de la Chapelle Lab
Dr. de la Chapelle’s laboratory focuses on the mapping, cloning and characterization of high- and low-penetrance genes for cancer predisposition. When new genes are identified, studies are directed to determine the pathophysiological role of the proteins or RNA molecules they encode, and the mechanisms by which mutations in the genes contribute to the cancer phenotype. Finally, there is an emphasis on translational aspects of the research, viz. the exploitation of laboratory discoveries toward new diagnostic and therapeutic procedures. Diseases under study include colorectal cancer, papillary thyroid cancer and acute myeloid leukemia.
Colorectal cancer (CRC) has high heritability. The putative mutations that likely cause many CRCs eluded the researchers for decades up to the year 1993 when several major discoveries were made implicating mismatch repair genes as culpable. These made it possible to classify tumors as either mismatch repair normal or abnormal. These findings had immediate clinical applications and also allowed epidemiological and screening procedures to diagnose gene carriers at high risk of cancer. The carriers of mismatch repair gene mutations are nowadays said to have Lynch syndrome.
The incentive to study the genetics of Lynch syndrome came from the fact that Dr. de la Chapelle (then at Helsinki) had played a central role in the gene discoveries. At The Ohio State University, the main emphasis was and continues to be on the translational level. The aim was to show how/if screening of all CRC cases on a statewide level could be practiced and whether such screening would be beneficial. As predicted, the concept was valid, and a large study was initiated with participation of patients and hospitals representing a subset of all CRCs in Ohio. The laboratory work was done at Ohio State. In total, 1066 patients were screened for Lynch syndrome, which was found in 23. Genetic counseling in the families of the patients resulted in 52 further cases diagnosed with Lynch syndrome (ref. 1). This was the first and largest study of its kind in the U.S. and stimulated similar screening to be implemented in the routine management all over the country and world. Work on CRC in the de la Chapelle lab gradually switched to application of the recently developed next generation DNA sequencing that allows greatly improved mutation detection. These studies have helped design new, better and cheaper methods of mutation detection (refs 2 and 3). Most recently, the lab has developed methods of mutation detection even more efficiently than before. Dr. de la Chapelle’s collaborations with Heather Hampel in the Division of Human Cancer Genetics has been a forerunner in the field.
These studies have not lost their burning actuality. As detected by others (mainly Dr. Vogelstein at Johns Hopkins University), it has become clear that tumors caused by mismatch repair deficiency respond unbelievably well to therapy with certain antibodies. Dr. de la Chapelle and colleagues have been part of these studies (ref. 4). One important fact is that mismatch repair gene defects do not occur only in CRC or Lynch syndrome but also in subsets of all cancers. Thus, thousands or hundreds of thousands of patients can be screened for a condition that carries a high risk of cancer and/or death. Individuals showing evidence of Lynch syndrome can benefit from surveillance, early cancer detection and adequate therapy if affected.
Papillary thyroid cancer (PTC) is diagnosed in some 50,000 individuals per year in the U.S. PTCs heritability is high, suggesting the occurrence of heritable mutations with high penetrance. As linkage analysis became practically applicable for mutation detection, it became evident that high-risk mutations in PTC did exist that accounted for some large families on record. However, they accounted for a minimal proportion, perhaps some 10% of all heritability of PTC. The de la Chapelle group postulated that instead common but low-penetrance mutations or variants might be responsible. The de la Chapelle lab has been the central player in three so-called Genome Wide Association Studies (GWAS) in search of low-penetrance genes. Indeed, at present, some 15 loci have been implicated as contributors to the risk of PTC. Of these loci, 11 were detected in the de la Chapelle lab. Present studies focus on two specific aims. First, can the effects of these low-penetrant genetic mutations be additive? The answer is a strong yes. The risk in carriers of the risk allele from 10 of these genes can be five- to ten-fold of those who do not carry the risk allele in the same loci. The de la Chapelle lab is planning to put together a panel for risk estimation in thyroid cancer. Second, recently whole genome or exome sequencing of members of 25 Papillary Thyroid Cancer (PTC) families led to the detection of 40 plausible genes showing mutations or variants. These are presently being evaluated as serious candidates for high-penetrance PTC predisposition. First, using targeted sequencing of the genes in large numbers (e.g. 1000) of PTC patients, the incidence of the mutations in sporadic disease is being evaluated. Second, functional assays are being used to determine what molecular functions are affected. Already it is clear that several candidate genes act through molecular pathways that have already been implicated in cancer. Our major aim of this research has to do with the molecular biology of the newly detected risk loci (ref. 5)
A puzzling fact is that thyroid cancer is vastly more common in females than in males. In fact, all common cancers are more common in males, whereas in thyroid cancer, females are three times more likely to have the disease than men. Surprisingly, to our knowledge, no experimental data explaining this disparity has been published. In fact, there are not many speculations as to possible causes. The de la Chapelle lab is presently busy setting up experiments to test the hypothesis that the answer will come from the study of the germline composition of the genome.
A GWAS would seem to be the first technique used to screen for structural variants that affect the two sexes differently. Alternatively, a gene on the Y chromosome that protects against PTC could be culpable. The reason why there appears to be no literature on the subject may be that there are no GWAS panels designed for the Y chromosome and no analytic packages for either the X or the Y chromosome. This is researchable in view of the fact that the X chromosome is well represented in the available probe sets, and the Y chromosome is represented albeit with a small probe set. The de la Chapelle lab is presently just beginning to analyze a series of patients with PTC (male and female) and a series of controls. The number of samples assembled for this purpose is around 1000 from females and about 500 from males. It is estimated that the first results will be available within a month. This experiment is being done by targeted sequencing of germline DNA from blood.
