Using Feature Extraction From Deep Convolutional Neural Networks for Pathological Image Analysis and Its Visual Interpretability

This dissertation presents a computer-aided diagnosis (CAD) system using deep learning approaches for lesion detection and classification on whole-slide images (WSIs) with breast cancer. The deep features being distinguishing in classification from the convolutional neural networks (CNN) are demonstrated in this study to provide comprehensive interpretability for the proposed CAD system using the domain knowledge in pathology. In the experiment, a total of 186 slides of WSIs were collected and classified into three categories: Non-Carcinoma, Ductal Carcinoma in Situ (DCIS), and Invasive Ductal Carcinoma (IDC). Instead of conducting pixel-wise classification (segmentation) into three classes directly, a hierarchical framework with the multi-view scheme was designed in the proposed system that performs lesion detection for region proposal at higher magnification first and then conducts lesion classification at lower magnification for each detected lesion. The majority voting scheme was adopted to improve the error tolerance of the system in lesion-wise prediction. For all collected 186 slides, the slide-wise prediction accuracy rate strikes to 95.16% (177/186) in binary classification to predict carcinoma (malignant) or non-carcinoma (benign), and the sensitivity for cases with carcinoma reaches 96.36% (106/110). In multi-classification, the accuracy rate is 92.47% (172/186) when predicting Non-Carcinoma, DCIS, and IDC for each slide. Most importantly, the interpretability for the mechanism of the proposed CAD system is provided from the pathological perspective. The experimental results show that the morphological characteristics and co-occurrence properties learned by the deep learning models for lesion detection and classification meet the clinical rules in diagnosis. Accordingly, the pathological interpretability of the deep features not only enhances the reliability of the proposed CAD system to gain acceptance from medical specialists, but also facilitates the development of deep learning frameworks for various tasks in pathology

Argyrophilic nucleolar organizer regions and bromodeoxyuridine and h3-thymidine labelling indices in colorectal cancer

The count of argyrophilic nucleolar organizer regions (AgNORs) has been proposed as a useful method for evaluating cell replication in human tumours. The current study was undertaken to compare AgNOR values in colorectal cancers with two better established methods for investigating cell proliferation such as bromodeoxyuridine (BrdUrd) and (3)[H]-thymidine ((3)[H]dT) labelling indices (LIs). Because some concern still exists regarding accuracy and reproducibility of AgNOR quantifying methods, we carried out a control study by independently repeating the same measurements (number, area and area per silver-stained NOR particle) in two centres with different operators and computer-assisted image analysers on 40 colorectal carcinomas. AgNOR values recorded in the two centres were strictly correlated (r = 0.75; P < 0.001 for number; r = 0.62, P < 0.01 for area; r = 0.63, P < 0.001 for area per silver-stained NOR particle) and the range of values were almost identical, Then, AgNOR values were compared with BrdUrd and (3)[H]dT LIs, respectively obtained by in vivo incorporation and in vitro incubation in the same series of colorectal carcinomas. No correlation was found between AgNOR values and BrdUrd or (3)[H]dT LIs. BrdUrd and (3)[H]dT LIs were instead reciprocally significantly correlated, No evident correlation was seen between LIs or AgNOR values and clinico-pathological parameters of the tumour. In conclusion, in colorectal neoplasms, AgNOR values did not appear to relate with more direct parameters of cell proliferation. It follows that AgNOR reliability as a biomarker of cell proliferation remains questionable

Wszystko co świeci w PET nie jest nowotworem złośliwym! Wychwyt 18F-deoksyglukozy a biologia nowotworu: incidentaloma przysadki mózgowej u chorego, który przebył dwie niezwiązane choroby nowotworowe

