Apparently, there is no relationship between the different haplogroups associated with protection against breast cancer. However, when we analyzed the sequence information, it is possible to observe polymorphisms commonly related to breast cancer. It is important to note that most of the samples have a European origin and these are similar to half of the population with breast cancer (44.9%) and to the sequence used as the rCRS reference genome in the database and genomic browsers.
Otherwise, of the 241 polymorphisms exclusive in neoplastic tissue, only 9 were repeated in more than 3 different sequences in our analysis: A16183C repeat in 11 different sequences, T16217C in 5, and T16298C in 4 sequences. Some of these changes in the mtDNA sequences are related with other malignant neoplastic diseases (49).
These variants in D310 were present in 98% of the analyzed sequences. Although most of these polymorphisms are commonly associated with specific haplogroups, it was identified that the 315.1C polymorphism, evolutionarily is associated with haplogroup H of Caucasian origin and infrequent in Indo-European haplogroups with a frequency lower than 1.5%. In our analysis in 99% of sequences of non-European origin with breast cancer.
It is an important focus that T16189C and T16311C are positioned in the HVR1 and T16519C is placed in a non-coding position in the control region. In our analysis we found a characteristic pattern related to breast cancer characterized by the presence of 315.1C and the absence of C309CCT and C310T; and in the same way, when polymorphisms C309CCT and C310T are present, 315.1C was invariably absent. Although when analyzed individually, each of these changes has no statistical significance (tables 5 and 6), the 315.1C polymorphism was identified related in the literature mainly to haplogroup H of Caucasian origin and infrequent in Indo-European haplogroups with a frequency lower than 1.5%, in our analysisit was found in 99% of the non-European sequences with breast cancer.
In a previous study, we identified that the polymorphism 315.1C is not associated with breast cancer. However, it has as areference two samples of a medium prevalence and very low for neoplastic disease (55). This change into the sequence is written 315.1C, where.1C means that a copy of the base C has been inserted at position 315 compared to the rCRS, so it is translated into these sequences and the rCRS is slightly (a base) more extensive than many other sequences in mitochondrial genomes.
The polymorphism 315.1C is considered to be one of the most recent mutations occurred in the last 60,000 years. This is the type of mutations, now well accepted and detailed in many of the phylogenetic trees, related to haplogroup H (56). Although this haplogroup is related to populations of ethnic origin, it has been found to have a high prevalence in Latin American mestizos and in other populations with different haplogroups (55–61).
The polymorphisms, 315.1C and C309CCT-T310C, which are found in the non-coding HVR2 fragment of the D-Loop at the mtDNA control region, are considered as an access point due to the high frequency of changes. Furthermore, the modifications of these have been given the go-ahead, may have implications with the appropriate transcription and regulation of mitochondrial genome expression. This Poly-C hotspot area is located in the mitochondrial genome between positions 303–315, defined as D310, and is considered very polymorphic and can be different between direct relatives by the mother line (48,62–64).
Due to the high prevalence in Caucasian groups, 315.1C usually is not considered during the bioinformatic analysis and is not used in the construction of phylogenetic trees. This is the reason why it is usually going unnoticed. However, there are reports in the literature where the 315.1C polymorphism is associated with various forms of cancer and other chronic-degenerative diseases (53,63) This poly-C tract in the mitochondrial D-Loop located commonly between 303 and 315 nucleotides has been identified as a frequent hotspot mutation region in human neoplasia, including breast cancer (56–58), suggesting that mtDNA instability in this site may be a common characteristic in this malignant disease.
In Mexico, there is a high prevalence and incidence of breast cancer, however, is lower than the United States of America or Western Europe, due to both populations have Caucasian ancestry. In the northern of Mexico there is a higher prevalence of breast cancer compared to central and southern of the country. This discrepancy could explain it because in the north there is European ancestry to difference to the south where is mainly indigenous and the principal variants are C309CCT-C310T, del306 and C310T-G306C, most commonly related to Amerindian populations with lower frequency of breast cancer (data not published by Baptista Rosas et al. 2019).
Is important to remark that in our analysis the presence of T16519C, was found in near 60% of the breast cancer sequences and less than 20% of controls sequences. Other studies have focused on this polymorphism, apparently, without relation with other polymorphisms previously described in the available literature (20,32–35,38). Moreover, the association of several variants resulted in a significant predictive breast cancer factor. Indeed, A10398G, usually associated with breast cancer in other studies, (28,29,31–34,52) was found only in 24% of the mtDNA sequences analyzed, without statistical significance and in association with other mutations such as T4216C, G9055A, A12308G or T16519C. It was found to increase the risk of developing breast cancer (36).
T16519C is associated in the Phylotree database between the branches to haplogroup L5 and Haplogroup L2 with other 11 mutations: T16311C, T16189C, C16187T, A15301G, C13506T, A13105G, T10810C, G10688A, C8655T, T825A, and G247A, back to its CRS value and usually found in Euro Asiatic mitogenomes. These ancient polymorphisms have arisen 140,000 years ago, and are considered part of the suggested Mitochondrial Eve genome, supporting the theory to first human migration outside of African continent (56).
Once again, the high number of mutations suggests that there was a significant bottleneck in human evolution at the time, perhaps around 120,000 years ago, which might have lasted for many thousands of years (56).
Finally, the molecular mechanisms underlying that increased risk of cancer, due to these specific mtDNA polymorphisms, are still unclear. The control region is important for the regulation of mitochondrial genome replication and expression. The polymorphisms in this region might affect mtDNA replication and lead to electron transport chain alteration, resulting in compensatory increases in glycolytic ATP production (66). However, one of the inevitable products of these alterations is an increased release of highly reactive oxygen species, which may lead to mitochondrial abnormalities. These abnormalities invoke a mitochondria-to-nucleus retrograde response and finallyresult in nuclear genome damage, which contributes to initial events related to carcinogenesis (67–69). The regulation of mitochondrial genome replication from the control region might also lead to the mtDNA damage (70–72) and, with a critical number of mitochondrial genome changes, to cellular apoptosis (73), which finally could induce cancer development.
The evidence so far suggests that these changes previously described in the literature and the findings in our analysis are probably theresult of damage by oxidative stress at the level of the mitochondrial genome rather than being the origin of the changes associated with carcinogenesis.
Further analysis is required with the objective to evaluate more sequences and calculate the correlation with the risk in the development of malignancy.
This approach will give us a general perspective about the importance of consolidating the evidence in specialized repositories and that has not been crossed yet. Finally, it is important to include populations of different origins than Caucasian with the purpose of showing the genetic differences related to breast cancer, regardless of high and low prevalence. With this focus, our understanding of these malignant diseases will improve through the interpretation of the complete mitogenome.