Involvement of centrosomes in nuclear irregularity of thyroid carcinoma cells

Artificial Intelligence Detected the Relationship Between Nuclear Morphological Features and Molecular Abnormalities of Papillary Thyroid Carcinoma

Papillary thyroid carcinoma (PTC) is the most common type of thyroid carcinoma and has characteristic nuclear features. Genetic abnormalities of PTC affect recent molecular target therapeutic strategy towards RET-altered cases, and they affect clinical prognosis and progression. However, there has been insufficient objective analysis of the correlation between genetic abnormalities and nuclear features. Using our newly developed methods, we studied the correlation between nuclear morphology and molecular abnormalities of PTC with the aim of predicting genetic abnormalities of PTC. We studied 72 cases of PTC and performed genetic analysis to detect BRAF p.V600E mutation and RET fusions. Nuclear features of PTC, such as nuclear grooves, pseudo-nuclear inclusions, and glassy nuclei, were also automatically detected by deep learning models. After analyzing the correlation between genetic abnormalities and nuclear features of PTC, logistic regression models could be used to predict gene abnormalities. Nuclear features were accurately detected with over 0.90 of AUCs in every class. The ratio of glassy nuclei to nuclear groove and the ratio of pseudo-nuclear inclusion to glassy nuclei were significantly higher in cases that were positive for RET fusions (p = 0.027, p = 0.043, respectively) than in cases that were negative for RET fusions. RET fusions were significantly predicted by glassy nuclei/nuclear grooves, pseudo-nuclear inclusions/glassy nuclei, and age (p = 0.023). Our deep learning models could accurately detect nuclear features. Genetic abnormalities had a correlation with nuclear features of PTC. Furthermore, our artificial intelligence model could significantly predict RET fusions of classic PTC.

Three-dimensional structural analysis of papillary thyroid carcinoma nuclei with serial block-face scanning electron microscopy (SBF-SEM)

Nuclear morphology of carcinoma cells is critical for the pathological diagnosis of papillary thyroid carcinoma (PTC). However, three-dimensional architecture of PTC nuclei is still elusive. In this study, we analyzed the three-dimensional ultrastructure of PTC nuclei using serial block-face scanning electron microscopy which takes advantage of the high-throughput acquisition of serial electron microscopic images and three-dimensional reconstruction of subcellular structures. En bloc-stained and resin-embedded specimens were prepared from surgically removed PTCs and normal thyroid tissues. We acquired two-dimensional images from serial block-face scanning electron microscopy and reconstructed three-dimensional nuclear structures. Quantitative comparisons showed that the nuclei of carcinoma cells were larger and more complex than those of normal follicular cells. The three-dimensional reconstruction of carcinoma nuclei divided intranuclear cytoplasmic inclusions into "open intranuclear cytoplasmic inclusions" connecting to cytoplasm outside the nucleus and "closed intranuclear cytoplasmic inclusions" without that connection. Cytoplasm with abundant organelles was observed in open inclusions, but closed inclusions contained fewer organelles with or without degeneration. Granules with a dense core were only observed in closed inclusions. Our observations suggested that open inclusions originate from nuclear invaginations, and disconnection from cytoplasm leads to closed inclusions.

Use of Artificial Intelligence for the Interpretable Prediction of the Pathologic Diagnosis and Molecular Abnormalities of Flat Urothelial Lesions

Flat urothelial lesions are important because of their potential for carcinogenesis and development into invasive urothelial carcinomas. However, it is difficult for pathologists to detect early flat urothelial changes and accurately diagnose flat urothelial lesions. To predict the pathologic diagnosis and molecular abnormalities of flat urothelial lesions from pathologic images, artificial intelligence with an interpretable method was used. Next-generation sequencing on 110 hematoxylin and eosin-stained slides of normal urothelium and flat urothelial lesions, including atypical urothelium, dysplasia, and carcinoma in situ, detected 17 types of molecular abnormalities. To generate an interpretable prediction, a new method for segmenting urothelium and a new pathologic criteria-based artificial intelligence (PCB-AI) model was developed. κ Statistics and accuracy measurements were used to evaluate the ability of the model to predict the pathologic diagnosis. The likelihood ratio test was performed to evaluate the logistic regression models for predicting molecular abnormalities. The diagnostic prediction of the PCB-AI model was almost in perfect agreement with the pathologists' diagnoses (weighted κ = 0.98). PCB-AI significantly predicted some molecular abnormalities in an interpretable manner, including abnormalities of TP53 (P = 0.02), RB1 (P = 0.04), and ERCC2 (P = 0.04). Thus, this study developed a new method of obtaining accurate urothelial segmentation, interpretable prediction of pathologic diagnosis, and interpretable prediction of molecular abnormalities.

