A Zombie LIF Gene in Elephants Is Upregulated by TP53 to Induce Apoptosis in Response to DNA Damage

Large-bodied organisms have more cells that can potentially turn cancerous than small-bodied organisms, imposing an increased risk of developing cancer. This expectation predicts a positive correlation between body size and cancer risk; however, there is no correlation between body size and cancer risk across species ("Peto's paradox"). Here, we show that elephants and their extinct relatives (proboscideans) may have resolved Peto's paradox in part through refunctionalizing a leukemia inhibitory factor pseudogene (LIF6) with pro-apoptotic functions. LIF6 is transcriptionally upregulated by TP53 in response to DNA damage and translocates to the mitochondria where it induces apoptosis. Phylogenetic analyses of living and extinct proboscidean LIF6 genes indicates that its TP53 response element evolved coincident with the evolution of large body sizes in the proboscidean stem lineage. These results suggest that refunctionalizing of a pro-apoptotic LIF pseudogene may have been permissive (although not sufficient) for the evolution of large body sizes in proboscideans.

TP53 copy number expansion is associated with the evolution of increased body size and an enhanced DNA damage response in elephants

A major constraint on the evolution of large body sizes in animals is an increased risk of developing cancer. There is no correlation, however, between body size and cancer risk. This lack of correlation is often referred to as 'Peto's Paradox'. Here, we show that the elephant genome encodes 20 copies of the tumor suppressor gene TP53 and that the increase in TP53 copy number occurred coincident with the evolution of large body sizes, the evolution of extreme sensitivity to genotoxic stress, and a hyperactive TP53 signaling pathway in the elephant (Proboscidean) lineage. Furthermore, we show that several of the TP53 retrogenes (TP53RTGs) are transcribed and likely translated. While TP53RTGs do not appear to directly function as transcription factors, they do contribute to the enhanced sensitivity of elephant cells to DNA damage and the induction of apoptosis by regulating activity of the TP53 signaling pathway. These results suggest that an increase in the copy number of TP53 may have played a direct role in the evolution of very large body sizes and the resolution of Peto's paradox in Proboscideans.

DOI:http://dx.doi.org/10.7554/eLife.11994.001

As time passes, healthy cells are more likely to become cancerous because more and more damaging mutations accumulate in the cell’s DNA. Assuming that all cells have a similar risk of acquiring mutations, larger and longer-lived animals – like elephants – should have a higher risk of cancer than smaller, shorter-lived animals – like mice. However, there does not appear to be any link between the size of an animal and its risk of developing cancer. Consequently, a key question in cancer biology is how very large animals protect themselves against these diseases.

One gene that is often damaged during an animal’s lifetime is called TP53. This gene normally produces a tumor suppressor protein that senses when DNA is damaged or a cell is under stress and either briefly slows the cell’s growth while the damage is repaired or triggers cell death if the stress is overwhelming. One way that large animals could reduce their risk of cancer is to have extra copies of TP53 or other genes that encode tumor suppressor proteins.

Here Sulak et al. used an evolutionary genomics approach to study TP53 in 61 animals of various sizes, including several large animals such as African elephants and Minke whales. All of the animals studied had at least one copy of TP53, and several had a few extra copies, known as TP53 retrogenes. African elephants – the largest living land mammal – had more retrogenes than any of the others with 19 in total. To investigate why African elephants have so many TP53 retrogenes, Sulak et al. also analyzed DNA from Asian elephants and several other closely related, but now extinct species, including the woolly mammoth. As expected, as species evolved larger body sizes they also evolved more TP53 retrogenes.

Further experiments indicate that several of the TP53 retrogenes in African elephants are likely to be able to produce the tumor suppressor protein and that they contribute to elephant cells being better equipped to deal with DNA damage. The next step following on from this work will be to find out exactly how TP53 retrogenes help to protect animals from cancer.

DOI:http://dx.doi.org/10.7554/eLife.11994.002

Decreased NAA in gray matter is correlated with decreased availability of acetate in white matter in postmortem multiple sclerosis cortex

