Molecular biology (III)

Below I have added a few quotes and links related to the last few chapters of the book‘s coverage.

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“Normal ageing results in part from exhaustion of stem cells, the cells that reside in most organs to replenish damaged tissue. As we age DNA damage accumulates and this eventually causes the cells to enter a permanent non-dividing state called senescence. This protective ploy however has its downside as it limits our lifespan. When too many stem cells are senescent the body is compromised in its capacity to renew worn-out tissue, causing the effects of ageing. This has a knock-on effect of poor intercellular communication, mitochondrial dysfunction, and loss of protein balance (proteostasis). Low levels of chronic inflammation also increase with ageing and could be the trigger for changes associated with many age-related disorders.”

“There has been a dramatic increase in ageing research using yeast and invertebrates, leading to the discovery of more ‘ageing genes’ and their pathways. These findings can be extrapolated to humans since longevity pathways are conserved between species. The major pathways known to influence ageing have a common theme, that of sensing and metabolizing nutrients. […] The field was advanced by identification of the mammalian Target Of Rapamycin, aptly named mTOR. mTOR acts as a molecular sensor that integrates growth stimuli with nutrient and oxygen availability. Small molecules such as rapamycin that reduce mTOR signalling act in a similar way to severe dietary restriction in slowing the ageing process in organisms such as yeast and worms. […] Rapamycin and its derivatives (rapalogs) have been involved in clinical trials on reducing age-related pathologies […] Another major ageing pathway is telomere maintenance. […] Telomere attrition is a hallmark of ageing and studies have established an association between shorter telomere length (TL) and the risk of various common age-related ailments […] Telomere loss is accelerated by known determinants of ill health […] The relationship between TL and cancer appears complex.”

“Cancer is not a single disease but a range of diseases caused by abnormal growth and survival of cells that have the capacity to spread. […] One of the early stages in the acquisition of an invasive phenotype is epithelial-mesenchymal transition (EMT). Epithelial cells form skin and membranes and for this they have a strict polarity (a top and a bottom) and are bound in position by close connections with adjacent cells. Mesenchymal cells on the other hand are loosely associated, have motility, and lack polarization. The transition between epithelial and mesenchymal cells is a normal process during embryogenesis and wound healing but is deregulated in cancer cells. EMT involves transcriptional reprogramming in which epithelial structural proteins are lost and mesenchymal ones acquired. This facilitates invasion of a tumour into surrounding tissues. […] Cancer is a genetic disease but mostly not inherited from the parents. Normal cells evolve to become cancer cells by acquiring successive mutations in cancer-related genes. There are two main classes of cancer genes, the proto-oncogenes and the tumour suppressor genes. The proto-oncogenes code for protein products that promote cell proliferation. […] A mutation in a proto-oncogene changes it to an ‘oncogene’ […] One gene above all others is associated with cancer suppression and that is TP53. […] approximately half of all human cancers carry a mutated TP53 and in many more, p53 is deregulated. […] p53 plays a key role in eliminating cells that have either acquired activating oncogenes or excessive genomic damage. Thus mutations in the TP53 gene allows cancer cells to survive and divide further by escaping cell death […] A mutant p53 not only lacks the tumour suppressor functions of the normal or wild type protein but in many cases it also takes on the role of an oncogene. […] Overall 5-10 per cent of cancers occur due to inherited or germ line mutations that are passed from parents to offspring. Many of these genes code for DNA repair enzymes […] The vast majority of cancer mutations are not inherited; instead they are sporadic with mutations arising in somatic cells. […] At least 15 per cent of cancers are attributable to infectious agents, examples being HPV and cervical cancer, H. pylori and gastric cancer, and also hepatitis B or C and liver cancer.”

