How 'Omics Technologies are Revolutionizing Colorectal Cancer Care in South Africa
Imagine a world where your cancer treatment is designed specifically for your unique genetic makeup, rather than following a one-size-fits-all approach. This is the promise of precision medicine—a promise that is gradually becoming reality in high-income countries but remains largely out of reach in many developing nations. Nowhere is this disparity more evident than in the battle against colorectal cancer (CRC), a disease whose burden is rapidly shifting toward low and middle-income countries.
CRC accounted for about 2,367 cases of the total 26,606 new cancer cases reported in South Africa in 1999, ranking as the sixth most common cancer 1 .
The incidence of CRC in South Africa more closely resembles that of developed nations than the low rates typically seen elsewhere in Africa 1 .
The term 'omics' refers to a suite of advanced technologies that allow scientists to comprehensively study the complete sets of biological molecules that govern our bodies. Think of it as moving from examining individual trees to mapping the entire forest.
The study of all our genes and their functions
The analysis of all RNA molecules that help express genetic information
The examination of complete protein profiles in our cells
The investigation of small molecules involved in cellular processes
"By providing a comprehensive molecular landscape of CRC, omics technologies enable the discovery of potential biomarkers for early non-invasive detection of CRC, definition of CRC subtypes, prediction of its staging, prognosis, and overall survival of CRC patients" 4 .
South Africa's healthcare system is famously divided between private and public sectors, creating a stark contrast in cancer outcomes. Research published in the South African Medical Journal reveals that in the privately insured population, the crude incidence of CRC increased from 18.9 to 21.3 per 100,000 between 2008 and 2015—figures that fall between the high rates of developed nations and the lower rates typical of sub-Saharan Africa 6 .
Cancer confined to colon or rectum
Patients with liver metastases
Patients with both liver and lung metastases
Source: South African Medical Journal 6
The same study uncovered striking differences in treatment patterns and outcomes. Among patients with metastatic disease to the liver or lungs, only 7.2% underwent surgical removal of these metastases—a figure notably lower than international trends 6 .
To understand how omics technologies are revolutionizing our understanding of CRC in African populations, let's examine a landmark study published in Nature Communications that analyzed colorectal cancer in Nigerian patients 7 . This research provides crucial insights relevant to the broader African context, including South Africa.
380 Nigerian CRC patients were enrolled, with specimens compared to 458 patients from Memorial Sloan Kettering Cancer Center (MSKCC) in the United States 7 .
Using genetically determined ancestry (GDA) to accurately determine the genetic background of participants 7 .
Next-generation sequencing via MSK-IMPACT to identify genetic mutations, immunohistochemistry to assess protein expression, and methylation analysis to study epigenetic modifications 7 .
Rigorous comparison of molecular and clinical features between the Nigerian and American cohorts 7 .
The findings challenged conventional wisdom about colorectal cancer. The rate of microsatellite instability (MSI-H)—a genetic signature important for treatment decisions—was significantly higher in Nigerian patients (28.1%) compared to both The Cancer Genome Atlas (14.2%) and MSKCC (8.5%) cohorts 7 .
| Molecular Feature | Nigerian Patients | MSKCC (USA) Patients | Statistical Significance |
|---|---|---|---|
| MSI-H Rate | 28.1% | 8.5% | P < 0.001 |
| APC Mutations (MSS tumors) | 39.1% | 76.0% | P < 0.001 |
| WNT Pathway Alterations | 47.8% | 81.9% | P < 0.001 |
| RAS Pathway Alterations | 76.1% | 59.6% | P = 0.03 |
| BRAF V600E Mutation (MSI-H tumors) | 0% | 25.8% | P = 0.01 |
These findings aren't just academically interesting—they have real-world implications for how colorectal cancer should be diagnosed and treated in African populations. The high rate of MSI-H in Nigerian patients suggests that immunotherapy, which works particularly well against MSI-H tumors, might benefit a larger proportion of patients than previously assumed 7 .
