Dr. Johan de Boer

Adjunct Associate Professor, Biology Department
member of the Consortium for Genomics Research on Atlantic Salmon Project (cGRASP)
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Phone: (250) 472-4079
Research area: DNA repair, prevention of cancer through diet, salmon genetics
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Research profile:

GRASP: Salmon transposons offer key to evolution

The more he looks at it the more Dr. Johan de Boer believes there is no such thing as junk DNA. He is currently looking at a genetic element often considered junk: transposons. Transposons account for up to 50 per cent of plant and animal DNA, even though they don’t code for plant or animal genes. They are called jumping genes because of their ability to excise themselves and move around in genomes. They act somewhat like a parasite in that they replicate themselves independently without an obvious benefit for the host.

De Boer is studying transposons in Atlantic salmon as part of the consortium for Genomic Research on All Salmon Project (cGRASP), a group of international researchers who are mapping all of the expressed genes of Atlantic salmon.

De Boer recently published a paper (BMC Genomics), giving strong evidence that transposons provide a mechanism for periods of rapid evolution. He found a several bursts of transposon activity that coincided with a period of rapid evolution in a salmon ancestor, leading to whitefish, graying and about 30 species of salmon and trout.

De Boer identified more than 14 transposon families in Atlantic salmon, and he tracked transposon activity by comparing transposon sequences across salmon species. He found transposons that seem to have replicated often, resulting in multiple copies, sometimes even copies within copies. Most have become inactive (with evidence of several insertion and deletion mutations) and their sequences have begun to diverge as the species have differentiated.

As interesting as de Boer finds this work, studying transposons has many applications beyond understanding evolution in salmon. By characterizing the sequences of transposons, de Boer will help geneticists streamline their DNA analysis by helping researchers recognize and exclude transposon sequences when they want to look at a species’ functional genes.

New Oncology and Nutrition group

Dr. Johan de Boer has extensive experience finding links between diet and cancer. He is following up on that experience as a member of a Michael Smith Team Planning group at the BC Cancer Agency to build a new Oncology Nutrition research group.

De Boer and his collaborators are interested in how diet can affect the recurrence rate of prostate, breast or colon cancer.

They recently submitted a review for publication that evaluates existing clinical studies related to this question. Nutrition and cancer is a notoriously complex problem to tackle and the group found that out of 34 published clinical trials related to prostate cancer recurrence, only eight were free from poor experimental design. They hope to use the review as a foundation to develop an Oncology Nutrition group.

Breast Cancer more than just genes

In another project, Dr. Johan de Boer has teamed up with CBR member Dr. Patrick MacLeod to study breast cancer.

They are looking at the well-known breast cancer genes BCRA1 and BCRA2. Women carrying a mutation in these genes have an increased risk for breast or ovarian cancer, but mutations in these genes only account for about five percent of breast cancer cases.

MacLeod and de Boer theorize that some breast cancers occur not because the gene is mutated but because the gene is never expressed.

One way in which genes are regulated is through methyl groups that bind to the regulatory region of the gene, blocking the gene’s expression.

In a preliminary study, de Boer and MacLeod explored ways to measure methylation on the regulatory region of the BCRA1 gene in breast cancer patients in the hope of expanding their studies of BCRA1 methylation this year.