About the Institute of Molecular and Clinical Pathology and Medical Genetics

Besides its research activities, the Institute of Pathology also provides a range of teaching at Bachelor's and Master's level. Teaching focuses on both theoretical and practical courses in pathology, which form part of the second year of all Bachelor's degree programmes and the third year of the Master's programme in General Medicine.

The Institute also carries out comprehensive diagnostics of biopsy tissues, including extensive perioperative diagnostics. It also conducts non-gynecological cytological tests and autopsy diagnostics for the clinics and departments of the Ostrava University Hospital. The Institute works closely alongside other institutions and pathology departments throughout the Czech Republic. It possesses high-quality modern equipment enabling it to apply standard and innovative new methods (immunohistochemical, histochemical, immunofluorescence, electron microscopy, molecular pathology, computer image analysis). We also use telepathology and virtual digital microscopy methods. We carry out around 18 000 biopsy tests every year, plus 2 000 cytological tests and 350 autopsies. Our team consists of 11 medical staff, 13 laboratory assistants, 5 practical assistants and 4 administrative staff.

Main activities of the department

Histopathological diagnostics

The Institute of Clinical and Molecular Pathology and Medical Genetics provides a wide range of biopsy diagnostics in a complete range for the entire FNO and external applicants. On average, we perform about 18,000 histological examinations annually.

In necessary cases (e.g. to determine the type of tumors), we use immunohistochemical or immunofluorescence examinations using a wide range of antibodies, the number of which is constantly expanding with new ones. We perform almost 30,000 immunohistochemical examinations annually.

An integral part of our daily work is the performance of intraoperative examinations, when the material is processed so-called "frozen". After rapid freezing of the delivered tissue directly from the operation, the preparation is stained and evaluated by a pathologist. From these samples, we are able to inform the surgeon in a moment, for example, about the biological nature of the operated lesion. We perform about 600 intraoperative examinations annually.

Thanks to the wide range of examined material, the Department of Pathology is a suitable place for further specialization of young pathologists and graduates of general medicine, as well as medical laboratory technicians.

Histotopogram (whole mount section)

This is a technique for processing samples into so-called megablocks, which are created from wide cross-sections of the examined organs and provide a better topographic overview of the location of the examined structures, most often tumors.

This is a more complex and financially demanding method of processing in the laboratory, requiring special material and technical facilities. At our workplace, we use histotopograms in the examination of prostate carcinomas in cooperation with imaging methods (MRI) and thanks to them, we are able to determine the exact localization of the tumor and the extent of damage to the prostate tissue. In the future, we plan to expand histotopogram examinations to the area of gynecological pathology (uterus, cervix) and mammary gland pathology.

Cytological diagnostics

The history of clinical cytodiagnostics is associated with the development of microscopic and staining techniques, currently with the possibility of immunohistochemistry. The beginnings of cytodiagnostics were applied mainly in gynecological diagnostics, currently pathology laboratories have been expanded to include a wide range of clinical cell collections in pneumology, urology, endocrinology, the digestive tract, cerebrospinal fluid examination, mammology and other systems.

Cytological collections are performed by clinics in various forms of smears and punctures. However, cytohistological correlations are essential for the pathologist for a certain number of false positive or negative findings in cytology.

During the performance of gynecological cytology in the FNO and in cooperation with private laboratories of gynecologists, some experience was gained with cervical smears. Thus, numerous collections of preparations were created, which are now used as part of the postgraduate education of laboratory technicians in the certified course Gynecological Cytodiagnostics.

Our laboratory currently processes non-gynecological cytology and its activities widely include immunohistochemical methods and, in selected cases, electron microscopy. The annual number of cytological examinations is on average 1,500 samples.

Electron microscopy

Electron microscopy has been performed within the Department of Pathology at the Ostrava - Zábřeh University Hospital since 1983. With the construction of a new building of the Institute of Pathology on the premises of the Ostrava - Poruba University Hospital, which began operations in 1993, this methodology continued to be used and further developed here as well.

Electron microscopy is a superior laboratory examination, performed mainly in a faculty-type hospital. It achieved significant development in the Czech Republic, especially in the 1980s and 1990s. This method requires significant financial costs for operation and considerable demands on the expertise of laboratory workers and doctors.