    Introduction: 18F-deoxy-glucose positron emission tomography combined with computed tomography (18F-FDG PET/CT) is routinely used in the detection of malignant disease based on the property of malignant cells to fuel their growth and replication by increased glucose uptake. Malignant lesions are rare in the sellar region, while pituitary adenomas are the most common pathology. These are benign neoplasms with insidious onset and low proliferation activity, and therefore are only exceptionally detected by 18F-FDG PET/CT. Studies that compare the biology of pituitary adenomas and their radiological properties using PET/CT are still lacking. Case report: We investigate and discuss tumour biology in light of increased 18F-FDG avidity in a symptom-free, 70-year-old male patient, previously treated for two different malignancies (lung and rectal). Increased tracer accumulation in the sellar region was incidentally detected on a follow-up 18F-FDG PET/CT scan. Additional MRI disclosed pituitary adenoma. Normal hormonal status was found, consistent with the diagnosis of non-functioning pituitary adenoma. Analysis of tumour tissue after pituitary surgery confirmed a silent gonadotroph adenoma with low proliferation index. Low expression of oncogene-induced senescence markers did not support senescence as the explanation for the tumour’s low proliferative activity although it was in consonance with the hormonal activity. Conclusions: Pituitary adenomas can manifest as hypermetabolic foci on 18F-FDG PET/CT imaging with increased tracer uptake even in indolent, clinically silent pituitary adenomas with low mitotic activity. Special attention should be paid to evaluation of 18F-FDG avid pituitary adenomas in patients with multiple malignancies, bearing in mind that avidity does not always mirror its biological behaviour.Wstęp: Pozytonowa tomografia emisyjna sprzężona z tomografią komputerową przy użyciu 18F-deoksy-glukozy (18F-FDG PET/CT) to metoda stosowana rutynowo do wykrywania nowotworów złośliwych, opierająca się na właściwościach komórek nowotworowych, których wzrost i replikacja wiąże się ze zwiększeniem wychwytu glukozy. Zmiany złośliwe występują rzadko w okolicy siodła tureckiego, natomiast do najczęstszych patologii należą gruczolaki przysadki mózgowej. Są to łagodne nowotwory z podstępnym początkiem choroby i małą aktywnością proliferacyjną, dlatego też są wykrywane wyjątkowa rzadko za pomocą badania 18F-FDG PET/CT. Nie przeprowadzono dotychczas badania porównującego cechy biologiczne gruczolaków przysadki mózgowej i ich właściwości radiologiczne z zastosowaniem techniki PET/CT. Opis przypadku: Autorzy zbadali i omówili biologię nowotworu w aspekcie zwiększonego wychwytu 18F-FDG u 70-letniego chorego bez objawów, leczonego wcześniej z powodu dwóch różnych nowotworów (płuca i odbytnicy). Zwiększony wychwyt znacznika w okolicy siodła tureckiego wykryto przypadkowo podczas kontrolnego badania 18F-FDG PET/CT. Wykonane dodatkowo badanie MRI ujawniło gruczolaka przysadki mózgowej. Stężenia hormonów u chorego były w normie, co było zgodne z rozpoznaniem nieczynnego gruczolaka przysadki mózgowej. Badanie tkanki guza po resekcji chirurgicznej potwierdziło diagnozę niemego klinicznie gruczolaka gonadotropowego o niskim wskaźniku proliferacji. Niska ekspresja markerów starzenia się indukowanego onkogenami nie potwierdziła hipotezy, że starzenie się może tłumaczyć małą aktywność proliferacyjną nowotworu, natomiast była zgodna z aktywnością hormonalną. Wnioski: Gruczolaki przysadki mózgowej mogą być widoczne w badaniu 18F-FDG PET/CT jako ogniska hipermetaboliczne o zwiększonym wychwycie znacznika nawet w przypadku nieczynnych, niemych klinicznie guzów przysadki o małej aktywności mitotycznej. Należy zwrócić szczególną uwagę na ocenę 18F-FDG-awidnych gruczolaków przysadki u chorych z wieloma nowotworami, pamiętając, że intensywność wychwytu znacznika nie zawsze odzwierciedla biologię nowotworu

