T-Cell Clonality And Genetic Heterogeneity In Cutaneous T-cell Lymphoma

  • Author / Creator
    Iyer, Aishwarya
  • Cutaneous T-cell lymphoma (CTCL) is heterogeneous form of T-cell lymphoma of which, Mycosis fungoides (MF) is the most common entity. In early stages MF presents on skin as a scaly plaques that in advanced stages develop into tumors and may disseminate to other sites such as lymph node and central nervous system. There no prognostic markers of disease progression. The disease is incurable, currently available therapies providing temporary remissions but the disease inadvertently relapses.

    The long-standing dogma in MF is that it develops from a mature, skin resident T-cell and progresses in a linear fashion from plaques to tumors and finally disseminated to extracutaneous sites. The purpose of this thesis was to critically test this assumption. Based on previous studies and clinical observations we formulated a working hypothesis that MF is a genetically and clonally heterogeneous disease. The testable consequence of this hypothesis was that MF does not develop from the skin-resident T-cell but must originate by seeding of transformed cells from the circulation to the skin leading to a multifocal development. 
    We decided to use whole exome sequencing (WES) as the primary research method taking advantage from the fact that WES allows to quantify the tumor cell fraction, identify spectrum of genomic mutations, cancer subclones and T-cell receptor (TCR) repertoire. We were able to show conclusively that MF is not a monoclonal lymphoproliferation but comprised multiple TCR- α, -β, and -ɣ clonotypes indicating presence of clonal heterogeneity. Next, we compared the TCR sequences from skin with those in the circulating blood and identified that neoplastic TCR clonotypes from skin are present in the circulation, even in the early stages of MF. Additional sampling of skin lesions from different areas on the body and longitudinal sampling presented a model of MF, in which the lesions do not arise from skin-resident T-cells but are initiated by seeding of transformed cells to the skin from the circulation. Further analysis of the molecular architecture of MF, we catalogued genetic abnormalities (somatic variants and copy number aberrations) and used this information to determine the fraction of genetic aberrations which are clonal (common in most of cancer cells) and that are subclonal (present in a subpopulation of malignant cells). We observed that significant proportion of mutations were present in the subclones indicating genetic heterogeneity. The phylogenetic deconvolution of the genetic aberrations presented MF to be evolved via unrestricted branched evolution producing an increasing heterogeneity and mutational complexity. Tumor cells in different lesions and in different tissue niches within the same lesion (epidermis vs dermis) showed independent evolution with no evidence of competition or cell transfer between the compartments.

    We believe that our studies meaningfully advance the knowledge on the molecular pathogenesis of MF. We propose a model for MF development, where the skin lesions originate by seeding from the pool of circulating precursor cells in the blood. Those cells proliferate in the skin, accumulate mutations and further branch into multiple genetic subclones. Our model might provide a better understanding of the mechanism of disease progression, treatment resistance and relapse. Further studies by single cell sequencing techniques would increase the accuracy of identifying clonal and subclonal populations for targeted therapies and immunotherapies. 

  • Subjects / Keywords
  • Graduation date
    Spring 2020
  • Type of Item
  • Degree
    Doctor of Philosophy
  • DOI
  • License
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