Transmission electron microscopy at the Department of Pathology at the Ostrava University Hospital focused mainly on the field of nephrological pathology. Later, this method was used in oncological diagnostics, in the evaluation of pathological processes of the nervous system and in the pathology of metabolic diseases. Currently, our department focuses on the use of this method in the examination of muscle biopsies and in studying the effect of nanoparticles on the organism. We also focus on the examination of lung tumors, intestinal biopsies and various pathological agents (e.g. Tropheryma whipplei). We also try to find certain connections between oncological cytology, immunohistochemical methods and electron microscopy.

Every year, our department processes around 50 cases using transmission electron microscopy. The time required to process individual cases is demanding and requires a longer time interval to establish a diagnosis. The processing of the material takes place in close cooperation between the laboratory worker and the physician. Electron microscopy helps in differential diagnostics to determine the histogenesis of tumor and inflammatory processes that cannot be observed by conventional histopathological examination (e.g. Whipple's disease, etc.). It helps to determine the correct diagnosis in findings that are limited by the ambiguity of immunohistochemical methods (e.g. mesothelioma vs. adenocarcinoma, neurosecretory tumors, etc.). One of the latest articles on this topic is presented by Vladimír Židlík, MD, who deals with the issue of Gaucher disease in the bone marrow of a 16-year-old girl.

Amyloid examination

Amyloid is a poorly defined protein, chemically it is more of a group of different proteins with a broken conformation. Amyloid is often part of the disease amyloidosis and its deposits are visible in various tissues.

In the basic histochemical staining hematoxylin-eosin amyloid has a pink color. It can be demonstrated by several methods including histochemical (Congo, Saturn red), immunohistochemical and immunofluorescence methods. Amyloid deposits can be demonstrated in various organs. Usually the kidneys are the first to be affected. Then any other organ.

At our workplace, in cooperation with the Clinic of Hemato-Oncology, we use the detection of amyloid in subcutaneous fat. Taking samples of adipose tissue is quite comfortable and less burdensome for the patient.

Probably the fastest and most reliable method of detecting amyloid is immunofluorescence examination. Native adipose tissue samples are processed frozen, stained with immunofluorescent antibodies, and viewed under a fluorescence microscope.

Neuropathology

Our department is part of a comprehensive neuro-oncology center at the FNO, where we collaborate with neurosurgeons, radiologists and oncologists and participate in multidisciplinary seminars at weekly intervals. We perform approximately 500 biopsy examinations of primary and metastatic CNS tumors including the spine and samples from endoscopic skull base surgery (pituitary surgery, etc.), including in pediatric patients. We use a wide panel of immunohistochemical examinations for their accurate diagnosis. We also perform intraoperative frozen section examinations.

Fetopathology

Is a field focusing on the study of the pathology of the newborn, fetus and placenta. We perform macroscopic and microscopic examinations with an emphasis on recognizing congenital anomalies, infections and pathological findings that led to complications during pregnancy and childbirth (preeclampsia, premature birth, fetal growth retardation, fetal or neonatal death), and which can predict the possible occurrence of subsequent complications. The number of mandatory autopsies of fetuses and children performed annually is around 100. The number of biopsy-examined placentas is on average 350 per year.

We closely cooperate with doctors from the Department of Medical Genetics, the Department of Obstetrics and Gynecology, the Department of Neonatology and with pediatric cardiologists in the diagnosis of congenital developmental defects, especially of the heart and large vessels. Clinicians participate in autopsies of the heart-lung complex in aborted fetuses with a developmental defect detected prenatally by ultrasound and also in fetuses with an increased risk of these defects (Down, Edwards and Patau syndrome and other chromosomal defects). In the differential diagnosis of developmental defects, especially of the CNS, we are also greatly helped by interdisciplinary cooperation with the Institute of Radiodiagnostics, which performs prenatal MRI.

Our goal is to provide accurate diagnostic information that may have an impact on the medical care of the mother, child and future pregnancies.

Hematopathology and bone marrow biopsy

Diagnosis of hematological diseases is very broad and far from limited to routine histological examination of submitted samples, although morphology is still the most important examination in most lesions. It is a complex diagnostic process in which we use cooperation with specialized laboratories, such as Spadia Lab (flow cytometry) and EUC laboratory (clonality examination, cytogenetics and molecular genetics).

The spectrum of diagnoses ranges from reactive and inflammatory lesions to malignant hematological diseases such as leukemias and lymphomas, for the typing of which we apply a wide range of immunohistochemical antibodies, which we constantly supplement as needed.

We also perform bone marrow examinations in the entire spectrum of hematooncological diagnostics for the Department of Hematooncology of the Havířov Hospital and, to a limited extent, for the Clinic of Hematooncology FNO and the Clinic of Pediatrics FNO.