Breast fibroblasts modulate epithelial cell proliferation in three-dimensional in vitro co-culture

BACKGROUND: Stromal fibroblasts associated with in situ and invasive breast carcinoma differ phenotypically from fibroblasts associated with normal breast epithelium, and these alterations in carcinoma-associated fibroblasts (CAF) may promote breast carcinogenesis and cancer progression. A better understanding of the changes that occur in fibroblasts during carcinogenesis and their influence on epithelial cell growth and behavior could lead to novel strategies for the prevention and treatment of breast cancer. To this end, the effect of CAF and normal breast-associated fibroblasts (NAF) on the growth of epithelial cells representative of pre-neoplastic breast disease was assessed. METHODS: NAF and CAF were grown with the nontumorigenic MCF10A epithelial cells and their more transformed, tumorigenic derivative, MCF10AT cells, in direct three-dimensional co-cultures on basement membrane material. The proliferation and apoptosis of MCF10A cells and MCF10AT cells were assessed by 5-bromo-2'-deoxyuridine labeling and TUNEL assay, respectively. Additionally, NAF and CAF were compared for expression of insulin-like growth factor II as a potential mediator of their effects on epithelial cell growth, by ELISA and by quantitative, real-time PCR. RESULTS: In relatively low numbers, both NAF and CAF suppressed proliferation of MCF10A cells. However, only NAF and not CAF significantly inhibited proliferation of the more transformed MCF10AT cells. The degree of growth inhibition varied among NAF or CAF from different individuals. In greater numbers, NAF and CAF have less inhibitory effect on epithelial cell growth. The rate of epithelial cell apoptosis was not affected by NAF or CAF. Mean insulin-like growth factor II levels were not significantly different in NAF versus CAF and did not correlate with the fibroblast effect on epithelial cell proliferation. CONCLUSION: Both NAF and CAF have the ability to inhibit the growth of pre-cancerous breast epithelial cells. NAF have greater inhibitory capacity than CAF, suggesting that the ability of fibroblasts to inhibit epithelial cell proliferation is lost during breast carcinogenesis. Furthermore, as the degree of transformation of the epithelial cells increased they became resistant to the growth-inhibitory effects of CAF. Insulin-like growth factor II could not be implicated as a contributor to this differential effect of NAF and CAF on epithelial cell growth

Investigation of nanoscale structural alterations of cell nucleus as an early sign of cancer

Background: The cell and tissue structural properties assessed with a conventional bright-field light microscope play a key role in cancer diagnosis, but they sometimes have limited accuracy in detecting early-stage cancers or predicting future risk of cancer progression for individual patients (i.e., prognosis) if no frank cancer is found. The recent development in optical microscopy techniques now permit the nanoscale structural imaging and quantitative structural analysis of tissue and cells, which offers a new opportunity to investigate the structural properties of cell and tissue below 200-250 nm as an early sign of carcinogenesis, prior to the presence of microscale morphological abnormalities. Identification of nanoscale structural signatures is significant for earlier and more accurate cancer detection and prognosis. Results: Our group has recently developed two simple spectral-domain optical microscopy techniques for assessing 3D nanoscale structural alterations - spectral-encoding of spatial frequency microscopy and spatial-domain low-coherence quantitative phase microscopy. These two techniques use the scattered light from biological cells and tissue and share a common experimental approach of assessing the Fourier space by various wavelengths to quantify the 3D structural information of the scattering object at the nanoscale sensitivity with a simple reflectance-mode light microscopy setup without the need for high-NA optics. This review paper discusses the physical principles and validation of these two techniques to interrogate nanoscale structural properties, as well as the use of these methods to probe nanoscale nuclear architectural alterations during carcinogenesis in cancer cell lines and well-annotated human tissue during carcinogenesis. Conclusions: The analysis of nanoscale structural characteristics has shown promise in detecting cancer before the microscopically visible changes become evident and proof-of-concept studies have shown its feasibility as an earlier or more sensitive marker for cancer detection or diagnosis. Further biophysical investigation of specific 3D nanoscale structural characteristics in carcinogenesis, especially with well-annotated human cells and tissue, is much needed in cancer research

The cell biology of basal cell carcinoma. relationship to histology and clinical outcome.

