Wednesday, 16 May 2012

Recent Advancement of Genome Sequencing and the Implications for the Tasmanian Devil


Recent Advancement of Genome Sequencing and the Implications for the Tasmanian Devil
By Cassie Dellit

One major driving factor of advancement in most fields is technology. Technology in genetics has lead to improved sequencing machines, which is now revolutionising scientists’ ability to reconstruct whole genomes [6]. In particular, scientists can now get a clear picture of a genotype of interest, detect mutations in genes, which is enabling broader understanding of individual organisms such as the Tasmanian Devil [6].

The Tasmanian Devil (Sarcophilus harrisii) is a carnivorous marsupial, generally acting as a scavenger by feeding off carcasses [3]. The Tasmanian Devil previously faced extinction in the early 1930s as early European settlers considered the species to be a pest [3]. However, in 1941 a law protecting Tasmanian Devils passed and the Devil’s population began to recover [3]. Due to the early culling, the Devil, once being spread over the Australian mainland, is now typically found in Tasmanian [3].

The Tasmanian Devil is again facing massive population decline, this time due to a cancer, which has been named devil facial tumour disease or DFTD as the cancer typically attacks the face in form of a tumour [3, 4]. Scientists believe the cancer has somehow evolved and spread as a clone [5]. It is an unusual cancer in that it is a transmissible cancer [4]. That is, the cancer cells are transmitted by biting and unlike most cancers which die with the host, DFTD does not [1, 2, 3, 4, 5]. This means the cancer can spread almost exponentially as Devil’s often bite each other from competition during mating and feeding [3].

The first observation of DFTD in Tasmanian Devils was in 1996, when the devil population was more prevalent [4, 5]. However, due to the low diversity of the devil, the disease has spread to over eighty percent of the geographic range, drastically dwindling the devil population, as devils affected by DFTD have only months to live [4]. The devil’s low diversity could also explain why its natural immune system did not fight the cancer [5].

By mapping the devil’s genome, scientists will have a better understanding of what is causing the cancer and give an insight as to how to prevent further cases of DFTD and treat existing ones if such a way exists [2, 3, 4, 5]. Elizabeth Murchison (geneticist) believes that DFTD can be traced back to a specific female devil [2].
Scientists recently, through the aid of technology, have been able to reconstruct the genome of the Tasmanian Devil [2, 6]. Two study groups were established; the first being two devils affected by DFTD and the second being two devils not affected by DFTD (only one geographic population of non-cancerous devils remains today) [2, 5, 6].

The genome sequencings between the two groups were compared to find variants to infer what the original founder genome would look like [5]. The results showed the gene responsible for the immune response system was absent in the tumour affected devils (group one), implying reason for devils lacking any response to tumour cells [2].  This correlates with other studies that have showed DFTD is closely linked to Canine Transmissible Venereal Tumour (CTVT) as both diseases exploit the major histocompatibility complex (MHC) gene and avoid detection by the immune system [1].

There was evidence of mutations in the genes of group one (which closely resembles the gene mutation in human cancers) [2]. This implies there could be defects in the DNA repair system (for example devils may lack a ‘proofreading’ enzyme) [5]. Scientists are still unsure what the effects of the mutations are on the tumour itself [2].

Scientists are hoping to either make linkages of DFTD to mutations present in human cancer cells, thereby creating a drug for DFTD, or by composing a vaccine from the genome sequences to boost the devils’ immune system and let it fight the tumour [2]. The recent technologically enhanced improvements of genome sequencing machines have aided in the creation of individual genomes which have led to important findings, answered some questions and have given rise for further research [2, 6].


 

BIBLIOGRAPHY
[1] Belov, K 2010, ‘The role of the Major Histocompatibility Complex in the spread of contagious            cancers’, Mammalian Genome, vol. 22, no. 1-2, pp. 83-90.
[2] Callaway, E 2012, ‘Field narrows in hunt for devil tumour genes’, Nature – International weekly journal of science, vol. 16th February 2012.
[3] The Department of Primary Industries, Parks, Water and Environment 2011, Save the Tasmanian Devil Program, viewed 8 March 2012, <http://www.tassiedevil.com.au>.
[4] Hamede, R, Lachish, S, Belov, K, Woods, G, Kreiss, A, Pearse, A-M, Lazenby, B, Jones, M and McCallum, H 2012, ‘Reduced Effect of Tasmanian Devil Facial Tumor Disease at the Disease Front’, Conservation Biology, vol. 26, iss. 1, pp. 124–134.
[5] Murchison, EP, Schulz-Trieglaff, OB, Ning, Z, Alexandrov, LB, Bauer, MJ, Fu, B, Hims, M, Ding, Z, Ivakhno, S, Stewart, C, Ng, BL, Wong, W, Aken, B, White, S, Alsop, A, Becq, J, Bignell, GR, Cheetham, RK, Cheng, W, Connor, TR, Cox, AJ, Feng, Z-P, Gu, Y, Grocock, RJ, Harris, SR, Khrebtukova, I, Kingsbury, Z, Kowarsky, M, Kreiss, A, Luo, S, Marshall, J, McBride, DJ, Murray, L, Pearse, A-M, Raine, K, Rasolonjatovo, I, Shaw, R, Tedder, P, Tregidgo, C, Vilella, AJ, Wedge, DC, Woods, GM, Gormley, N, Humphray, S, Schroth, G, Smith, G, Hall, K, Searle, SMJ, Carter, NP, Papenfuss, AT, Futreal, PA, Campbell, PJ, Yang, F, Bentley, DR, Evers, DJ, Stratton, MR 2012, ‘Genome Sequencing and Analysis of the Tasmanian Devil and Its Transmissible Cancer’, Cell Press, vol. 148, iss. 4, pp. 780-791.
[6] Pareek, CS, Smoczynski, R, Tretyn, A 2011, ‘Sequencing Technologies and Genome Sequencing’, Journal of Applied Genetics, vol. 52, iss. 4, pp. 413-435.

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