The VarSite Database and Potential Future Investigations of Pirin

        Last week I utilized EBI’s database to research the pathologies associated with pirin in the human body. This week I will continue to use EBI’s database, specifically VarSite, a portion of the EBI database concerned with cataloging disease-associated variants in humans (Laskowski, Stephenson, Sillitoe, et al., 2020). I will be using this database to further research pirin-associated pathologies as well as its catalytic activity and tissue specificity. 

When searching for pirin on the VarSite database I was immediately given pirin’s ID number (O0065), its VarSite ID number (PIR_Human), as well as a brief description of pirin’s tissue specificity and tissue related pathology that reads as follows “[Pirin is] highly expressed in a subset of melanomas. Detected at very low levels in most tissues (at protein level). Expressed in all tissues, with highest level [sic] of expression in heart and liver.” This description fits with my research on pirin thus far. Clicking on pirin’s ID number directs me to an info sheet containing information on pirin’s disease associations, catalytic activity, cofactors, and tissue specificity.

The database states that pirin has no known associated diseases, though as seen in the last blog post, there are several diseases in which research has suggested pirin association. I assume that the database marks pirin as having no associated diseases because of the novelty of the protein and the need for more research to establish more certainty in suggested pirin-pathology associations. The database also mentions the quercetin 2,3-dioxygenase catalytic activity that was mentioned in the first week of this blog as catalyzing the metabolism of the flavonoid quercetin. In addition, the VarSite database lists ferric iron as being a pirin cofactor, which also supports the research I conducted during the first week of this blog.

Perhaps the most interesting information relayed to me through the VarSite database was data concerning the tissue specificity of pirin, which is a characteristic of pirin that I have not studied yet. The database states that pirin is highly expressed in some subsets of melanoma, a fact that I came across during last week’s research. Furthermore, VarSite emphasises that pirin has a low level of expression in most tissue in the human body, while significantly higher levels of expression in heart and liver tissue. While pirin does demonstrate at least some level of expression in most tissue, it is notably absent in most tissues in the throat (The pharynx, larynx, esophagus and trachea), eye tissue, tissue in parts of the inner brain, and bone tissue.

The absence of pirin in bone tissue is specifically interesting, as previous research has established possible increases in PIR transcription during in vitro maturation of precursor hematopoietic cells, indicating lapses in our understanding of pirin’s tissue specificity in relation to its function (Licciulli, Cambiaghi, Scafetta, et al., 2010), or perhaps merely suggests incongruencies between the data compiled in VarSite and the actual body of literature on the topic. The role pirin may play in the maturation and differentiation of myeloid cells is an aspect of pirin that I am interested in researching further, particularly due to the emergence of studies in the last 15 years that have suggested that reductions in pirin expression correlate with the development of adult acute myeloid leukemia (Ibid.). 

Similarly, pirin’s speculated role as an inhibitor of ferroptosis (Hu, Bai, Dai, et al., 2020) and the potentially related oncogenic pathologies that may result from its decentralized over-expression (Licciulli, Luise, Zanardi, et al., 2010) are also areas that I am eager to further explore. Essentially, I think that I would enjoy further researching how pirin expression may be used to detect malignant neoplasm, as well as how pirin’s presence may contribute to some cancers such as melanoma, while its absence has been associated with other cancers such as leukemia.

 Perhaps it would be possible to utilize an in vitro expression system to observe how pirin down-regulation influences the protection and repair of hematopoietic and white blood cells, and by extension potentially protects hematopoietic and white blood cells against leukemia. Previously on this blog I discussed how pirin may be a transcription coregulator for the protein complex NF-κB, which is known to transcribe DNA that plays a heavy role in adapting to stress stimuli that may contribute to the development of leukemia. Specifically, NF-κB has been linked to cellular responses to irradiation as well as redox regulation (Liu, Rehmani, Esaki, et al., 2013). Pirin regulates NF-κB by principle of its Fe cofactor; essentially, ferrous iron acts as an allosteric inhibitor to pirin-NF-κB binding, thereby disabling NF-κB form forming the proper structure needed to fulfill its transcriptional functions. However, ferric iron enhances pirin-NF-κB’s affinity and by extension the entire supramolecular complex’s ability to bind and transcribe κB DNA (Adeniran & Hamelberg, 2017). That is to say that as the ferrous iron bound to pirin is reduced to ferric iron, pirin inhibition is eliminated, allowing it to act as transcriptional coregulator to NF-κB. The implication here is that pirin binding to NF-κB is redox specific; pirin will cease to function under conditions in which Fe(III) is oxidized to Fe(II). If down-regulated pirin is associated with the development of myeloid leukemia as well as NF-κB down-regulation (Which, as previously mentioned, is associated with poor cellular stress stimuli response linked to leukemia development), and pirin becomes downregulated in oxidant environments, there may be associations between leukemic progression and/or white blood cell damage and either myeloid redox states or NF-κB transcription activity.

References 

Adeniran C, Hamelberg D. Redox-Specific Allosteric Modulation of the Conformational
Dynamics of κB DNA by Pirin in the NF-κB Supramolecular Complex.
Biochemistry. 2017 Sep 19;56(37):5002-5010. doi:
10.1021/acs.biochem.7b00528. Epub 2017 Sep 6. PMID: 28825294.

Hu N, Bai L, Dai E, Han L, Kang R, Li H, Tang D. Pirin is a nuclear redox-sensitive
modulator of autophagy-dependent ferroptosis. Biochem Biophys Res Commun.
2021 Jan 15;536:100-106. doi: 10.1016/j.bbrc.2020.12.066. Epub 2020 Dec 26.
PMID: 33373853.

Laskowski, RA,  Stephenson, JD,  Sillitoe, I,  Orengo, CA,  Thornton, JM.  VarSite:
Disease variants and protein structure. Protein Science.  2020; 29: 111– 119. 

https://doi.org/10.1002/pro.3746
Licciulli S, Cambiaghi V, Scafetta G, Gruszka AM, Alcalay M. Pirin downregulation is a
feature of AML and leads to impairment of terminal myeloid differentiation.
Leukemia. 2010 Feb;24(2):429-37. doi: 10.1038/leu.2009.247. Epub 2009 Dec
10. PMID: 20010624.

Licciulli, S., Luise, C., Zanardi, A., Giorgetti, L., Viale, G., Lanfrancone, L., Carbone, R.,
& Alcalay, M. (2010). Pirin delocalization in melanoma progression identified by
high content immuno-detection based approaches. BMC cell biology, 11, 5.
https://doi.org/10.1186/1471-2121-11-5
Liu F, Rehmani I, Esaki S, Fu R, Chen L, de Serrano V, Liu A. Pirin is an iron-dependent
redox regulator of NF-κB. Proc Natl Acad Sci U S A. 2013 Jun
11;110(24):9722-7. doi: 10.1073/pnas.1221743110. Epub 2013 May 28. PMID:
23716661; PMCID: PMC3683729.