Jeffrey S. Buguliskis Ph.D. Technical Editor Genetic Engineering & Biotechnology News

Research Shows that Many Carcinogenic Mutations Are Not Derived from Either Parent

Conventional wisdom has steered scientists for many years toward the assumption that disease-triggering genetic mutations were inherited by offspring from existing mutations within parental DNA, and that these mutations reside within all somatic cells, eventually emerging due to some perturbation of the cellular environment. However, over the past several years experimental and genomic data has shown that many of the mutations that lead to carcinogenesis originate somatically, i.e., de novo  mutations generated in offspring that are undetectable in either parent.

While inherited (germline) mutations are ascribable, since they follow familial genetic patterns, the underlying causes and traceability of somatic mutations has been problematic for many years. However, due to the increased accessibility and cost effectiveness of next-generation sequencing (NGS) techniques such as whole- genome sequencing (WGS) and whole-exome sequencing (WES), researchers have been able to readily identify somatic mutations and begin to categorize them based on the nature of the mutation, as well as the tissue from where it was derived.      

Reporting in the February issue of Nature for example, scientists at Harvard University and the Broad Institute analyzed 173 cancer genomes from eight different cancer types, which represented a wide array of tissue origins. The researchers compared the distribution of mutations in these cancer genomes to 424 epigenetic markers from similar tissue origins where the cancers were derived. The researchers found that the genomic dispersal of epigenetic features aligned to the tumor’s tissue and cell type origin. This led the authors to conclude that “the DNA sequence of a cancer genome encompasses a wealth of information about the identity and epigenomic features of its cell of origin.”  


Who’s Driving this Bus?

Many cancers emanate from somatically acquired changes within the DNA of cancer cells. Yet, not all of the somatic abnormalities that have been identified in the cancer genome are involved in carcinogenesis. Indeed, a fair amount have made no contribution at all. To address this phenomenon, scientists have developed terminology that groups somatic mutations into two categories, drivers and passengers.

Driver mutations contribute to oncogenesis by conferring an advantage to cancerous cells, allowing them to rapidly adapt to local microenvironments, as well as bestowing an abnormally high mutation rate upon the molecular machinery. This allows the carcinogenic process to be driven by a handful of mutations and chromosomal abnormalities.  

Conversely, a passenger mutation retains no growth advantage to be selected for and is, therefore, not thought of as being a contributing factor toward cancer development. Passenger mutations are, however, found within the cancer genome since somatic mutations often occur during cell division without functional consequences. Hence, a cell that contains a passenger mutation will clonally expand carrying the mutation within all of the cells from that point forward.

Until recently, identifying and distinguishing driver from passenger mutations was difficult. However, in 2004 a database was created to deposit genetic information connected with somatic mutations in cancer. The catalogue of somatic mutations in cancer (COSMIC) began with data from just four genes known to be involved in tumorigenesis. Currently, the database describes over two million point mutations from more than one million tumor samples. While COSMIC has greatly aided in the identification of some driver mutations, many still remain elusive. Yet, algorithms are being continuously created to improve the accuracy of driver recognition.  


By studying epigenetic phenomena, i.e., the modulation of gene expression by the methylation of a DNA segment, scientists believe they can gain a better understanding of the development of somatic mutations. [Media Bakery]

Epigenetics Takes Place

One of the more current strategies for identifying drivers of somatic mutations in cancer has come from studies observing the increased role that epigenetic mutations play. Epigenetics typically refers to, although not exclusively, the modulation of gene expression through direct DNA methylation or changes in chromatin structure by histone modifications without changing the genetic sequence.

Recent evidence has shown that alterations in the epigenome are associated with all aspects of cancer, from initiation of tumors, to cancer progression and metastasis. Moreover, NGS has identified a number of driver mutations within epigenetic regulators, which provides a molecular link between the normal and cancer epigenome. “Detection of mutations in genes responsible for epigenetic modification is also an important aspect of designing therapeutic approaches,” said Maher Albitar, M.D., chief medical officer and director of research and development for NeoGenomics Laboratories.

It is important to understand the structural nature of packaged DNA within the nucleus, as this is where the majority of epigenetic regulation takes place. Briefly, condensed DNA, or chromatin, is composed of thousands of functional units—nucleosomes—which are composed of core histone proteins arranged in an octameric structure that is encircled by 147 base pairs of DNA. This packaging mechanism is performed by all eukaryotic cells to not only contain the massive length DNA, which is roughly 300 times longer than the average diameter of a nucleus, but to protect the genetic code from damage and control rates of replication and expression.

Epigenetic regulation of nucleosomes often occurs in the form of protein/DNA modifications through methylation, acetylation, sumoylation, ubiqutination, and phosphorylation by enzymes that either add or remove functional groups from DNA or histone proteins. The activity of these enzymes ultimately changes the structure of chromatin, which in turn modifies the accessibility to DNA promoter regions for gene transcription, as well as regulating the replication and genomic maintenance molecular mechanisms.


Driving Toward an Underlying Mechanism

Some of the earliest molecular features observed in cancer cells were aberrant methylation patterns, but it wasn’t until several decades later that the intrinsic nature of epigenetic changes would be fully understood. Recently, WGS and WES studies have not only demonstrated that mutations in epigenetic regulators are linked to an array of cancerous tumors, such as adenoid cystic and renal carcinoma, they have identified the driver mutations that are promoting tumorigenesis for these cancers. 

In a recent example from the scientific literature, Australian scientists from Monash University reported this March in Nucleic Acids Research how phosphorylation of the histone variant H3.3 is critical for chromatin maintenance and survival of human ALT cancer cells. This study identified a new role for the histone kinase CHK1, showing its increased phosphorylation activity on serine 31 of H3.3 in ALT cancer cells. The researchers surmise that alterations to H3.3 may drive cancer progression in ALT cells, since it showed a similar role in pediatric glioblastoma. Furthermore the Monash teams stated that this was “the first evidence of the existence of aberrant epigenetic histone modification profiles in ALT cells” and that it could provide “a promising new therapeutic target for treatment of ALT cancers.”

Additionally, another Australian research group from the University of Sydney discussed the role of the methyltransferase EZH2 in the development of malignant melanoma in Pigment Cell & Melanoma Research last June. The scientists explained how incremental increases in activity for EZH2 were observed when cells advanced from benign nevi to metastatic melanoma, leading to the conclusion that EZH2 has a strong association with the progression of melanoma. Furthermore, the authors examined approaches for developing inhibitors to this enzyme and the potential therapeutic value they hold.

These are just two examples describing the influence of epigenetic regulators on somatic mutations of cancer. The epigenome exerts a huge influence over a multitude of genetic diseases and we are just beginning to fully understand the circuitous nature of its regulatory power. “It is a very exciting time for medicine and oncology,” explained Dr. Albitar. “However, more work is needed to understand the interaction between various molecular abnormalities.”

With the exponential utilization of NGS techniques to identify driver mutations, a comprehensive map linking epigenetic regulators and somatic mutations of cancer should develop quickly, hopefully identifying new drug targets along the way. 







































Jeffrey S. Buguliskis, Ph.D. (jbuguliskis@genengnews.com), is Technical Editor of GEN and Clinical OMICs. 

This article was originally published in the April 2015 issue of Clinical OMICs. For more content like this and details on how to get a free subscription to this digital publication, go to www.clinicalomics.com.