic males remained largely asymptomatic, females developed abdominal swellings caused by benign ovarian teratomas that were under-represented for paternally- and placentally-expressed transcripts. Plcz1 was not overexpressed in the ovaries of LT/Sv or in human germline ovarian tumours. The narrow spectrum of PLCZ1 activity indicates that it is modulated by tissue-restricted accessory factors. This work characterises a novel model in which parthenogenesis and tumourigenesis follow full meiotic maturation and are linked to fertilisation by PLCZ1.

Acute blood neutrophilia induced by short-term compost dust exposure in previously unexposed healthy individuals.

OBJECTIVES: Systemic effects of organic dust inhalation have been described in farming environments. The purpose of this study was to examine whether a single exposure at a biowaste composting facility could also exert systemic effects in healthy volunteers not previously exposed to organic dust from such facilities. METHODS: Seventeen subjects (age 20-35 years) were exposed to organic dust for 2 h (exposure day) during moderate exercise; 12 of these subjects also took part in a control experiment (control day). Spirometry was performed before and immediately after the exposure. White blood cell counts and levels of tumor-necrosis factor-alpha (TNF-alpha), interleukin-1beta (IL-1beta) and interleukin-6 (IL-6) in peripheral blood were determined before and 3 h after exposure. RESULTS: Exposures did not result in significant changes in lung function or blood cytokine levels. In contrast, the number and percentage of neutrophils increased during the exposure day [median (range) percent change of percentages 14 (-2; 67) %; P=0.002], but not during the control day [5 (-22; 35) %; P=0.66). Furthermore, there was a decrease in the number and percentage of eosinophils during the exposure day [-47 (-57; 0.0) %; P=0.002], whereas the change during the control day was smaller [-8 (-56; 71) %; P=0.68]. CONCLUSION: Short-term exposure of healthy, young subjects to organic dust from composting facilities had opposite effects on the numbers of blood neutrophils and blood eosinophils. These effects, though mild, suggest that even during a limited period of moderate work a sufficient amount of bioactive material can be deposited in the lung to elicit acute systemic alterations.