Research Projects

Gastric cancer research – Prof Richard Naidoo

Gastric cancer research – Prof Richard Naidoo

Prof Richard Naidoo

Professor Richard Naidoo

  • Associate Professor and Medical Scientist, Faculty of Health Science, Division of Anatomical Pathology, Clinical and Laboratory Sciences, University of Cape Town
  • E-mail

Title of the project

Molecular analysis and identification of biomarkers from formalin fixed paraffin embedded gastric cancers.

Project description

Gastric carcinoma is rated as the second most frequent carcinoma worldwide (Parkin, 2001).  This carcinoma is also very commonly encountered in the Western Cape.  The tumour can be broadly classified into 2 categories, those that have well-differentiated or intestinal type morphology and those having a poorly differentiated or diffuse type morphology.  The incidence of this carcinoma varies geographically, with high incidences of the disease seen in Japan, China, South and Eastern Europe and Central America. It is also prevalent in the older age group (ie individuals over 50 years)

The aetiology of this carcinoma involves environmental and genetic risk factors. The important environmental factors include tobacco smoking, obesity and diet. In addition, Helicobacter pylori (H.pylori) have also been implicated in the development of this carcinoma (Milne et al., 2009). Furthermore, the influence of molecular genetic alterations in the development of gastric carcinoma has become significant over recent years and will greatly impact on future diagnostic and prognostic processes.

Gastric carcinoma has both a familial and a sporadic arm. About 10% of all gastric carcinomas are attributed to familial clustering. The E-Cadherin gene (CDH1) encodes for a cell adhesion protein and is a key component of the Wnt signalling pathway. Studies have shown a strong association between familial gastric carcinoma and mutations in the CDH1 gene (Oliveira et al., 2009). Decreased E- Cadherin expression has been associated with diffuse gastric carcinomas and E-Cadherin positive tumours have been shown to have a significantly better 3-5 year survival.

Other genetic factors that influence development and progress of gastric carcinoma include aberrations in the DNA repair genes (Keller et al., 1996), polymorphisms in the cytochrome P450 genes (Cai et al., 2005) and polymorphisms in the IL β1 gene (Milne et al., 2009)). Microsatellite instability and DNA loss have also been associated with the development of the disease (Oki et al., 2009).

The high mortality rate seen in gastric carcinoma has been ascribed to the lack of early diagnosis. It is evident that earlier diagnosis of carcinomas lead to better survival. This project aims to identify molecular markers which are present in tumour tissue, using high throughput biomarker identification methods

The most significant medical advance in the last decade has been increasing identification and characterisation of the human genome. Since the completion of the Human Genome Project (Collins et al., 2003), it is now estimated that there are approximately 50,000 to 60, 000 genes that encode the various proteins found in human cells. Emerging from this research is clear evidence that most diseases and disorders are controlled by specific genes. This may be inherited or may be in response to environmental stresses.

The completion of the human genome project has spawned the development of a number of high throughput molecular technologies. These new technologies include a number of genomic and proteomic methodologies. The isolation of the protein complement from tissue would allow for interrogation of proteins that are present in various carcinomas. It is well publicized that the molecular signature of malignant tissue, ie the protein complement is unique and different from their corresponding normal tissue.

Identification of biomarkers is important in addressing specific clinical phenotypes and disease progression. The identification of biomarkers in cancers has tremendous potential for the development of new and earlier diagnostic tests (Tainsky, 2009). Biomarker identification has primarily been conducted using fresh and frozen tissue samples which are obtained at the time of surgery.  Formalin fixed paraffin embedded tissue is also an excellent source of genetic material which may also be used for these studies. There are a number of studies which have used this type of starting material for biomarker identification (Crockett et al. 2005; Hood et al, 2005). Several spin-offs emerge from these studies. These include:

1.         Early detection of cancers

2.         The development of new clinical tests

3.         Long term optimal and targeted therapy

Non-scientific report

My research focuses on a range of studies using state-of-the-art matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) to identify proteins and peptides in cancer tissue. The recent emergence of MALDI imaging mass spectrometry has made it possible to study more complex proteomic patterns directly in tissue. These studies typically have used fresh tissue obtained from surgical resections.  We intend to investigate the use of formalin fixed paraffin embedded (FFPE) tissue for identification of proteins/peptides and potential biomarkers unique to cancer using the above technology. Whilst, FFPE tissue has not been used in the past because of the potential problems associated with formalin fixing, we have established a method to improve protein/peptide access in this tissue prior to MALDI analysis.

We would like to use matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-imaging) to study more complex proteomics patterns directly on histology tumour tissue. This will be followed by analysis and interpretation of the data acquired using advanced computational methods.

I am currently involved with research projects related to molecular changes in gastric cancer and HIV and non-HIV related lymphomas. Claudia Vet (Honours student) has completed her project and written up her thesis. She has generated some interesting data related to PTEN gene expression in gastric cancer. However, this warrants some additional work before being submitted for publication. One of my master’s students (Anelisa Jaca) has completed her thesis and we plan to publish at least 2 papers from this project. Riyaadh Roberts (MMED student) has completed all his experimental work and will also be writing up his thesis at the end of 2013. In addition, I am also expecting a publication from his work. Pumza Phillips (PhD) student has commenced with a project related to biomarker identification in HIV and Non-HIV related lymphomas.


  • Biomarker identification in formalin fixed paraffin embedded tissue using proteomics methods.  R Naidoo, A Padayachie, M Locketz, P Govender and D Govender. Pathology Conference 2010
  • A novel proteomics assay using formalin fixed paraffin embedded tissue.  R Naidoo, A Padayachie, M Locketz, P Govender and D Govender. Laboratory Medicine Conference 2011
  • MALDI imaging in Histopathology. R Naidoo, M Locketz and T Govender. Laboratory Medicine. Laboratory Medicine Conference 2013
  • Sequence analysis of the E-cadherin (CDH1) gene in a cohort of gastric cancers seen in the Western Cape. A Jaca, M Locketz and R Naidoo. Laboratory Medicine. Laboratory Medicine Conference 2013
  • A method to increase DNA yield from formalin fixed paraffin–embedded (FFPE) Tissue.  P. Govender and R Naidoo. Laboratory Medicine. Laboratory Medicine Conference 2013


  • Attended the Laboratory Medicine Congress at the Sandton Convention Centre from 31 August–4 September 2011. Presentation and abstract title: A NOVEL PROTEOMICS ASSAY USING FORMALIN FIXED PARAFFIN EMBEDDED TISSUE.



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