Teasing apart which is which remains challenging. Regardless of what factors contribute to homoplasmy, the process appears to take considerable time. Greaves et. al. showed that in normal colon, homogeneously COX1staining crypts do not appear until after the age of 40 and that these divide to form small clusters of related crypts that increase in size with age [79]. Presumably crypt division begins at a younger age but is not yet histochemically visible because the COX1- genotype has not had sufficient time to propagate to homoplasmy within the crypt stem cells. This is one illustration of a general consideration for all markers of cell lineage that is discussed further below he inability to detect a clonal marker is not de facto evidence for the absence of a clone. The temporal delay of homoplasmy makes mitochondrial mutations a potentially problematic tool for identifying early neoplastic clones in the young. Emerging sequencing technologies [87] and other techniques capable of high resolution mutation analysis [74] are beginning to permit detailed investigation of low-frequency, heteroplasmic mtDNA mutations, which may partially obviate this concern in the future.NIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author ManuscriptSemin Cancer Biol. Author manuscript; available in PMC 2011 October 15.Salk and HorwitzPage7. EpimutationsAnother sometimes forgotten source of molecular information that is Chloroquine (diphosphate) manufacturer heritably transmitted during cell division is DNA methylation. Following genome replication, DNA methyltransferases copy the methylcytosine profile of the parent molecule to the newly synthesized daughter strand. While a relatively accurate process (approximately 1? mistakes introduced per 105 residues copied [90]), it remains considerably more error-prone than DNA replication itself (rates variably estimated to be from 10-9-10-11 per base per cell division in normal tissues [91]). De novo methylation tends to increase with age [92], most specifically, mitotic age [93]. Thus, just as with DNA mutations, methylation error patterns serve as a record of somatic cell ancestry. Silencing of gene expression through hypermethylation is a common phenomenon observed in cancer [94]. There have been a variety of reports of similar epigenetic changes in nondysplastic tissue surrounding tumors. Shen et al identified methylation of the MGMT gene promoter in normal-appearing tissue flanking sporadic colorectal cancers [95]. Ushijima and colleagues have demonstrated promoter methylation of both protein-coding genes and microRNAs in non-cancerous mucosa around gastric cancers associated with helicobacter infection [96]. Similar epigenetic changes have been observed in tissues adjacent to cancers in liver [97], esophagus [98,99], lung [100], breast [101], kidney [102], and bladder [103], among others. Interpreting the results of many of these studies in terms of clonality is complicated. While “fields” of methylation changes certainly exist around some cancers, it is difficult to know that these necessarily represent clonal entities from which the cancer evolved. The predominantly used technique (order Cycloheximide methylation-specific PCR) can detect epigenetic changes in a small percentage of cells in a population and offers a general assessment of methylation across a CpG island rather than a readout of specific methylated bases that would be needed for rigorous lineage assessment. Without this information, it is conceivable that such signals might result from agg.Teasing apart which is which remains challenging. Regardless of what factors contribute to homoplasmy, the process appears to take considerable time. Greaves et. al. showed that in normal colon, homogeneously COX1staining crypts do not appear until after the age of 40 and that these divide to form small clusters of related crypts that increase in size with age [79]. Presumably crypt division begins at a younger age but is not yet histochemically visible because the COX1- genotype has not had sufficient time to propagate to homoplasmy within the crypt stem cells. This is one illustration of a general consideration for all markers of cell lineage that is discussed further below he inability to detect a clonal marker is not de facto evidence for the absence of a clone. The temporal delay of homoplasmy makes mitochondrial mutations a potentially problematic tool for identifying early neoplastic clones in the young. Emerging sequencing technologies [87] and other techniques capable of high resolution mutation analysis [74] are beginning to permit detailed investigation of low-frequency, heteroplasmic mtDNA mutations, which may partially obviate this concern in the future.NIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author ManuscriptSemin Cancer Biol. Author manuscript; available in PMC 2011 October 15.Salk and HorwitzPage7. EpimutationsAnother sometimes forgotten source of molecular information that is heritably transmitted during cell division is DNA methylation. Following genome replication, DNA methyltransferases copy the methylcytosine profile of the parent molecule to the newly synthesized daughter strand. While a relatively accurate process (approximately 1? mistakes introduced per 105 residues copied [90]), it remains considerably more error-prone than DNA replication itself (rates variably estimated to be from 10-9-10-11 per base per cell division in normal tissues [91]). De novo methylation tends to increase with age [92], most specifically, mitotic age [93]. Thus, just as with DNA mutations, methylation error patterns serve as a record of somatic cell ancestry. Silencing of gene expression through hypermethylation is a common phenomenon observed in cancer [94]. There have been a variety of reports of similar epigenetic changes in nondysplastic tissue surrounding tumors. Shen et al identified methylation of the MGMT gene promoter in normal-appearing tissue flanking sporadic colorectal cancers [95]. Ushijima and colleagues have demonstrated promoter methylation of both protein-coding genes and microRNAs in non-cancerous mucosa around gastric cancers associated with helicobacter infection [96]. Similar epigenetic changes have been observed in tissues adjacent to cancers in liver [97], esophagus [98,99], lung [100], breast [101], kidney [102], and bladder [103], among others. Interpreting the results of many of these studies in terms of clonality is complicated. While “fields” of methylation changes certainly exist around some cancers, it is difficult to know that these necessarily represent clonal entities from which the cancer evolved. The predominantly used technique (methylation-specific PCR) can detect epigenetic changes in a small percentage of cells in a population and offers a general assessment of methylation across a CpG island rather than a readout of specific methylated bases that would be needed for rigorous lineage assessment. Without this information, it is conceivable that such signals might result from agg.