It is also important to note the cooperation with consulting departments, which are primarily the Department of Pathology of the University Hospital Olomouc and the Department of Pathology of the University Hospital Brno (Bohunice).

Pneumopathology

We examine cytological and biopsy material from bronchoscopic samples and also from thoracoscopic biopsies. To differentiate primary lung tumors from metastases, we use a standard panel of recommended immunohistochemical methods. We also evaluate surgical resections of lung carcinomas and tumor affections of the pleura from needle biopsies using immunohistochemistry.

We examine tumor lesions of the pleura from surgical specimens and also from needle biopsies using immunohistochemistry. It is important here to differentiate the mesothelial and epithelial origin of the captured elements and eventually determine the primary origin of the metastatic carcinoma.

Diagnostics of non-tumor lesions is carried out at the cytological, histological and histochemical levels. As part of the differential diagnosis of bronchial asthma, we examine bronchoscopic samples from the bronchial mucosa, where the evaluation focuses on determining the presence of goblet cell hyperplasia in the epithelial cover, the morphometry of the basement membrane, the nature of the inflammatory infiltrate, the presence of hyperplasia of the bronchial salivary glands and mucosal muscle. All examinations are performed in close clinical cooperation with pulmonologists, radiologists and thoracic surgeons (Selected cases are discussed in the framework of clinical-pathological seminars).

Head and Neck Tumors

Thanks to close cooperation with the Department of Oral, Maxillofacial and Facial Surgery, as well as grant activities and interregional cooperation, we are dedicated to the possibilities of clarifying the factors leading to perineural invasion of head and neck squamous cell carcinoma tumors, we are trying to contribute to the understanding of the principle of molecular margins in surgical therapy and we are also collaborating on the pathogenesis of ankylosing spondylitis and dental cysts.

A multidisciplinary cooperative group has been established dedicated to the diagnosis of tumor diseases, but also, for example, in the area of oral leukoplakia.

Nephropathology

Part of the examination at the Department of Oral and Maxillofacial Surgery is the histopathological examination of renal biopsies, especially transplanted kidneys. As part of this assessment, changes associated with graft rejection by the recipient are monitored. Changes typical of acute or chronic rejection are monitored. The presence of deposits of the complement subunit C4d, typical of humoral rejection, is observed using immunohistochemical and immunofluorescence examinations. Specific stromal, intratubular round cell cellularization or vascular involvement typical of cellular rejection and other histopathological signs are monitored using optimized histochemical stains, taken over from the Department of Clinical and Transplant Pathology, IKEM, Prague. Part of the standard protocol is IHC staining for the detection of polyomavirus or CMV. The processed material is regularly consulted at the Institute of Clinical and Molecular Pathology, University Hospital Olomouc.

Mammary gland pathology

At the Department of Otolaryngology and Oncology, we examine mammary gland samples from a wider range of samples. These include cytological examinations, e.g. nipple secretions, punctures of suspicious formations, samples taken as a core-cut biopsy (CCB) and, last but not least, from larger resections (quadrantectomy, lumpectomy) or complete mastectomies.

Although the primary aim is to determine the presence of a malignant tumor, the lesions examined include a wide range of diagnoses from benign processes (e.g. adenosis, mastopathy, hyperplasia, fibroadenomas) to malignant tumor lesions.

The examination includes the most accurate morphological description of the examined sample, in the case of malignant tumors, determination of differentiation (grading according to the Nottingham classification) and subsequent evaluation of the expression of female hormonal receptors (estrogen, progesterone), with which we simultaneously evaluate the expression of the c-erb oncoprotein using special immunohistochemical antibodies.

According to the prescribed guidelines, in certain cases we continue with the examination of the Her2/neu oncoprotein and the molecular genetic examination FISH (fluorescence in situ hybridization), which we send to cooperating reference laboratories (AGEL Laboratories, EUC Laboratory).

The biopsy examination itself from receipt of the sample to the final diagnosis, including immunohistochemical examination, usually takes about 3-4 days.

Dermatopathology

The field of dermatopathology itself is a very broad discipline covering a number of benign and malignant processes from inflammatory lesions (dermatitis), autoimmune diseases, adnexal and primary epithelial tumors, hematopathological diseases and melanocytic tumors.

We examine the latter in large numbers in cooperation with the melanoma advisory center of the ÚP FNO together with the examination of the so-called sentinel node and, upon request by the clinician, also by examining BRAF mutations (and others), which we send to a cooperating reference laboratory (EUC laboratory). The lesions described include common benign melanocytic nevi (so-called moles) through various transitional forms to cutaneous melanomas, for which we determine prognostic factors such as depth of invasion (Clark, Breslow), signs of angioinvasion, superficial ulcerations, presence of inflammatory infiltrate, etc.

