The new biology: histopathology

Serum Tumor Markers: Past, State of the Art, and Future

Serum determinations of tumor markers are indispensable in the diagnosis and management of cancer, and therefore play an important role in clinical practice. After a short historical survey, we systematically review a number of contemporary aspects of serum tumor markers related to various organ systems, and briefly indicate possible future developments.

More than meets the eye: the changing face of histopathology

This personal reflection on trends in histopathology over the past 50 years draws upon experience of professional training and practice in the specialty in the UK. Developments during this period often resulted from new therapies (and their adverse effects) necessitating greater precision in the histopathological classification of disease, for which morphology alone can be insufficient. Conversely, histopathology has contributed to advances in our understanding of disease, leading directly to novel and more effective treatments. New infections, some involving histopathology in their discovery, have also led to fresh diagnostic challenges. Increasingly, patients have benefited from fundamental changes in professionalism in pathology. Through audit, external quality assurance, continuing professional development, standardized reporting, and increasing specialization, the consistency and reliability of histopathological diagnoses have steadily improved. Regarding the specialty's future, some now see rivalry between the morphological and molecular approaches to diagnosis and classification, particularly for neoplastic disease. An integrated strategy led by the specialty is more likely to strengthen histopathology and ultimately to have the greatest benefit for patients.

New Biotechnologies: Spin-off on Health and Society

New biotechnologies and the new biology deriving from them are having a revolutionary impact on economy and society and are consequently transforming the role of researchers, which is changing continually to meet the competence required. The advances in human genetics on the other hand make it necessary to look for different approaches and new rules in bioethics. Comprehensive views and careful considerations are therefore needed in order that this new biology may have a positive impact on health, being respectful of the social and ethical principles of human beings.

Defining a molecularly normal colon

As techniques evolve that allow molecular characterization of disease processes such as cancer, definition of "normal" at a molecular level becomes increasingly important. Increasingly large numbers of mutations are found at the genomic level, but whether all of those mutations contribute to the malignant state of a carcinoma cell is not clear. Without knowledge of what constitutes normality on the proteomic level in an organ or cell, we cannot determine what genomic changes are physiologically important. Traditionally, colon cancer is identified and classified by histological criteria. Margins of the colon are defined as "grossly uninvolved" when the histology is indistinguishable from that of normal (free from disease) colon. By using molecular pathology techniques and working backward from colon adenocarcinoma to hypoplastic polyps to presumably normal mucosa, we defined some of those protein differences. Our results may provide a molecular basis for identifying tumor formation and progression in situ.(J Histochem Cytochem 49:667-668, 2001)

Will the “new biology” Affect the Future of Histopathology?

The technologies used in histopathology are changing as a consequence of the current revolutionary progress in several areas of biology. It is likely that general cancer management will improve because of the impact of molecular techniques and immunohistochemistry on tumor diagnosis and classification and on the determination of prognosis and response to therapy. Moreover, as therapies are starting to be modelled after the distinctive molecular characteristics of a specific tumor, the availability of molecular tests to all patients will become a matter of great importance.

Identity testing in cervical carcinoma in case of suspected mix-up

The histopathologic diagnosis is the cornerstone of modern oncology. But mix-ups of specimens can occur at any stage. The resection of a 1.2 cm polypoid cervical mass in a 25-year-old woman showed a poorly differentiated adenocarcinoma prospectively staged as T1b1 (International Federation of Gynecology and Obstetrics IB1). Even after complete embedding and serial sectioning of the whole cervix of the hysterectomy specimen after radical hysterectomy, only adenocarcinoma in situ, but no invasive tumor, was seen. To exclude a mix-up of the specimens, identity testing of the paraffin-embedded material was performed by microsatellite analysis. For both materials, we established identical results after testing the microsatellite loci HumTH01, HumVWA, HumFGA, HumACTBP2, HumF13B, and HumD8S1132. The resulting probability of identity came to 99.9999%, excluding a mix-up of the specimens. Archival paraffin-embedded specimens can be used to establish identity and can prevent the wrong patient from having major surgery.

