Epigenetics & Biology of Cutaneous T-cell Lymphomas

Written by

Pierluigi Porcu, MD, Sidney Kimmel Cancer Center

Anjali Mishra, PhD, Ohio State University Comprehensive Cancer Center

Cutaneous T-cell Lymphomas (CTCL) are a family of extranodal T-cell non-Hodgkin’s lymphomas (NHL) affecting primarily the skin that derive from skin-homing mature T-cells.

While the skin is the main site of disease, CTCL are a type of blood cancer. The most common type of CTCL is Mycosis Fungoides (MF), which represents approximately 70% of all CTCL. In approximately two thirds of the cases, MF presents with early stage disease (stage IIA or less), causes a flat, scaly, rash, and has an indolent clinical course, with good prognosis. However, in a significant fraction of patients, after a variable interval from diagnosis, the disease progresses to advanced stage (stage IIB or greater), with tumor lesions in the skin, extracutaneous dissemination (blood, lymph nodes, visceral organs), and large cell transformation (LCT), all of which are associated with a worse prognosis. Patients with Sezary syndrome (SS) represent a very small but distinct subset of advanced stage CTCL, with extensive blood involvement. SS may arise de novo (i.e from the onset) or evolve from pre-existent MF.
 

What triggers the development of MF, drives its progression from early to advanced stage, leads to the development of SS, and determines its sensitivity or resistance to the treatments available in the clinic has remained for a long time a mystery.

However, over the past 2 years, a number of breakthrough molecular genetic studies have been published by several research groups worldwide that begin to shed some light on these critical aspects of the disease, and offer guidance for additional studies focused on new therapies that are likely to change its natural history, and positively impact patients’ lives.1-7

Most of these studies have focused on patients with advanced stage MF and SS thus offering an important but relatively narrow view of the abnormal molecular landscape of these lymphomas. In aggregate, these studies provide valuable insight on the spectrum and the frequency of the mutations that accumulate in the tumor cell’s DNA over the long trek from early onset, limited-stage disease, all the way to advanced stage, treatment-resistant, poor-risk disease. Many of these mutations no doubt represent “background noise” or genomic “wear and tear”, and some reflect the expected DNA damage resulting from life-long exposure of the skin to sunlight. Separating the wheat from the chaff - a task not always easy - is obviously a crucial part of this work. Some mutations, however, appear to affect parts of the cancer cell genome that contain bona fide or candidate “driver” cancer genes, that is genes that, once mutated, drive - or initiate - the cancer process. These are the genes that, once clearly identified, are expected to produce “dividends” in our search for a cure.
 

Some driver genes are the target of so-called gain-of-function (GOF) mutations. These are genes that stimulate normal cells’ growth and replication when expressed at the right time and in the right place. GOF mutations cause these genes to be switched into a constitutive “on” status. So altered, they are no longer responsive to physiologic feedback control loops and consequently cannot be turned “off”. Other genes become “drivers” by loss-of-function (LOF) mutations. These are cellular genes that normally repress abnormal cell growth, and when mutated or deleted can no longer exert their physiologic function, leading to uncontrolled cell proliferation.

While the precise hierarchy of driver genes and mutations in different cancers - including CTCL - remains to be defined, the knowledge gained from these studies is already being used to develop and test new drugs, and drug combinations, in clinical trials.

The mutational landscape analysis provided by these studies, however, is not informative about the early events leading to the initial development of CTCL, which occur years, possibly decades before progression to advanced stage disease. To gain some insight on the early mechanisms that trigger the development of CTCL and determine how they lead to disease progression, the best tools we currently have are spontaneous animal models of CTCL. By creating a genetically engineered mouse that constitutively produces large amounts of interleukin 15 (IL-15), a regulator of T-cell growth that is overexpressed in CTCL patients, our group was able to demonstrate that within 4-6 weeks of life, the IL-15 mice start to develop a T-cell lymphoma that replicates most of the features of human CTCL, including classical findings on skin biopsy, severe itching, and development of tumor lesions.8 Treatment of the IL-15 mice with drugs approved for human CTCL (romidepsin, vorinostat) within 4-6 weeks stops disease progression, whereas all mice treated with placebo die.8
 

How does IL-15 produce CTCL in mice?

Our studies show that constant exposure of normal T-cells to IL-15 over time, leads to dramatic changes in the epigenetic control of thousands of genes, some of which belong to the same family of driver cancer genes that were found to be mutated in the CTCL genomic studies cited above. It is also of great interest that three of the genes that are highly overexpressed in CTCL as a consequence of chronic IL-15 exposure - histone deacetylase (HDAC) 1, HDAC2, and HDAC6 – are the primary target of romidepsin and vorinostat, suggesting a mechanism for the clinical efficacy of these drugs.9 HDAC1 and HDAC2, in turn, directly induce the expression of a well-known cancer-promoting gene called miR-21, which had been shown by several groups to be upregulated in CTCL. With more effective HDAC1 and HDAC2 inhibitors in clinical development,10 and with new drugs able to counteract the cancer-inducing effect of miR-21 on the horizon,11 the possibility of a combined inhibition of these key CTCL-inducing genes will soon be a reality.

