When assistant professor Dr. Rogier Louwen uploaded the human genome in the CRISPRCasFinder software program, and thousands of hits came back on his computer screen, he experienced a moment of excitement.
The discovery contradicted the consensus in biology that the CRISPR-Cas system is only present in the genetic material of bacteria, archaea, and plants as a system used for defense against viruses. Nowadays, CRISPR-Cas is widely used in the scientific world as a tool to generate DNA changes in a simple, accurate and effective manner.
Louwen and his colleagues found 12,572 CRISPR elements in the human genome and reported their findings in the scientific journal Nature Communications Biology. A CRISPR element is a piece of DNA with a distinctive repeating sequence. The human CRISPRs, as the scientists have named them, are randomly distributed throughout the chromosomes.
What is CRISPR-Cas?
CRISPR-Cas is a complex of a protein (Cas) that works like a scissor and a guiding RNA (CRISPR) that enables scientists to cut any piece of DNA of interest in a specific and precise manner. The CRISPR-Cas system was discovered in bacteria, which use it as a defense mechanism against viruses. Nowadays, many scientists use the CRISPR-Cas system to edit DNA, for example, for gene therapy purposes to cure genetic disorders.
The scientists came across the human CRISPRs through their earlier work when they discovered that the bacterium Campylobacter causes intestinal damage by cutting human DNA with the Cas protein, named Cas9. ‘I found that so remarkable because, at that time, we only knew that Cas9 could only function in combination with a guiding RNA (CRISPR). This made us question the scientific consensus that there are no CRISPRs in the human genome, says Louwen. Their current work reveals that it was a valid question to ask; the presence of CRISPRs in the human genome is now a scientific fact.
Where the human CRISPR elements come from and what they are used for exactly in the human cells is not yet clear. Some of them may originate from infections with retroviruses, which have left their footprint on the human DNA. Retrotransposons are another possibility: pieces of genetic material that spread, multiply and build themselves into the DNA of microorganisms, plants, and eukaryotes. ‘Future research will have to show how this works exactly,’ says Louwen.
However, the scientists already see a possible application of their discovery. They have found that the CRISPR elements in the DNA are transcribed and converted into so-called small non-coding RNAs. It was striking that the expression of these RNAs differed between healthy and prostate tumor tissue. It is, therefore, possible that human CRISPRs could serve as diagnostic markers for cancer and other diseases, the researchers say.
Using a simple test, similar to a rapid corona test or a pregnancy test, the researchers can detect the RNAs that are actively expressed in tissue. The researchers are now working on a way to make this happen in body fluids, such as urine.
This research was the result of a collaboration between the departments of Urology (Prof. Guido Jenster), Pathology/Bioinformatics (Prof. Peter van der Spek), Center of Biomics (Dr. Wilfred van Ijcken), and Medical Microbiology and Infectious Diseases of Erasmus MC. (Dr. Rogier Louwen). The Rotterdam researchers have worked closely together with teams in Amsterdam, Leiden, Dhaka (Bangladesh), and Michigan (USA).