Challenge of investigating biologically relevant functions of virulence factors in bacterial pathogens

Recent innovations have increased enormously the opportunities for investigating the molecular basis of bacterial pathogenicity, including the availability of whole-genome sequences, techniques for identifying key virulence genes, and the use of microarrays and proteomics. These methods should provide powerful tools for analysing the patterns of gene expression and function required for investigating host-microbe interactions in vivo. But, the challenge is exacting. Pathogenicity is a complex phenotype and the reductionist approach does not adequately address the eclectic and variable outcomes of host-microbe interactions, including evolutionary dynamics and ecological factors. There are difficulties in distinguishing bacterial 'virulence' factors from the many determinants that are permissive for pathogenicity, for example those promoting general fitness. A further practical problem for some of the major bacterial pathogens is that there are no satisfactory animal models or experimental assays that adequately reflect the infection under investigation. In this review, we give a personal perspective on the challenge of characterizing how bacterial pathogens behave in vivo and discuss some of the methods that might be most relevant for understanding the molecular basis of the diseases for which they are responsible. Despite the powerful genomic, molecular, cellular and structural technologies available to us, we are still struggling to come to grips with the question of 'What is a pathogen?'

Molecular pathology and future developments

There has already been a 'molecular' revolution in pathology. Demonstrating transcription of specific single genes or small gene sets and their protein products by in situ hybridisation and immunocytochemistry is routine in diagnostic and experimental pathology. A perhaps-greater revolution is imminent with the application of more recently established and emergent technologies in pathology. These include new approaches to polymerase chain reaction (PCR); simultaneous studies of multiple genes and their expression using oligonucleotide and cDNA arrays; serial analysis of gene expression (SAGE); expressed sequence tag (EST) sequencing, subtractive cloning and differential display; high-throughput sequencing; comparative genomic hybridization, multiplex fluorescence in situ hybridisation (FISH) (spectral karyotyping); reverse chromosome painting; knockout and transgenic organisms; laser microdissection and micro-machining; and new methods in bio-informatics, 'data mining' and data visualisation. Molecular methods will profoundly change diagnosis, prognosis and treatment targeting in oncology and elucidate fundamental mechanisms of neoplastic transformation. Individual susceptibility to specific diseases will become assessable and screening will be refined. The new molecular biology will be most fruitful in partnership with classical approaches to pathology: the expectation that molecular methods alone will answer all pathological questions is unrealistic. A further challenge for the biomedical community in the 'genome era' will be to ensure that the benefits of these sophisticated technologies are enjoyed globally.

Visualisation of biomedical datasets by use of growing cell structure networks: a novel diagnostic classification technique

BACKGROUND

Medical research produces large multivariable datasets that are difficult to visualise and interpret intuitively. We describe a novel growing cell structure (GCS) technique that compresses multidimensional datasets into two dimensional maps with colour overlays that can be visually interpreted.

METHODS

The two-dimensional map is self-discovered from the training set by distribution of cases to different nodes according to similarity between the cases at each node. Nodes are added to the map until there is no further significant reduction in error. The Parzen window method is used to estimate the probability distribution of the training cases, and this probability is converted to posterior class probabilities by use of Bayes' theorem. Classification performance can be assessed by means of receiver operating characteristic (ROC) curves. Colour maps of the values of each input variable at each node are constructed, which illustrate the relation between each input variable and the overall distribution of cases in the network map.

FINDINGS

From a dataset of 11 input variables from 692 fine-needle aspirate samples from breast lesions, a 32-node network produced an area under the ROC curve of 0.96, which was not significantly different from that for logistic regression (0.98, z=1.09, p>0.05). Colour maps of the input variables showed that some variables had discrete distributions over exclusively benign or malignant areas of the network, and were thus discriminant, whereas others, such as foamy macrophages, covered both benign and malignant regions.

INTERPRETATION

This technique produces dimensional compression that allows multidimensional data to be displayed as two-dimensional colour images. This envisioning of information allows the highly developed visuospatial abilities of human observers to perceive subtle inter-relations in the dataset.