From hot springs to personalised cancer treatment

We’re campaigning to #KeepResearchCurious: highlighting the importance of curiosity-driven cancer research.

In this series of articles we highlight how fundamental research driven by curiosity can lead to advances in medicine, sometimes in unpredictable ways.

This article tells the story of the history and impact of DNA sequencing and PCR (polymerase chain reaction) technology on cancer research and treatment. It tracks how DNA sequencing enabled the identification of cancer-associated genes, facilitating the development of targeted therapies, and routine sequencing of tumor DNA. It also discusses how this laid the groundwork for current multi-omics approaches in cancer research.

Nowadays everybody knows about PCR, and I don’t mean all scientists. Almost every person in the world must have at least heard of PCR. Granted this has more to do with the recent COVID-19 pandemic rather than cancer research, nonetheless, this does not undermine the importance and popularity of this technique for clinical practice in cancer care. For scientists in general, and those familiar with molecular biology techniques in particular, the integral role of PCR in increasing the efficacy of DNA sequencing techniques is no secret.

The Sequencing Revolution: Unlocking the Secrets of the Cancer Genome

For the past couple of decades, the role of sequencing has become increasingly important in cancer research and cancer care. The completion of the human genome project in 2001 [1], opened the stage for understanding how DNA alterations are linked to certain diseases, including cancer. Many other revolutionary projects followed, such as the 1000 and the 100.000 human genome projects [2-4], the HapMap project [5] or ENCODE [6] – helping understand healthy, normal genetic variation in the human population and looking at characterising the functional side of the human genome, respectively.

The possibility to identify cancer-specific DNA alterations was a major breakthrough in cancer research. It allowed for the identification of genetic risk factors and thus facilitated early diagnosis of several cancer types through genetic screening. Classical examples are BRCA1/2 genes for breast and ovarian cancer [7-9] or MLH1, MSH2, EPCAM, MSH6, and PMS2 for colon cancer [10]. The identification of cancer-specific DNA alterations also enabled the development of targeted therapies with trastuzumab (an anti-HER2 humanised monoclonal antibody) [11] and imatinib (a tyrosine kinase inhibitor) [12] being the first targeted therapies approved for metastatic breast cancer and chronic myeloid leukaemia respectively, as early as 1998 and 2001.

Sequencing the Path to Precision Oncology

The genome of a tumour sample was first sequenced in 2008, proving that tumour DNA holds valuable information regarding the drivers of oncogenesis and other mutational events that characterise the disease [13]. Hence, sequencing the DNA extracted from the tumour can offer valuable information about actionable mutations present in the tumour thus allowing for risk stratification, informing therapy choice and predicting response to therapy. Two classical examples in this sense are testing for EGFR mutations in lung cancer to predict treatment response to EGFR tyrosine kinase inhibitors in non–small cell lung cancer patients [14] and gene expression profiling of a panel of genes, including proliferation, invasion, oestrogen and HER2 status marker in breast cancer to predict the response to chemotherapy and recurrence risk [15].

We have come a long way from the first sequencing of a tumour genome, and nowadays tumour sequencing, even if just for a panel of genes, is common practice in many clinical centres. Several large-scale cancer sequencing projects are now looking at optimising the use of NGS in cancer patient care. A good example of such an ambitious project is CGI-Clinics which, through the use of whole-genome sequencing and automatic learning, aims to develop a tool for systematic interpretation, which, through systematic learning, in time, would also uncover the significance of genomic features currently of unknown significance [16].

Multi-Omics: The Next Frontier in Cancer Research

Tumour sequencing is expected to keep revolutionising cancer care in the future. We are now transitioning from a genomics to a multi-omics era. The picture drawn by the genomic discoveries over the past few decades is being completed nowadays by epigenetic and transcriptomics studies. This is possible due to other technological advances such as ChipSeq [17, 18], chromosome conformation capture techniques [19], techniques that capture histone modifications [20] or RNA-seq [21], just to name a few.

Mining Blood for Cancer Clues: The Rise of Liquid Biopsies

Revolution in cancer care might also come in light of the rather old discovery (1977) that tumour cells, like other healthy cells, shed DNA into the bloodstream (cell free tumour DNA; ctDNA) [22]. Although progress regarding the characterisation and utility of such DNA fragments was slow for a rather long time due to technological limitations, the genomic era brings new meaning for ctDNA to patient monitoring and offers the opportunity to monitor treatment response in terms of the development of chemotherapeutic resistance and/or detection of early onset of tumour recurrence [23]. An example in this sense is Galleri, the multi-cancer early-detection blood test developed by GRAIL, currently in clinical trials [24]. This test promises to detect more than 50 different types of samples based on the methylation patterns of ctDNA found in the blood.

Accidental Discoveries to Nobel Prizes: Serendipity in Science

The popularity of genomics in clinical practice in general and cancer care in particular is due to the development of next-generation sequencing (NGS), which increased sequencing efficiency whilst significantly decreasing its costs. However, one must keep in mind that not even the first high-throughput sequencing methods, nonetheless long-read sequencing [25], could have been developed if Sanger hadn’t developed the ‘dideoxy’ chain-termination method coupled with electrophoretic size separation for sequencing DNA molecules in 1977, nor if Paul Berg wouldn’t have developed in 1972 the technology to isolate defined DNA fragments, or Kary Mullis wouldn’t have developed the PCR technique in 1985 [26-29]. Today, we can’t imagine molecular biology without any of these three techniques, but likewise nor could any of these Nobel Prize winners imagine at the time the revolution that their work would bring to biosciences and clinical practice. They were driven by the curiosity to better understand the world around them and determined to find the answer to their questions, not realising how many other questions their work would end up solving in time.

If you wish to go a step further, or backwards in this instance, if not for another unrelated discovery in the late 1960s, Kary Mullis’s PCR would’ve remained a tedious technique that required constant supervision and monitoring to top-up the enzyme in the PCR mix as needed [28, 30]. In 1967, Thomas Brock and Hudson Freeze, through sheer curiosity to find out what organisms might live in the hot springs from Yellowstone discovered Thermus aquaticus, the bacteria from which the DNA polymerase, so crucial for PCR, has been extracted [30-32]. Needless to say, their discovery didn’t gain much attention at the time nor were they able at the time to envision the technological advances their discovery would eventually enable.

As you can see from these paragraphs, the journey from ground-breaking discoveries to finding their clinical applications often takes decades. The road to discovering the translational potential isn’t quite linear either, as progress can sometimes be hindered by the technology available. And equally important, the long-term implications of a new discovery are often unpredictable. This is why it’s so important to invest both time and money in open-question research and to allow scientists to satisfy their curiosities. We at the EACR truly believe that the fundamental, curiosity-driven research of today is the translational and clinical research of tomorrow. And through this ‘Sparks of Curiosity‘ series of mini-articles, we hope to convince you as well.

by Dr. Alexandra Boitor, EACR Scientific Officer

We’d like to thank René Bernards (Netherlands Cancer Institute) for reviewing this article.

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