Genomics of profound shock and trauma

The human genome

The genome is the complete set of information in an individual’s DNA. In humans, the genome contains approximately 22,000 protein-coding genes, which, with transcriptional variants and posttranslational modifications, give rise to the millions of physiologically acting proteins in the human proteome. These protein-coding genes are the most studied yet only account for approximately 1.5% of the genome. Our knowledge of the genome has made remarkable advancements since the identification of the structure of DNA in 1953, but our understanding of the remaining 98% is still quite limited. The investigation into the noncoding segment of the genome and its variations may be the key to determining an individual’s susceptibility to disease as well as why different individuals respond differently to physiologic stress.

Protein coding gene structure and function has been examined extensively. The basic composition includes a promoter (located on the upstream or 5′ end), followed by the coding sequence, then a terminator region (on the downstream, 3′ end). The promoter is a DNA base-pair sequence that specifies where transcription begins. This region binds proteins known as transcription factors, which recruit RNA polymerase. The complex subsequently initiates the generation of messenger RNA (mRNA). The following coding sequence contains regions of nucleotides that are coding (exons) and noncoding (introns). Introns are removed during RNA splicing allowing for exons to be joined together forming a contiguous coding sequence. The terminator region is a nucleotide sequence that specifies the end of the mRNA transcript. The resultant mRNA strand is later translated to a sequence of amino acids during protein synthesis. The translation process is terminated when a particular sequence of nucleotides, known as a “stop codon,” is encountered.

The function of noncoding DNA sequences remain less well understood. Most of these sequences exist between genes on the chromosomes and most have no currently known function. Studies in comparative genomics, the study of evolutionary DNA conservation, have demonstrated there are highly conserved noncoding DNA sequences, sometimes on time scales of hundreds of millions of years. This implies that these regions are under strong evolutionary pressure and positive selection. Studies have suggested that some disease-causing genetic variants are not the result of aberrant proteins but rather due to variations in the noncoding DNA. Noncoding polymorphisms have been shown to play a role in an individual’s susceptibility to certain infectious diseases, such as hepatitis C, as well as certain cancers, including Ewing sarcoma.

Variability in DNA macrostructure also contributes to the functional regulation of the genome. Histones are proteins that provide structural support to a chromosome. Linear DNA molecules wrap around histone protein complexes allowing for a more compact shape. While initially thought to only serve a structural purpose, histones have been shown to play an important role in gene regulation and expression. Histone modification with subsequent interference of the DNA-histone interaction can cause alterations in chromatin compaction, nucleosome dynamics, and transcription. This dysregulation can shift the balance of gene expression contributing to or directly causing many known disease processes. Mutations in chromatin-bound proteins are among the top frequently mutated targets in cancer.

Genetic divergence

Our genetic composition contributes to all disease processes, or lack thereof, by inherent or acquired differences in our DNA. Some of these differences may render an individual more susceptible to a particular disease while others may be protective against an unrelated disorder. Other factors, such as environmental exposures, contribute to these susceptibilities though an individual’s response to such an exposure may vary based on their DNA. For example, many cancers result from an accumulation of genetic changes, influenced by environmental factors that occur over one’s lifetime.

While researchers are still determining key functional aspects of the human genome, the genetic basis of disease has been studied. Single-gene disorders are perhaps the simplest to understand. They have a relatively straightforward inheritance pattern (dominant, recessive, X-linked) and while a single gene primarily causes them, different mutations can result in varying degrees of severity and phenotype. Single-gene disorders are individually rare but account for 80% of rare disorders, of which there are several thousand. Examples include cystic fibrosis and hemochromatosis.

The most common type of DNA variation results from single nucleotide polymorphisms, or SNPs. A SNP is a single-nucleotide (A, T, C, or G) difference in a particular sequence of DNA. At least 1% of a population must contain the same nucleotide variation for it to be considered an SNP. These occur normally throughout a person’s DNA, and most have no effect on health or development. SNPs are hereditary and are shared by individuals of common descent thus allowing them to be used as a way to track ancestry, especially as greater than 99% of the human genome is identical among individuals. Certain SNPs may predict an individual’s risk of developing certain diseases, responses to certain medications, and susceptibility to environmental factors.

SNPs can occur within introns or exons. Of those found in exons (coding regions), they may or may not affect protein sequence (synonymous vs. nonsynonymous). Examples of nonsynonymous SNPs (those that affect protein sequence) include missense mutations, nonsense mutations, and nonstop mutations. Missense mutations result in a change in the amino acid in a protein. This is the least common form but can have the greatest effect on protein structure/function (e.g., sickle cell disease, epidermolysis bullosa). Nonsense mutations occur when a codon is changed to a premature stop codon causing truncation of the resulting protein. Nonstop mutations cause a deletion of a stop codon resulting in a longer, nonfunctional protein. Synonymous SNPs, while they do not affect protein sequence, can affect the binding of transcription factors, gene splicing, and mRNA degradation. The gene expression that is affected by this type is known as an expression SNP and may be either upstream or downstream from the gene. SNPs that are found in the coding or promotor regions of genes for Toll-like receptor 1 and tumor necrosis factor alpha proteins have been shown to correlate with increased mortality after trauma/sepsis.

Additional genetic variants include microsatellite polymorphisms and insertion/deletion polymorphisms. A microsatellite is a tract of DNA that contains sequences that are serially repeated (typically 5–50 times). A “mini” satellite is similar in that it is a microsatellite but much longer. These micro/minisatellites have a higher mutation rate due to the loss/gain of an entire repeat unit resulting in increased genetic diversity. If these changes occur in promoter areas, gene expression can be significantly altered.

Insertion/deletion polymorphisms (or “indels”) are a type of genetic variation in which a specific nucleotide sequence is either present (insertion) or absent (deletion). These account for approximately 3 million of the 15 million known genetic variants. Frameshift mutations are the most common indel and occur when a DNA segment is inserted/deleted that is not a multiple of three. As a result, the reading frame is shifted and the transcript sequence may code for an entirely different set of amino acids or result in a premature stop codon. Indel variants with multiples of three nucleotides may result in a protein with extra or fewer amino acids. This may or may not affect the structure and function of the resultant protein.