“There are about 10 million different sites at which people can vary in their DNA sequence withing the 3 billion bases in our DNA. […] A few, but highly variable sequences or minisatellites are chosen for DNA profiling. These give a highly sensitive procedure suitable for use with small amounts of body fluids […] even shorter sequences called microsatellite repeats [are also] used. Each marker or microsatellite is a short tandem repeat (STR) of two to five base pairs of DNA sequence. A single STR will be shared by up to 20 per cent of the population but by using a dozen or so identification markers in profile, the error is miniscule. […] Microsatellites are extremely useful for analysing low-quality or degraded DNA left at a crime scene as their short sequences are usually preserved. However, DNA in specimens that have not been optimally preserved persists in exceedingly small amounts and is also highly fragmented. It is probably also riddled by contamination and chemical damage. Such sources of DNA sources of DNA are too degraded to obtain a profile using genomic STRs and in these cases mitochondrial DNA, being more abundant, is more useful than nuclear DNA for DNA profiling. […]  Mitochondrial DNA profiling is the method of choice for determining the identities of missing or unknown people when a maternally linked relative can be found. Molecular biologists can amplify hypervariable regions of mitochondrial DNA by PCR to obtain enough material for analysis. The DNA products are sequenced and single nucleotide differences are sought with a reference DNA from a maternal relative. […] It has now become possible for […] ancient DNA to reveal much more than genotype matches. […] Pigmentation characteristics can now be determined from ancient DNA since skin, hair, and eye colour are some of the easiest characteristics to predict. This is due to the limited number of base differences or SNPs required to explain most of the variability.”

“A broad range of debilitating and fatal conditions, non of which can be cured, are associated with mitochondrial DNA mutations. […] [M]itochondrial DNA mutates ten to thirty times faster than nuclear DNA […] Mitochondrial DNA mutates at a higher rate than nuclear DNA due to higher numbers of DNA molecules and reduced efficiency in controlling DNA replication errors. […] Over 100,000 copies of mitochondrial DNA are present in the cytoplasm of the human egg or oocyte. After fertilization, only maternal mitochondria survive; the small numbers of the father’s mitochondria in the zygote are targeted for destruction. Thus all mitochondrial DNA for all cell types in the resulting embryo is maternal-derived. […] Patients affected by mitochondrial disease usually have a mixture of wild type (normal) and mutant mitochondrial DNA and the disease severity depends on the ratio of the two. Importantly the actual level of mutant DNA in a mother’s heteroplas[m]y […curiously the authors throughout the coverage insist on spelling this ‘heteroplasty’, which according to google is something quite different – I decided to correct the spelling error (?) here – US] is not inherited and offspring can be better or worse off than the mother. This also causes uncertainty since the ratio of wild type to mutant mitochondria may change during development. […] Over 700 mutations in mitochondrial DNA have been found leading to myopathies, neurodegeneration, diabetes, cancer, and infertility.”

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Links:

Dementia. Alzheimer’s disease. Amyloid hypothesis. Tau protein. Proteopathy. Parkinson’s disease. TP53-inducible glycolysis and apoptosis regulator (TIGAR).
Progeria. Progerin. Werner’s syndrome. Xeroderma pigmentosum. Cockayne syndrome.
Shelterin.
Telomerase.
Alternative lengthening of telomeres: models, mechanisms and implications (Nature).
Coats plus syndrome.
Neoplasia. Tumor angiogenesis. Inhibitor protein MDM2.
Li–Fraumeni syndrome.
Non-coding RNA networks in cancer (Nature).
Cancer stem cell. (“The reason why current cancer therapies often fail to eradicate the disease is that the CSCs survive current DNA damaging treatments and repopulate the tumour.” See also this IAS lecture which covers closely related topics – US.)
Imatinib.
Restriction fragment length polymorphism (RFLP).
CODIS.
MC1R.
Archaic human admixture with modern humans.
El Tor strain.
DNA barcoding.
Hybrid breakdown/-inviability.
Trastuzumab.
Digital PCR.
Pearson’s syndrome.
Mitochondrial replacement therapy.
Synthetic biology.
Artemisinin.
Craig Venter.
Genome editing.
Indel.
CRISPR.
Tyrosinemia.