Inflammatory diseases (dermatitis) together with autoimmune diseases or skin manifestations of systemic diseases are examined using the entire spectrum of histochemical and immunohistochemical methods, including direct immunofluorescence (e.g., bullous diseases IgG, IgM, IgA, C3c).

Within dermatopathology, we organize regular training courses for doctors specializing in dermatology.

Pathology of the gastrointestinal tract

Investigation of pathological processes in the gastrointestinal tract is one of the routinely performed examinations at the Department of Gastroenterology, FNO. In cooperation with the internal medicine clinic, we mainly examine samples taken by endoscopic approach with a focus on inflammatory lesions of the GIT from the esophagus to the rectum, such as esophagitis, gastritis with determination of Helicobacter pylori colonization, gluten enteropathy, ulcerative colitis and Crohn's disease. At the request of clinicians, in intestinal inflammatory processes, we determine the presence of CMV both immunohistochemically and subsequently by verification using PCR by sending the sample to the Ostrava Health Institute.

Another broader area of examination is precancerous lesions of the GIT (dysplasia, adenomas) or malignant tumors of epithelial (adenocarcinomas), mesenchymal (GIST) and hematological origin (lymphomas).

In cooperation with the surgical clinic, we mainly examine large resections, most often with malignant etiology, mainly from the colon and biliary tract.

The examination of adenocarcinomas includes RAS mutations examined in our cooperating reference laboratory (EUC laboratory) and, upon request by the clinician, also examination of microsatellite instability proteins (MSI) performed by immunohistochemical methods at our workplace.

Autopsy diagnostics

Autopsy examinations are an important part of clinical-pathological cooperation. Their task is to inform clinics about the correctness of the therapy and also to educate young doctors, including pathologists. The number of autopsies is constantly decreasing annually, yet we perform 300 autopsies at our institute annually.

Molecular genetic diagnostics

As part of comprehensive diagnostics and care for oncological patients, specific diagnostics based on molecular pathology and cytogenetics are necessary - i.e. genetic analysis of the somatic genome (tumors), which is then followed by further medical care for the patient with regard to the genotype of the given tumor.

A great benefit is the introduction of so-called predictive diagnostics with a connection to the indication of targeted biological treatment of oncological patients. Specifically, or dominantly, it concerns predictive diagnostics of the following genes: BRCA1, BRCA2, KRAS, NRAS, EGFR, BRAF, ALK-IHC, ALK-ISH, HER2-IHC, HER2-ISH, ROS1-IHC and ROS1-ISH.

Molecular genetic diagnostics is performed in the molecular pathology laboratory, which uses the following examination methods:

• Performing chromosome examinations by classical cytogenetic analysis
• Performing cytogenetic analysis of peripheral lymphocytes
• Performing chromosome examinations by FISH method
• Performing microarray analyses
• Performing molecular genetic examinations by reverse hybridization methods
• Fragmentation analyses using capillary electrophoresis
• MLPA
• Real-time PCR
• Direct sequencing according to Sanger
• Massively parallel sequencing
  
  

Teaching Pathology

Due to the relocation of the equipment of the Department of Pathology of the Faculty of Medicine, students of the Medical Laboratory Technician program can improve their skills in laboratory techniques and in the 3rd year they can work on their bachelor's theses in the new laboratories.

Students of the Master's Program in General Medicine are allowed to participate in autopsies and demonstrations of interesting cases from pathological medical practice in the microscope room, where teaching takes place using modern imaging techniques.

Scientific research activities are focused on the field of special pathology and cytology, especially pneumopathology, dermatopathology, gynecology, pathology of the breast and thyroid gland. To a large extent, members of the Institute also deal with neonatology, neuroendocrine tumors, nanopathology, neoplasms in the context of molecular pathology and immunohistochemistry, amyloidosis, or bariatric treatment of the obese, which is currently being processed in the form of a grant.

The team of the Institute of Pathology also organizes seminars, conferences, and other professional events.

Together with the Institute of Pathology of the Faculty of Medicine, the Faculty of Medicine of the University of Ostrava organizes interdisciplinary seminars. Another important joint event of the Institute of Pathology of the Faculty of Medicine and the Faculty of Medicine is the Interregional Biopsy Seminar or Cytology Day.

Updated: 15. 04. 2025