"The findings suggest a unique biology of CRC in Nigeria, which emphasizes the need for regional data to guide diagnostic and treatment approaches for patients in West Africa" 7 —a conclusion that applies equally to South Africa.
Research in Cape Town is addressing another critical challenge in implementing precision medicine: the interpretation of genetic variants in underrepresented populations. A recent study from the University of Cape Town highlighted the problem of variants of uncertain significance (VUS) in indigenous African patients with early-onset colorectal cancer 5 .
| Genetic Finding | Number of Patients | Percentage | Notes |
|---|---|---|---|
| Pathogenic Variants | 5 | 16% | Genes: C6, FAT1, LZTR1, PYCR1, UGT1A7 |
| "Leaning Pathogenic" VUS | 15 | 47% | Potential for reclassification as pathogenic |
| Genes with VUS | 17 | - | Included ASXL1, CHEK2, ERBB2, NOTCH1, others |
This research underscores a critical equity issue in the genomic revolution: without adequate representation of African genomes in reference databases, patients of African descent may not fully benefit from precision medicine approaches. As the authors note, there's an "urgent need for population-specific genomic research and the development of inclusive variant databases" 5 .
What does it take to conduct this cutting-edge cancer research in a developing world context? Here's a look at the essential tools and technologies:
| Tool/Technology | Primary Function | Application in CRC Research |
|---|---|---|
| Next-Generation Sequencing (NGS) | High-throughput DNA sequencing | Identifying mutations in cancer-related genes |
| Formalin-Fixed Paraffin-Embedded (FFPE) Tissues | Long-term preservation of tissue samples | Enabling retrospective studies from archived samples |
| MSK-IMPACT | Targeted sequencing platform | Comprehensive genomic profiling of tumors |
| Ion AmpliSeq Exome Kit | Whole exome sequencing | Capturing protein-coding regions of the genome |
| Immunohistochemistry | Visualizing protein expression | Assessing mismatch repair protein deficiency |
| Mass Spectrometry | Identifying and quantifying molecules | Proteomic and metabolomic profiling |
These technologies have become increasingly accessible, enabling researchers in places like Cape Town to conduct world-class cancer genomics research. As noted in one methodological paper, careful quality control measures—such as checking DNA concentration and purity—are essential for generating reliable results 3 .
The path toward implementing omics-based approaches in routine clinical care in the developing world faces several significant hurdles:
Advanced genomic technologies require substantial financial investment and stable infrastructure
The analysis of large omics datasets requires specialized computational skills
Developing appropriate guidelines for clinical application of genomic data
Incorporating molecular diagnostics into existing healthcare pathways
Despite these challenges, the potential benefits are tremendous. As one review noted, omics technologies "hold transformative potential to revolutionize the management of this disease" by enabling early detection, guiding treatment selection, and monitoring treatment response 4 .
In South Africa, initiatives are already underway to bridge these gaps. The pathology-supported genetic testing framework represents one approach to integrating genetic testing into clinical practice in a resource-appropriate manner 9 .
The journey to bring the benefits of omics technologies to colorectal cancer patients in South Africa and the broader developing world is well underway. Research from Cape Town, Nigeria, and other African centers is revealing a complex molecular landscape of colorectal cancer that differs in important ways from what we've learned from Western populations.
This new understanding is paving the way for more effective, targeted treatments that could significantly improve survival and quality of life for African cancer patients. While challenges remain, the dedicated work of scientists across the continent brings hope that the promise of precision medicine will become a reality for all patients, regardless of where they live.
As the global scientific community increasingly recognizes the importance of including diverse populations in genomic research, we move closer to a future where geography no longer determines destiny in cancer care. The work happening today in Cape Town's laboratories is not just transforming our understanding of colorectal cancer—it's helping to build a more equitable future for cancer patients across Africa and beyond.