Pathologic Image Classification of Flat Urothelial Lesions Using Pathologic Criteria-Based Deep Learning

OBJECTIVES

Pathologic diagnosis of flat urothelial lesions is subject to high interobserver variability. We expected that deep learning could improve the accuracy and consistency of such pathologic diagnosis, although the learning process is a black box. We therefore propose a new approach for pathologic image classification incorporating the diagnostic process of the pathologist into a deep learning method.

METHODS

A total of 267 H&E-stained slides of normal urothelium and urothelial lesions from 127 cases were examined. Six independent convolutional neural networks were trained to classify pathologic images according to six pathologic criteria. We then used these networks in the main training for the final diagnosis.

RESULTS

Compared with conventional manual analysis, our method significantly improved the classification accuracy of images of flat urothelial lesions. The automated classification showed almost perfect agreement (weighted κ = 0.98) with the consensus reading. In addition, our approach provides the advantages of reliable diagnosis corresponding to histologic interpretation.

CONCLUSIONS

We used deep learning to establish an automated subtype classifier for flat urothelial lesions that successfully combines traditional morphologic approaches and complex deep learning to achieve a learning mechanism that seems plausible to the pathologist.

Microtubule-organizing center-mediated structural atypia in low- and high-grade urothelial carcinoma

Urothelial carcinoma (UC) comprises two subtypes, low grade (LG-UC) and high grade (HG-UC), with different pathological and clinical behavior. LG-UC and HG-UC are classified based on cellular and structural atypia of pathological findings. The mechanisms responsible for maintaining structural atypia, such as the disturbance of nuclear polarity, remain unclear. In this study, we studied microtubule-organizing center (MTOC)-mediated nuclear polarity in UC subtypes. We evaluated six cases with normal urothelium (NU), 10 LG-UC cases, and 10 HG-UC cases by double immunofluorescence staining of γ-tubulin as a marker of MTOC and E-cadherin as a marker of each cell border. The number and position of γ-tubulin dots of expression in more than 100 cells per case were assessed using the spatial relationship with the nucleus and surface-basal axis. We found one γ-tubulin dot in most normal and tumor cells, and more than two γ-tubulin dots in 4.6% of NU cells, 6.1% of LG-UC cells, and 9.8% of HG-UC cells. More than three γ-tubulin dots were found only in 1.2% of HG-UC cells. Surface side positioning of γ-tubulin was found in 77.4% of normal urothelial cells, 63.8% of LG-UC cells, and 39.2% of HG-UC cells, whereas aberrant lateral and basal side positioning of γ-tubulin was found in 22.6% of normal urothelial cells, 36.1% of LG-UC cells, and 60.8% of HG-UC cells. We concluded that numerical and positional aberrations of MTOC in UC cases were strongly correlated with both cellular and structural atypia as well as abnormal cell proliferation.

Correlation analysis of nuclear morphology, cytokeratin and Ki-67 expression of urothelial carcinoma cells

We aimed to delineate the morphogenesis of aberrant nuclear features of urothelial carcinoma (UC) cells in association with cytokeratin (CK) expression patterns and cell proliferation activity. Correlation analysis of the nuclear area by morphometry and the expression patterns of CK5, CK20 and Ki-67 by triple immunofluorescence analysis was applied to 1699 cells from five low-grade and seven high-grade cases of UC. The majority of UC cells showed aberrant cellular differentiation represented by abnormal CK expression patterns of CK5+ / CK20+ (40.5%) or CK5- / CK20+ (56.0%). CK5+ / CK20- cells, a phenotype of cancer stem/progenitor cells, represented a very small population (1.9%) and showed a low proliferation activity. Ki-67+ cells showed a significantly different CK expression pattern compared with that of Ki-67(-) cells. The nuclear areas of CK5- / CK20+ cells (71.3 ± 25.9 μm2) were significantly larger than those of CK5+ / CK20+ cells (66.6 ± 25.5 μm2). Negativity for CK5 was related to the grade of UC and an increased number of CK5- / CK20+ / Ki-67+ cells was related to a higher malignant potential. We conclude the nuclear morphology is related to cell differentiation represented by CK expression and cell proliferative activity.