Finally, what is the reason for the overproduction of IL-15 in CTCL patients? Using purified tumor samples, we were able to show that in CTCL patients ZEB1, an important negative regulator of IL-15, is prevented from exerting its normal function due to the aberrant DNA methylation of the control region (promoter) for the IL-15 gene.8 In the absence of the repressive effect of ZEB1, human T-cells start producing large amounts of IL-15, activating the same cancer-inducing pathways (HDAC1, HDAC2, miR-21) that we had carefully characterized in the IL-15 mice. These observations have important treatment implications because drugs that decrease DNA methylation may be able to restore ZEB1’s physiologic repression of IL-15, thus interrupting this cancer signaling loop. The story comes full circle with the observation that many of the genomic CTCL studies cited above showed that ZEB1 was one of the most common cancer suppressor genes subject to LOF mutations, supporting its important role in the development of CTCL.

These are exciting times in CTCL research. The hard work of laboratory and clinical investigators worldwide is starting to bear fruit, and a number of basic discoveries in the genetic and epigenetic foundations of CTCL are now being translated into novel therapies, with great impact for patients.

 

References

1 Ungewickell A, Bhaduri A, Rios E, Reuter J, Lee CS, Mah A, Zehnder A, Ohgami R, Kulkarni S, Armstrong R, Weng WK, Gratzinger D, Tavallaee M, Rook A, Snyder M, Kim Y, Khavari PA. Genomic analysis of mycosis fungoides and Sézary syndrome identifies recurrent alterations in TNFR2. Nat Genet. 2015 Sep;47(9):1056-60

2 Choi J, Goh G, Walradt T, Hong BS, Bunick CG, Chen K, Bjornson RD, Maman Y, Wang T, Tordoff J, Carlson K, Overton JD, Liu KJ, Lewis JM, Devine L, Barbarotta L, Foss FM, Subtil A, Vonderheid EC, Edelson RL, Schatz DG, Boggon TJ, Girardi M, Lifton RP. Genomic landscape of cutaneous T cell lymphoma. Nat Genet. 2015 Sep;47(9):1011-9

3 Wang L, Ni X, Covington KR, Yang BY, Shiu J, Zhang X, Xi L, Meng Q, Langridge T, Drummond J, Donehower LA, Doddapaneni H, Muzny DM, Gibbs RA, Wheeler DA, Duvic M. Genomic profiling of Sézary syndrome identifies alterations of key T cell signaling and differentiation genes. Nat Genet. 2015 Dec;47(12):1426-34.

4 da Silva Almeida AC, Abate F, Khiabanian H, Martinez-Escala E, Guitart J, Tensen CP, Vermeer MH, Rabadan R, Ferrando A, Palomero T. The mutational landscape of cutaneous T cell lymphoma and Sézary syndrome. Nat Genet. 2015 Dec;47(12):1465-70

5 Kiel MJ, Sahasrabuddhe AA, Rolland DC, Velusamy T, Chung F, Schaller M, Bailey NG, Betz BL, Miranda RN, Porcu P, Byrd JC, Medeiros LJ, Kunkel SL, Bahler DW, Lim MS, Elenitoba-Johnson KS. Genomic analyses reveal recurrent mutations in epigenetic modifiers and the JAK-STAT pathway in Sézary syndrome. Nat Commun. 2015 Sep 29;6:8470

6 McGirt LY, Jia P, Baerenwald DA, Duszynski RJ, Dahlman KB, Zic JA, Zwerner JP, Hucks D, Dave U, Zhao Z, Eischen CM. Whole-genome sequencing reveals oncogenic mutations in mycosis fungoides. Blood. 2015 Jul 23;126(4):508-19

7 Woollard WJ, Pullabhatla V, Lorenc A, Patel VM, Butler RM, Bayega A, Begum N, Bakr F, Dedhia K, Fisher J, Aguilar-Duran S, Flanagan C, Ghasemi AA, Hoffmann RM, Castillo-Mosquera N, Nuttall EA, Paul A, Roberts CA, Solomonidis EG, Tarrant R, Yoxall A, Beyers CZ, Ferreira S, Tosi I, Simpson MA, de Rinaldis E, Mitchell TJ, Whittaker SJ. Candidate driver genes involved in genome maintenance and DNA repair in Sézary syndrome. Blood. 2016 Jun 30;127(26):3387-97

8 Mishra A, La Perle K, Kwiatkowski S, Sullivan LA, Sams GH, Johns J, Curphey DP, Wen J, McConnell K, Qi J, Wong H, Russo G, Zhang J, Marcucci G, Bradner JE, Porcu P, Caligiuri MA. Mechanism, Consequences, and Therapeutic Targeting of Abnormal IL15 Signaling in Cutaneous T-cell Lymphoma. Cancer Discov. 2016 Sep;6(9):986-1005

9 L.K. Ferrarelli. HDAC inhibitors in solid tumors and blood cancers. Sci. Signal. 20 Sep 2016: Vol. 9, Issue 446, pp. ec216

10 Halsall JA, Turner BM. Histone deacetylase inhibitors for cancer therapy: An evolutionarily ancient resistance response may explain their limited success. Bioessays. 2016 Nov;38(11):1102-1110

11 Chen Y, Yang F, Zubovic L, Pavelitz T, Yang W, Godin K, Walker M, Zheng S, Macchi P, Varani G. Targeted inhibition of oncogenic miR-21 maturation with designed RNA-binding proteins. Nat Chem Biol. 2016 Sep;12(9):717-23

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