Roessner, P. M. | bioRxiv Science

bioRxiv2020

EOMES and IL-10 regulate anti-tumor activity of PD-1+ CD4+ T-cells in B-cell Non-Hodgkin lymphoma

The transcription factor Eomesodermin (EOMES) promotes IL-10 production of CD4+ T-cells, which has been linked to immunosuppressive and cytotoxic activities. We detected EOMES-expressing CD4+ T-cells in lymph node samples of patients with chronic lymphocytic leukemia (CLL) or diffuse large B-cell lymphoma. This was in line with an observed expansion of EOMES-positive CD4+ T-cells in leukemic E{micro}-TCL1 mice, a well-established model of CLL, and upon adoptive transfer of TCL1 leukemia in mice. Transcriptome and flow cytometry analyses revealed that EOMES does not only drive the transcription of IL-10, but rather controls a unique differentiation program in CD4+ T-cells. Moreover, EOMES was necessary for the accumulation of a specific CD4+ T-cell subset that expresses IFN{gamma} and IL-10, as well as inhibitory receptors, like PD-1 and LAG3. T-cell transfer studies in leukopenic Rag2-/- mice showed that EOMES-deficient CD4+ T-cells were inferior in controlling TCL1 leukemia development compared to wildtype T-cells, even though expansion of Eomes-/- CD4+ T-cells was observed. We further showed that control of TCL1 leukemia was driven by IL-10 receptor-mediated signals, as Il10rb-deficient CD4+ T-cells showed impaired anti-leukemia activity. Altogether, our data suggest that IL-10 producing PD-1+ CD4+ T-cells contribute to CLL control in an EOMES- and IL-10R-dependent manner.

cancer biology↗

bioRxiv2020

Methylome-based cell-of-origin modeling (Methyl-COOM) identifies aberrant expression of immune regulatory molecules in CLL

BackgroundIn cancer, normal epigenetic patterns are disturbed and contribute to gene expression changes, disease onset and progression. The cancer epigenome is composed of the epigenetic patterns present in the tumor-initiating cell at the time of transformation, and the tumor-specific epigenetic alterations that are acquired during tumor initiation and progression. The precise dissection of these two components of the tumor epigenome will facilitate a better understanding of the biological mechanisms underlying malignant transformation. Chronic lymphocytic leukemia (CLL) originates from differentiating B cells, which undergo extensive epigenetic programming. This poses the challenge to precisely determine the epigenomic ground-state of the cell-of-origin in order to identify CLL-specific epigenetic aberrations. MethodsWe developed a linear regression model, methylome-based cell-of-origin modeling (Methyl-COOM), to map the cell-of-origin for individual CLL patients based on the continuum of epigenomic changes during normal B cell differentiation. ResultsMethyl-COOM accurately maps the cell-of-origin of CLL and identifies CLL-specific aberrant DNA methylation events that are not confounded by physiologic epigenetic B cell programming. Furthermore, Methyl-COOM unmasks abnormal action of transcription factors, altered super-enhancer activities, and aberrant transcript expression in CLL. Among the aberrantly regulated transcripts were many genes that have previously been implicated in T cell biology. Flow cytometry analysis of these markers confirmed their aberrant expression on malignant B cells at the protein level. ConclusionsMethyl-COOM analysis of CLL identified disease-specific aberrant gene regulation. The aberrantly expressed genes identified in this study might play a role in immune-evasion in CLL and might serve as novel targets for immunotherapy approaches. In summary, we propose a novel framework for in silico modeling of reference DNA methylomes and for the identification of cancer-specific epigenetic changes, a concept that can be broadly applied to other human malignancies.

cancer biology↗