Microtubule-organizing center-mediated nuclear polarity in various normal and neoplastic human tissues

Nuclear polarity is characterized by intracytoplasmic nuclear positioning and alignment in the tissue. The mechanisms responsible for maintaining nuclear polarity in normal cells and its disturbance in neoplastic cells are not understood. We studied microtubule-organizing center (MTOC) positioning-mediated nuclear polarity in various normal and neoplastic human tissues, as well as in cultured cells. To visualize the MTOC in cells, gamma-tubulin and pericentrin were immunohistochemically stained by fluorescence and non-fluorescence methods. Position of MTOC in normal and neoplastic tissue was assessed by spatial relationship with nucleus and apico-basal axis. We found MTOC positioning to be related to morphogenesis in various normal and neoplastic human tissues, as well as in cultured cells. MTOC positions were different between two-dimensional cultured isolated cells and three-dimensional cultured gland-formed cells. The MTOC position was specific depending on the cell type in the tissue structure. In particular, glandular and urothelial epithelium had a strong relationship with preservation of nuclear polarity and MTOC positioning. Carcinoma cells showed an irregular position or absence of the MTOC depending on poorer differentiation and higher grade of carcinomas. In conclusion, the position of the MTOC affects regulation of nuclear polarity and morphogenesis of normal and pathological tissue structure.

The diagnostic pathology of the nuclear envelope in human cancers

Cancer is still diagnosed on the basis of altered tissue and cellular morphology. The criteria that pathologists use for diagnosis include many morphologically distinctive alterations in the nuclear envelope (NE). With the expectation that diagnostic NE changes will have biological relevance to cancer, a classification of the various types of NE structural changes into three groups is proposed. The first group predicts chromosomal instability. The changes in this group include pleomorphism of lamina size and shape, as if constraints to maintain a spherical shape were lost. Also characteristic of chromosomal instability are the presence of micronuclei, a specific structural feature likely related to the newly described physiology of chromothripsis. The second group is predicted to be functionally important during clonal evolution, because the NE changes in this group are conserved during the clonal evolution of genetically unstable tumors. Two examples of this group include increased ratio of nuclear volume to cytoplasmic volume and the relatively fragile nuclei of small-cell carcinomas. The third and most interesting group develops in a near-diploid, genetically stable background. Many of these (perhaps ultimately all) are directly related to the activation of particular oncogenes. The changes in this group so far include long inward folds of the NE and spherical invaginations of cytoplasm projecting partially into the nucleus ("intranuclear cytoplasmic inclusions"). This group is exemplified by papillary thyroid carcinoma in which RET and TRK tyrosine kinases, and probably B-Raf mutations, directly lead to diagnostic longitudinal folds of the lamina ("nuclear grooves") and intranuclear cytoplasmic inclusions. B-Raf activation may also be linked to intranuclear cytoplasmic inclusions in melanoma and to nuclear grooves in Langerhans cell histiocytosis. Nuclear grooves in granulosa cell tumor may be related to mutations in the FOXL2 oncogene. Uncovering the precise mechanistic basis for any of these lamina alterations would provide a valuable objective means for improving diagnosis, and will likely reflect new types of functional changes, relevant to particular forms of cancer.

MUC1 expression in papillary thyroid carcinoma is associated with BRAF mutation and lymph node metastasis; the latter is the most important risk factor of relapse

BACKGROUND

The incidence of papillary thyroid carcinoma (PTC) has increased over the past 30 years in Western countries. PTC is usually associated with a good prognosis, but there is a wide range of aggressiveness, and some patients develop distant metastasis and/or resistance to standard treatment. Early identification of these high-risk tumors is a current challenge for appropriate patient management. MUC1 expression has been studied previously in thyroid cancer, but its prognostic value remains controversial. Here, we correlated MUC1 expression in PTC with clinical and pathological features and with the presence of the BRAF(V600E) mutation.