Basal cell carcinomas presents with extremely diverse clinical and histological appearances and behaviour. Currently there is little understanding of the biological processes that determine these variations. In an attempt to understand these differences, this thesis evaluated some aspects of the cell biology of BCC both a prospective series and in archival specimens. A variety of measurements were assessed in combination with patient factors (age, presentation etc.) and medical factors (type and adequacy of treatment). The cell kinetics of BCC was studied in vivo following administration of bromodeoxyuridine, which was analysed by flow cytometry. The growth fraction (Ki-67 immunohistochemistry) and the contribution of cell loss to the overall tumour kinetics were studied by evaluating apoptosis (morphologically) and the bcl-2, bax and p53 protein expression, using immunohistochemistry, in both the prospective and archival specimens (including non recurrent, recurrent and horrifying BCCs). It was apparent that BCCs are highly proliferative tumours with a median Ts of 7.6 hours (range 5.0-14-6), Tpot 2.8 days (range 4.0-18.3 days), LI 14%, and Gf 32%. Cell production rates were related to the histological growth pattern with infiltrative and morpheic tumours having a higher Gf than the nodular tumours (p<0.01) and a shorter Tc and Tpot. Cell proliferation was not related to differentiation status. The median apoptotic index was 1% (range l%-5%) and in the absence of apoptotic rate measurements, it was difficult to equate the contribution of apoptosis to the paradox of the slow clinical growth of BCCs. However, the concept of a high apoptotic rate was not supported by bcl-2 and bax protein expression. 88% of BCCs expressed bcl-2 and 23% expressed bax. The relationship between p53 expression and apoptosis was unclear since there was no correlation of p53 with bax, bcl-2 or apoptosis. The apoptotic parameters displayed some relationship to the histological growth patterns. The infiltrative and morpheic tumours exhibited the least apoptosis and least bcl-2 expression (p=0.02), but p53 did not correlate with tumour histology. The contribution of biological factors in determining outcome (the development of recurrence or a horrifying tumour) in BCC are limited because patient factors (late presentation) and treatment factors are dominant. Incomplete excision was associated with recurrence and the development of a horrifying tumour when compared to non recurrent tumours (p<0.01). Primary radiotherapy was also associated with the development of a horrifying tumour (p<0.01). A novel treatment modality, the optomechanically flash scanned carbon dioxide laser, was evaluated to assess its ability to completely ablate BCCs. Complete ablation was associated with ablation depth (p<0.01) and tumour type (p=0.01). Superficial BCCs were most suitable for this modality but required lasering to the middle dermis or deeper for complete eradication. Identification of problem BCCs at an early stage still requires further research but this thesis highlights the need for further improvement in surgical treatment

Colorectal Cancer Through Simulation and Experiment

Colorectal cancer has continued to generate a huge amount of research interest over several decades, forming a canonical example of tumourigenesis since its use in Fearon and Vogelstein’s linear model of genetic mutation. Over time, the field has witnessed a transition from solely experimental work to the inclusion of mathematical biology and computer-based modelling. The fusion of these disciplines has the potential to provide valuable insights into oncologic processes, but also presents the challenge of uniting many diverse perspectives. Furthermore, the cancer cell phenotype defined by the ‘Hallmarks of Cancer’ has been extended in recent times and provides an excellent basis for future research. We present a timely summary of the literature relating to colorectal cancer, addressing the traditional experimental findings, summarising the key mathematical and computational approaches, and emphasising the role of the Hallmarks in current and future developments. We conclude with a discussion of interdisciplinary work, outlining areas of experimental interest which would benefit from the insight that mathematical and computational modelling can provide