Explore the relationship between mitochondrial DNA variants and complex diseases through our interactive tools and graph-based databases to better understand the connections between genes and mitochondrial DNA variants behind complex diseases.
Diseases Covered
Gastric cancer
Gastric cancer or stomach cancer, is a malignancy that develops in the lining of the stomach. It is a serious disease that can have a high risk of spreading to other parts of the body. The disease is also often associated with vague symptoms in its early stages, making early detection difficult. In Brazil, the disease stands out in the north and northeast regions.
Study proposal
The association studies brought about by this tool can help in better understanding the genetic factors that can increase the risk of this disease.
These studies may help identify genetic markers that could be used in the early detection and personalized treatment of gastric cancer.
Parkinson's disease
Parkinson's disease is a chronic neurodegenerative disorder that primarily affects the central nervous system and causes symptoms such as tremors, muscle stiffness, and movement difficulties. As it progresses, Parkinson's disease can affect people's quality of life and limit their ability to carry out everyday tasks.
Study proposal
The relevance of studying genetic associations, in this case more specifically relationships with mtDNA, and Parkinson's disease is related to the search for genetic factors that contribute to the risk of developing this disease. Research in this field may shed light on how mtDNA mutations affect neuronal function and ultimately contribute to Parkinson's disease.
Studying the relationships between mtDNA and neurodegenerative diseases such as Parkinson's is important to better understand the underlying mechanisms of the disease and could potentially lead to better diagnosis and the development of more effective treatments in the future, such as possible targeted therapies.
Leprosy
Hanseniasis, also known as leprosy, is a chronic infectious disease caused by the bacteria Mycobacterium leprae. It mainly affects the skin and peripheral nerves, and can cause skin lesions and neurological damage. Hanseniasis is a contagious disease, but it is rare and is usually transmitted through prolonged contact with an infected person.
Study proposal
A relevant study of associations between mtDNA variants and infectious diseases, such as leprosy, lies in understanding how this area of genetics can influence susceptibility to this disease. These studies can clarify whether some people are more likely to contract the disease and help develop prevention and treatment strategies.
Studying these diseases from an association perspective with mitochondrial DNA variants can provide valuable information on the genetic factors that contribute to their development and progression. This research can have a significant impact on the prevention, diagnosis, and treatment of these diseases.
Data source
The data initially used as a basis for creating the data sets used in creating the network graphs for the diseases mentioned above, originated in other works already produced or produced in parallel to this one.
Attention: The variants present in all data sets published here are only the variants (somatic and germline) identified in the disease study samples represented by the central nodes, in green, of the association networks, which means that no variants were included exclusive to other diseases present in the association networks, but only the variants shared with the diseases mentioned above.
For more details about the data used, click read more.
References
• Cavalcante, G.C., Ribeiro-dos-Santos, Â. & de Araújo, G.S. Mitochondria in tumour progression: a network of mtDNA variants in different types of cancer. BMC Genom Data 23, 16 (2022). https://doi.org/10.1186/s12863-022-01032-2
• Cavalcante GC, Marinho ANR, Anaissi AK, et al. Whole mitochondrial genome sequencing highlights mitochondrial impact in gastric cancer. Sci Rep. 2019;9(1):15716. Published 2019 Oct 31. doi:10.1038/s41598-019-51951-x
• Yuan Y, Ju YS, Kim Y, et al. Comprehensive molecular characterization of mitochondrial genomes in human cancers [published correction appears in Nat Genet. 2020 Feb 11;:] [published correction appears in Nat Genet. 2020 Apr 27;:]. Nat Genet. 2020;52(3):342-352. doi:10.1038/s41588-019-0557-x
• de Souza, F.G., da Silva, M.B., de Araújo, G.S. et al. Whole mitogenome sequencing uncovers a relation between mitochondrial heteroplasmy and leprosy severity. Human Genomics 17, 110 (2023). https://doi.org/10.1186/s40246-023-00555-8
• Matos, G.B., Dos Santos C.S., De Sousa, T.P. et al. 2024. “Dynamic shifts of mitogenome-wide mutation repertoire in progression of Parkinson´s Disease”. Preprint, submitted on May 10, 2024
Gastric cancer samples
The mutation-cancer network, based on two datasets, is a graph G(V, E), where V comprises two distinct sets of nodes: mitochondrial mutations (u) and cancers (v).
The research of the gastric cancer study where the samples were collected included:
Case (n = 40) and control (n = 50) groups with gastric tissue samples (tumor, adjacent and normal). Sequencing details and primary analyzes are provided by Cavalcante et al. (2019).
The other types of cancer added to the network came from data extracted from The Cancer Mitochondrial Atlas - TCMA.
Parkinson samples
The data samples comprise 96 individuals, divided into case and control. The case group comprises 48 patients with idiopathic Parkinson's disease, with 27 not presenting levodopa-induced dyskinesia (LID) and 21 presenting LID. The control group consists of 48 individuals without Parkinson's disease or other neurodegenerative diseases (Santos et al., 2023, under review).
Hanseniasis samples
Composed of blood samples of leprosy patients (case group, n = 33) and control individuals, healthy household contacts (control group, n = 37). The group of cases is subdivided into three subgroups according to the type of leprosy: borderline lepromatous (BL) leprosy (n = 12), lepromatous (LL) (n = 11) and borderline tuberculoid (BT) leprosy (n = 10) ( Souza et al., 2023).
Our Developers
Gilderlanio Araújo
labored on all versions of tool
PhD in Bioinformatics (UFMG) allocated at LGHM and associated with the PPG in Genetics and Molecular Biology at UFPA. Currently is a visiting teacher working in the area of computational biology.
Letícia C. de Macêdo
labored on second version of tool
Graduating in biomedical engineering from UFPA. Currently works as a scholarship holder for the Fapespa scientific initiation program in the area of web development, in the bioinformatics sector at LGHM.
Ândrea R. dos Santos
labored on all versions of tool
PhD in Genetics (USP) and Post-Doctor (Indiana University). Currently a full teacher and coordinator, both at UFPA, of the Postgraduate Program in Genetics and Molecular Biology (PPGBM) at LGHM.
Giovanna Cavalcante
labored on first version of tool
PhD in Genetics and Molecular Biology (UFPA) with sandwich period at the Winship Cancer Institute of Emory University (Atlanta, USA). Was a visiting teacher linked to PPGBM/UFPA at LGHM.