It is possible that the number of cases, especially males, is too small to make firm conclusions. However, even if below-significance association peaks are produced, they will serve as an incentive to analyze further samples and to do so by full-scale GWAS rather than the present targeted approach.
When significant association is established for a gene, its structure and function will be “annotated,” and eventually, the effect of variants (SNPs) on function will be characterized. In the ideal scenario, a regular protein-coding gene will be found to occur only on the Y chromosome but not the X, and one of its alleles will be found more often in affected than unaffected males. Such a finding would then rapidly lead to further functional assays but also animal experiments to prove the hypothesis.
Acute Myeloid Leukemia
In acute myeloid leukemia, the group previously cloned a novel gene, BAALC (Brain and Acute Leukemia, Cytoplasmic), that is expressed in early hematopoietic progenitor cells and in a subset of acute myeloid and lymphoid leukemias. Ongoing studies seek to understand the role of BAALC in leukemogenesis. The hypothesis is that BAALC is a marker of, or even a contributor to, blocked differentiation of these cells. Surprisingly, in vitro and in vivo studies have implicated miR-3151 in the development of acute myeloid leukemia. This miR is “hosted” by the BAALC gene being located in intron 1 of BAALC. It appears that the major pathogenic player is miR-3151 rather than BAALC. More recently, a GWAS of AML patient revealed variants in at least three chromosomal loci (19q, 19p, 1q) that associate with AML risk (ref. 6) These are the first low penetrance, high frequency genomic changes that have been identified in AML. Functional assays are being done to determine the underlying molecular mechanisms.
In summary, the de la Chapelle laboratory is devoted to the detection of genes that when mutated cause cancer risk. This mostly suggests changes in the germline with implications for diagnostic work. As somatic (acquired) mutations are found, they may lead to a better understanding of the malignant process. In the best-case scenario, both types of mutations can inform successful drug development.
1. Hampel H, Frankel WL, Martin E, Arnold M, Khanduja K, Kuebler P, Nakagawa H, Sotamaa K, Prior TW, Westman J, Panescu J, Fix D, Lockman J, Comeras I, de la Chapelle A: Screening for the Lynch Syndrome (Hereditary Nonpolyposis Colorectal Cancer) New Engl J Med 352:1851-1860, 2005
2. Hampel H, Pearlman R, Beightol M, Zhao W, Jones D, Frankel WL, Goodfellow PJ, Yilmaz A, Miller K, Bacher J, Jacobson A, Paskett E, Shields PG, Goldberg RM, de la Chapelle A, Shirts BH, Pritchard CC for the Ohio Colorectal Cancer Prevention Initiative Study Group: Assessment of tumor sequencing as a replacement for Lynch syndrome screening and current molecular tests for patients with colorectal cancer. JAMA Oncology 4:806-813, March, 2018
3. He H, Li W, Liyanarachchi S, Jendrzejewski J, Srinivas M, Davuluri RV, Nagy R, de la Chapelle A: Genetic predisposition to papillary thyroid carcinoma: involvement of FOXE1, TSHR and a novel lincRNA gene, PTCSC2. J Clin Endo Metab 100(1):E164-72, 2014
4. Le DT, Uram JN, Wang H, Bartlett BR, Kemberling H, Eyring AD, Skora AD, Luber BS, Azad NS, Laheru D, Biedrzycki B, Donehower RC, Zaheer A, Fisher GA, Crocenzi TS, Lee JJ, Duffy SM, Goldberg RM, de la Chapelle A, Koshiji M, Bhaijee F, Huebner T, Hruban RH, Wood LD, Cuka N, Pardoll DM, Papadopoulos N, Kinzler KW, Zhou S, Cornish TC, Taube JM, Anders RA, Eshleman JR, Vogelstein B, Diaz LA Jr.: PD-1 blockade in tumors with mismatch-repair deficiency. New Engl J Med 372:2509-2520, 2015
5. He H, Li W, Liyanarachchi S, Jendrzejewski J, Srinivas M, Davuluri RV, Nagy R, de la Chapelle A: Genetic predisposition to papillary thyroid carcinoma: involvement of FOXE1, TSHR and a novel lincRNA gene, PTCSC2. J Clin Endo Metab 100(1):E164-72, 2014
6. Walker CJ, Oakes CC, Genutis LK, Giacopelli B, Liyanarachchi S, Nicolet D, Eisfeld AK, Scholz M, Brock P, Kohlschmidt J, Mrózek K, Bill M, Carroll AJ, Kolitz JE, Powell BL, Wang ES, Niederwieser DW, Stone RM, Byrd JC, Schwind S, de la Chapelle A, Bloomfield CD. Genome-wide association study identifies an acute myeloid leukemia susceptibility locus near BICRA Leukemia 33:771-775, 2019
Huiling He, MD – research scientist
Sandya Liyanarachchi, MS – research scientist
Taina Nieminen, PhD – visiting scholar
Ann-Kathrin Eisfeld, MD – clinical fellow
Wei Li, MD – research associate
Jan Lockman, BS – research associate, lab manager
Daniel Comiskey, PhD – postdoctoral researcher
Alaa Ali, MD – postdoctoral researcher
Ravi Patel – postdoctoral researcher
Barbara Fersch – assistant to Dr. de la Chapelle