METHODS

We performed a clinical and morphological analysis of 190 thyroid tumors (95 PTCs and 95 adenomas). MUC1 immunohistochemistry was carried out on a tissue microarray using different antibodies. The presence of the BRAF(V600E) mutation was investigated by pyrosequencing. MUC1 mRNA levels were assessed by quantitative reverse transcription polymerase chain reaction on a subset of PTC.

RESULTS

MUC1 expression was observed in 49% of PTCs and was found to correlate with the presence of papillary architecture, a stromal lymphoid infiltrate, aggressive histological subtypes, extrathyroidal extension, lymph node metastasis, nuclear pseudoinclusions, lymphovascular invasion, and the presence of the BRAF(V600E) mutation (p<0.0001). MUC1 was abundant in nuclear pseudoinclusions. Multivariate analysis showed a strong association of MUC1 expression with the presence of the BRAF(V600E) mutation and lymph node metastasis (p<0.0001). Lymph node metastasis was the most important risk factor of relapse.

CONCLUSIONS

Our study shows an association between MUC1 expression and the presence of the BRAF(V600E) mutation in PTC. Analysis of MUC1 expression could improve the risk stratification of PTCs.

Pitfalls in the diagnosis of follicular epithelial proliferations of the thyroid

The diagnosis of follicular epithelial neoplasms is an area of controversy. We provide our experience with common problems that practising pathologists face when confronted with follicular epithelial proliferations. One of the major issues is the recognition of the diagnostic nuclear features of papillary thyroid carcinoma and reactive cytologic atypia. We discuss the definitions of capsular invasion, vascular invasion, and extrathyroidal extension and their implications in cancer diagnosis and staging. We propose unified terminology for benign follicular epithelial proliferations in the setting of multinodular goiter. We also review challenges related to oncocytic change, malignant transformation in benign nodules, focal dedifferentiation, and the application of ancillary tools in thyroid pathology. We believe that this review contains comprehensive and up to date information that will be of value to pathologists who practice surgical pathology of thyroid.

Significant Correlation between Chromosomal Aberration and Nuclear Morphology in Urothelial Carcinoma

We aimed to identify whether there is any correlation between chromosomal/genetic changes, nuclear morphology and the histological grade of urothelial carcinomas of the urinary bladder. Morphometry and multicolour fluorescence in situ hybridisation (FISH) techniques were applied to 250 cells in five low-grade cases and 350 cells in seven high-grade cases of urothelial carcinoma. Compared with low-grade carcinomas, most high-grade cases showed larger and more variable nuclear size, more frequent polysomy of centromere enumeration probes (CEPs) 3, 7 and 17, and the loss of the 9p21 locus. The number of CEP signals in cells was increased as the nuclear area of the cells became larger. Cells with gains in two or more types of CEP had significantly larger nuclei than cells with normal FISH signal patterns. In conclusion, the present study indicates that there was a correlation between nuclear morphology and chromosomal/genetic changes which were related to histological grading. Thus, we show that differences in the chromosomal/genetic aberrations present in low- and high-grade tumours can affect not only nuclear morphology but also the histopathological and clinical behaviour of urothelial carcinomas.

Centrosomal and mitotic abnormalities in cell lines derived from papillary thyroid cancer harboring specific gene alterations

BACKGROUND

Differentiated thyroid carcinoma offers a good model to investigate the possible correlation between specific gene mutations and chromosome instability. Papillary thyroid neoplasms are characterized by different mutually exclusive genetic alterations, some of which are associated with aneuploidy and aggressive phenotype.

RESULTS

We investigated the centrosome status and mitotic abnormalities in three thyroid carcinoma-derived cell lines, each maintaining the specific, biologically relevant gene alteration harbored by the parental tumors: RET/PTC1 rearrangement in TPC1; heterozygous and homozygous BRAFV600E mutation in K1 and in B-CPAP, respectively. B-CPAP cells showed a statistically significant (P < 0.01) higher frequency of abnormal mitotic figures compared to TPC1 and K1 cells.

CONCLUSIONS

Our data indicate that RET/PTC1 oncogenic activity is not related to mitotic chromosome impairment and missegregation whereas, based on the consistent difference in types/frequencies of centrosome and spindle abnormalities observed between K1 and B-CPAP cells, the hetero/homozygous allelic status of BRAFV600E mutation seems to be not irrelevant in respect to chromosomal instability development.