Personalized treatment of Sézary syndrome by targeting a novel CTLA4:CD28 fusion

Abstract

Matching molecularly targeted therapies with cancer subtype-specific gene mutations is revolutionizing oncology care. However, for rare cancers this approach is problematic due to the often poor understanding of the disease's natural history and phenotypic heterogeneity, making treatment of these cancers a particularly unmet medical need in clinical oncology. Advanced Sézary syndrome (SS), an aggressive, exceedingly rare variant of cutaneous T-cell lymphoma (CTCL) is a prototypical example of a rare cancer. Through whole genome and RNA sequencing (RNA-seq) of a SS patient's tumor we discovered a highly expressed gene fusion between CTLA4 (cytotoxic T lymphocyte antigen 4) and CD28 (cluster of differentiation 28), predicting a novel stimulatory molecule on the surface of tumor T cells. Treatment with the CTLA4 inhibitor ipilimumab resulted in a rapid clinical response. Our findings suggest a novel driver mechanism for SS, and cancer in general, and exemplify an emerging model of cancer treatment using exploratory genomic analysis to identify a personally targeted treatment option when conventional therapies are exhausted.

Keywords: CD28; CTLA4; Sézary syndrome.

Figure 1

Identification of an amplified CTLA4-CD28 fusion (A) CNV plot of chromosome 2. The identified amplification (blue arrow) contains only the two fused genes, CTLA4 and CD28. The y-axis indicates the normalized log2 fold difference in copy number between the normal and tumor samples, inferred from sequencing read depth. (B) CD28 and CTLA4 loci and the chimeric product of gene fusion. (C) RNA-seq reads confirmed an in-frame fusion between CTLA4 and CD28. The breakpoint is marked with a dotted line. (D) Sanger sequencing validation of a reverse transcribed copy of the fusion transcript. The chromatogram shows the junction between CTLA4 and CD28. (E) The chimeric CTLA4-CD28 transcript is the predominant form of CTLA4RNA expressed in the examined tissues. This is despite the fact that ∽40% of the tumor is normal infiltrate, which is expected to express wild-type CTLA4.

Figure 2

DNA and RNA sequencing evidence of CTLA4-CD28 fusion (A) In normal T cells, activation of CD28 stimulates proliferation, whereas activation of CTLA4 inhibits. (B) In SS T cells expressing the chimera, CTLA4 activation would aberrantly stimulate proliferation through the intracellular CD28 domain. (C) Model of ipilimumab's inhibition of SS proliferation. In normal cells (left), binding of ipilimumab to CTLA4 blocks the inhibitory CTLA4 signaling. In SS cells (right), ipilimumab is predicted to inhibit proliferation by blocking the aberrant stimulatory signaling delivered by the chimeric protein.

Figure 3

Clinical response to ipilimumab (A) A pre-ipilimumab photo of the patient's calf is shown and displays generalized erythroderma and ulcerated cutaneous tumors. (B) Following ipilimumab treatment, the patient experienced a reduction in pruritus and erythema as well as healing of ulcerated tumors and a decrease in overall tumor number and size.