Multiple sclerosis (MS) is an inflammatory neurodegenerative disease of the central nervous system (CNS) which leads to progressive neurological disability. Our previous studies have demonstrated mitochondrial involvement in MS cortical pathology and others have documented decreased levels of the neuronal mitochondrial metabolite N-acetyl aspartate (NAA) in the MS brain. While NAA is synthesized in neurons, it is broken down in oligodendrocytes into aspartate and acetate. The resulting acetate is incorporated into myelin lipids, linking neuronal mitochondrial function to oligodendrocyte-mediated elaboration of myelin lipids in the CNS. In the present study we show that treating human SH-SY5Y neuroblastoma cells with the electron transport chain inhibitor antimycin A decreased levels of NAA as measured by HPLC. To better understand the significance of the relationship between mitochondrial function and levels of NAA and its breakdown product acetate on MS pathology we then quantitated the levels of NAA and acetate in MS and control postmortem tissue blocks. Regardless of lesion status, we observed that levels of NAA were decreased 25 and 32 % in gray matter from parietal and motor cortex in MS, respectively, compared to controls. Acetate levels in adjacent white matter mirrored these decreases as evidenced by the 36 and 45 % reduction in acetate obtained from parietal and motor cortices. These data suggest a novel mechanism whereby mitochondrial dysfunction and reduced NAA levels in neurons may result in compromised myelination by oligodendrocytes due to decreased availability of acetate necessary for the synthesis of myelin lipids.

Analysis of the mitochondrial proteome in multiple sclerosis cortex

Mitochondrial dysfunction has been proposed to play a role in the neuropathology of multiple sclerosis (MS). Previously, we reported significant alterations in the transcription of nuclear-encoded electron transport chain genes in MS and confirmed translational alterations for components of Complexes I and III that resulted in reductions in their activity. To more thoroughly and efficiently elucidate potential alterations in the expression of mitochondrial and related proteins, we have characterized the mitochondrial proteome in postmortem MS and control cortex using Surface-Enhanced Laser Desorption Ionization Time of Flight Mass Spectrometry (SELDI-TOF-MS). Using principal component analysis (PCA) and hierarchical clustering techniques we were able to analyze the differential patterns of SELDI-TOF spectra to reveal clusters of peaks which distinguished MS from control samples. Four proteins in particular were responsible for distinguishing disease from control. Peptide fingerprint mapping unambiguously identified these differentially expressed proteins. Three proteins identified are involved in respiration including cytochrome c oxidase subunit 5b (COX5b), the brain specific isozyme of creatine kinase, and hemoglobin β-chain. The fourth protein identified was myelin basic protein (MBP). We then investigated whether these alterations were consistent in the experimental autoimmune encephalomyelitis (EAE) mouse model of MS. We found that MBP was similarly altered in EAE but the respiratory proteins were not. These data indicate that while the EAE mouse model may mimic aspects of MS neuropathology which result from inflammatory demyelinating events, there is another distinct mechanism involved in mitochondrial dysfunction in gray matter in MS which is not modeled in EAE.

Optical coherence tomography of the Ex-PRESS miniature glaucoma implant

PURPOSE

To describe the localisation of the Ex-PRESS miniature glaucoma implant with an experimental setup for optical coherence tomography (OCT) of the anterior segment of the eye.

METHODS

An OCT scanner, central wavelength 1,280 nm, bandwidth 60 nm, resolution of 12 microm, was built onto a slitlamp to scan the anterior segment of the eye. Five ex-vivo porcine eyes received an Ex-PRESS miniature glaucoma implant and were used as a model to visualise the position of the implant in the anterior segment.

RESULTS

In the ex-vivo porcine eyes, the OCT images showed the anatomy of the anterior segment in great detail. The anterior segment OCT was able to visualise the whole outline and position of the implant. The abrupt change in reflectivity going from tissue to the implant resulted in a clear border along the circumference of the whole device.

CONCLUSION

In this paper, we have shown that we were able to outline the Ex-PRESS miniature glaucoma implant in the anterior segment of the ex-vivo porcine eye by using an experimental OCT setup built onto a slitlamp. The acquisition time of 0.8 s is short enough to allow for the scanning of patients, and anterior segment OCT is expected to aid in providing answers to the question regarding which parameters will determine the success or failure of such a device.

Inhibitor of kappaB kinase is required to activate a subset of interferon gamma-stimulated genes

IkappaB kinase (IKK), discovered as the major activator of NF-kappaB, plays additional roles in signaling. By using mouse embryo fibroblasts (MEFs) lacking both the alpha and beta subunits of IKK, we find that these proteins are required for induction of a major subset of IFNgamma-stimulated genes and that this requirement is independent of NF-kappaB activation. Furthermore, there is no defect in IFNgamma-stimulated signal transducer and activator of transcription 1 (Stat1) activation or function in the IKKalpha/beta-null MEFs. Therefore, although activated Stat1 dimers are necessary for the activation of these genes in response to IFNgamma, they are not sufficient. These results reveal an important additional pathway for IFNgamma-stimulated gene expression in which an NF-kappaB-independent function of IKK is required.