Charting heterogeneity in pediatric malignancies at the single cell level

  • Regev, Aviv A. (CoPI)
  • Stamenkovic, Ivan (PI)

Project Details


Pediatric cancers are the leading cause of death from disease among children in the United States and Europe. Despite affecting young individuals, pediatric cancers have not attracted the kind of attention that the more frequent adult tumors command and there has been less interest both from the pharmaceutical industry and academic research funding agencies in investing resources toward the discovery of effective therapies for these relatively uncommon malignancies. For the patients who suffer from these tumors, however, statistics are irrelevant and more effort needs to be directed toward elucidating the biology of pediatric cancers and developing effective therapeutic strategies. Moreover, whereas application of conventional chemotherapy to childhood leukemias meets with high therapeutic success, the same cannot be said for solid tumors. With relatively few exceptions and similar to adult malignancies, solid pediatric cancers respond poorly to conventional chemotherapy and the majority of targeted therapies have not lived up to their promise. Several reasons can be invoked for therapeutic failure, a major - and perhaps the principal - one being tumor heterogeneity, wherein malignant cell sub-populations display highly variable sensitivity to cytotoxic drugs. Tumor heterogeneity is shaped by genetic evolution of cancer cells as well as by non-genetic programs, such as those that govern tissue development. In cancers that mimic normal tissue organization, subpopulations of cells endowed with self-renewal (cancer stem cells, CSC) and tumor initiating (TIC) capacity tend to resist conventional chemotherapies and repopulate the tumor, giving rise to more aggressive progeny. While it has profound implications for therapeutic management, as pioneering studies in leukemias have demonstrated, the cancer stem cell model remains controversial in solid human malignancies. One of the reasons is that relating genetic and non-genetic determinants of cancer cell properties has been limited by technical challenges. It is therefore imperative to precisely identify and functionally assess the subpopulations of cells that compose solid tumors in a completely unbiased way. To address this issue directly, we propose to characterize a selection of solid pediatric tumors that bear unique signature oncogenic events by leveraging single-cell RNA sequencing technologies, which currently provide the only means to obtain unbiased and comprehensive assessment of tumor cell heterogeneity. We have chosen to work on three pediatric malignancies: diffuse intrinsic pontine gliomas (DIPG), Ewing sarcoma family tumors (ESFT) and synovial sarcoma (SS). All three tumors are driven by unique and highly specific genetic events: lysine-to-methionine mutations in histone 3.3 and 3.1 side chains (H3 K27M) in more than 90% of DIPG; the chromosomal translocation t(11;22)(q24;q12), in 85-90% of ESFT, which generates the EWS-FLI1 fusion gene that encodes an aberrant transcription factor whose oncogenic properties underlie ESFT pathogenesis; and the chromosomal translocation t(X;18)(p11;q11) in more than 90% of SS, which results in the fusion of the ubiquitously expressed SS18/SYT gene to one of the SSX family members that generates an aberrant transcriptional regulator responsible for transformation of permissive primary cells and tumor development. All three tumors share a relatively quiescent genetic landscape aside from the mutations that are responsible for their pathogenesis and display a strong tendency to relapse (and form early metastasis in the case of ESFT and SS) despite aggressive multimodal therapy. Prognosis is therefore somber for patients afflicted with any one of these tumors and the need for more effective treatment is obvious as options are currently limited. The main goals of the proposal are to determine the extent and pattern of tumor cell heterogeneity at the single cell level in these three pediatric malignancies; to identify subpopulations of cells that are responsible for tumor progression and resistance to therapy; to design novel therapeutic approaches that can target these subpopulations in pre-clinical assays; and to apply these therapeutic strategies in the clinic. The quiescent genetic landscape and unique oncogenic drivers of DIPG, ESFT and SS are responsible for relatively limited genetic inter-tumor variability within their respective classes. They are therefore ideal candidates for assessment of heterogeneity at the single cell level. The approach we propose to apply will reveal differences in gene expression repertoires among the different cell subpopulations within each tumor type as well as the underlying epigenetic, posttranscriptional and genetic events. Moreover, we will determine how tumor heterogeneity adapts to therapy and identify the mechanisms responsible for chemoresistance, relapse and dissemination, which will in turn provide the means to design novel therapeutic strategies. The project hinges on the synergy between three distinct disciplines, which in practice virtually never converge onto a single common goal: 1) a powerful technological and bioinformatics platform that has developed and continues to improve technology for single cell analysis; 2) a molecular/cell biology laboratory focused on cancer biology that will address functional properties of the relevant tumor cell populations and identify their sensitivities to diverse therapeutic regimens; 3) an expert pediatric clinical oncology team whose members will design and apply candidate therapies in pre-clinical assays and in the clinic. Success of the project therefore depends on synergy between three disciplines with distinct structures and conceptual as well as operational modes of function.

Effective start/end date1/02/1831/01/22


  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung: $2,452,984.00


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