Assessing Neanderthal Components of Human DNA With Innovative Software
Our close evolutionary cousins, the Neanderthals, gifted us some interesting alleles through hybridization. Image Source: Flickr User: erix!
Neanderthals may have died out 40,000 years ago, but we’re still seeing a their impact on our lives today. Some alleles of Neanderthalic origin have been associated with fat metabolism, depression, and schizophrenia, but the mechanisms contributing to this correlation have been hard to decipher. Researchers have recently reported on differences in expression between Neanderthal and modern human alleles in various genes.1 Bearing this in mind, researchers can move forward using tools like modern lab software to unearth a better understanding of these differences and aim to develop new therapeutics specifically targeting these previously unknown mechanisms.
Homo sapiens didn’t exist in some sort of evolutionary bubble apart from their close evolutionary relatives. In fact, since humans had enough genetic similarity to a number of their cousins, modern humans have benefitted from a bit of interspecies mingling. For example, the introgression of a particularly unusual haplotype containing a hypoxia pathway gene, EPAS1, in Tibetans, thanks to another hominin species, Denisovan, has allowed Tibetans to survive in a high-altitude environment.2
Innovative lab software has allowed scientists to delve in and assess the genomes of Neanderthals, identifying a number of genes that humans have nabbed. Some pertinent examples include the Neanderthal related catabolic genes found at higher concentration in Europeans.3 This may be an area of interest and further research. There are signs of recent positive selection and, as the lipid concentration in the brain is different, this may have bearing on brain composition and potentially its function. This could have further implications in mental health concerns or dementia, but this research is in its early days. As researchers continue to analyze and compare these genetic sequences, comprehensive lab software will be crucial to correctly identifying correlations and seeking explanations which prove causation.
Changes in Mechanisms of Expression
The aforementioned recent study on differential expression between human and Neanderthalic alleles in various genes looked at expression of the two different lineages in 52 different tissues. One of the genes assessed in this study is ADAMTSL3, and it was found that the Neanderthal allele, similar to other alleles, can decrease risk of schizophrenia while influencing height. Previous studies had suggested that the allele affected alternative splicing, which is supported with this new information, in addition to providing a causal explanation. Modern lab software can help researchers assess these differences and draw conclusions more easily. By having access to all this information—from sequences to full protein models in one program—it becomes far more straightforward to draw conclusions about the downstream effects of different alleles.
Additionally, the Neanderthal alleles appear to be upregulated in 49.8% and downregulated in 50.2% of SNPs, which indicate significant allele specific expression (ASE), with no overall directional bias. The mechanisms which are causing this ASE are not fully understood, but with the aid of innovative lab software, it may be possible to better assess all components of genomic data sets and identify underlying mechanisms which sway expression one way or another. For example, introgressed variants exhibiting significant ASE have been linked to human disease traits, and it is possible that through better understanding these genes and the processes contributing to their differential expression, researchers can identify new therapeutics targets for many of these diseases and develop new therapeutics for these illnesses.
BIOVIA Biologics Discovery is a common platform with capabilities that can assist researchers hone in on key targets in a sea of data. With predictive analytics, sequence data mining capabilities and workflow and data management, this technology is what is needed to move these projects forward. This will help carry your lab from target discovery to biologic therapeutic development. Please contact us today to learn more about how our software options can support the efforts of your lab.
- “Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression,” February 23, 2017, http://www.sciencedirect.com/science/article/pii/S0092867417301289 ↩
- “Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA,” August 14, 2014, http://www.nature.com/nature/journal/v512/n7513/full/nature13408.html ↩
- “Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans,” April 1, 2014, http://www.nature.com/articles/ncomms4584 ↩