Impact of tumor heterogeneity and microenvironment in identifying neoantigens in a patient with ovarian cancer.

Identification of neoepitopes as tumor-specific targets remains challenging, especially for cancers with low mutational burden, such as ovarian cancer. To identify mutated human leukocyte antigen (HLA) ligands as potential targets for immunotherapy in ovarian cancer, we combined mass spectrometry analysis of the major histocompatibility complex (MHC) class I peptidomes of ovarian cancer cells with parallel sequencing of whole exome and RNA in a patient with high-grade serous ovarian cancer. Four of six predicted mutated epitopes capable of binding to HLA-A*02:01 induced peptide-specific T cell responses in blood from healthy donors. In contrast, all six peptides failed to induce autologous peptide-specific response by T cells in peripheral blood or tumor-infiltrating lymphocytes from ascites of the patient. Surprisingly, T cell responses against a low-affinity p53-mutant Y220C epitope were consistently detected in the patient with either unprimed or in vitro peptide-stimulated T cells even though the patient's primary tumor did not bear this mutation. Our results demonstrated that tumor heterogeneity and distinct immune microenvironments within a patient should be taken into consideration for identification of immunogenic neoantigens. T cell responses to a driver gene-derived p53 Y220C mutation in ovarian cancer warrant further study.

Follicular Dendritic Cell Sarcoma of the Tonsil: A Multimodality Approach.

Follicular dendritic cell sarcoma (FDCS) accounts for < 0.4% of soft tissue sarcomas. Only 35 cases of tonsillar FDCS have been reported, and majority had localized presentation. We present a case of FDCS of the tonsil, wherein a well-coordinated trimodality approach provided good disease control in advanced disease. A 53-year-old man presented with a painless and enlarging neck mass of 11-month duration, with no other symptoms. Close examination revealed a 10 × 5 cm mass at the left carotid triangle, and a 3.2 × 2.2 cm mass at the left tonsillar fossa. Imaging revealed the tumor to be unresectable due to its attachment to the great vessels. There were no distant metastases. Biopsy and immunohistochemistry were initially deemed consistent with an undifferentiated sarcoma. Palliative chemotherapy was given using single agent doxorubicin and subsequent dacarbazine, resulting in partial response and stable disease, respectively. Pathological re-evaluation was pursued because of the uncharacteristic slow progression of the tumor, revealing diffuse positivity for CD21 and negative for CD1A and CD34, consistent with FDCS. The patient underwent three cycles of gemcitabine plus docetaxel resulting in 50% regression. This allowed dissection of level IB-V lymph nodes and subsequent radiotherapy for the neck and tonsillar mass, with weekly gemcitabine as a radiosensitizer. Evaluation 8 months post-treatment showed no signs of disease progression. Treatment-related complications included radiation dermatitis and swallowing dysfunction, which both resolved on follow-up. This case highlights the multidisciplinary management of a rare type of sarcoma in an uncommon anatomic location. Precise pathologic diagnosis is important in soft tissue sarcoma because of its therapeutic implications. For FDCS, effective response may still be achieved in the third-line setting.

Resistance to TRK inhibition mediated by convergent MAPK pathway activation.

TRK fusions are found in a variety of cancer types, lead to oncogenic addiction, and strongly predict tumor-agnostic efficacy of TRK inhibition1-8. With the recent approval of the first selective TRK inhibitor, larotrectinib, for patients with any TRK-fusion-positive adult or pediatric solid tumor, to identify mechanisms of treatment failure after initial response has become of immediate therapeutic relevance. So far, the only known resistance mechanism is the acquisition of on-target TRK kinase domain mutations, which interfere with drug binding and can potentially be addressable through second-generation TRK inhibitors9-11. Here, we report off-target resistance in patients treated with TRK inhibitors and in patient-derived models, mediated by genomic alterations that converge to activate the mitogen-activated protein kinase (MAPK) pathway. MAPK pathway-directed targeted therapy, administered alone or in combination with TRK inhibition, re-established disease control. Experimental modeling further suggests that upfront dual inhibition of TRK and MEK may delay time to progression in cancer types prone to the genomic acquisition of MAPK pathway-activating alterations. Collectively, these data suggest that a subset of patients will develop off-target mechanisms of resistance to TRK inhibition with potential implications for clinical management and future clinical trial design.

Establishing and Maintaining an Extensive Library of Patient-Derived Xenograft Models.

Patient-derived xenograft (PDX) models have recently emerged as a highly desirable platform in oncology and are expected to substantially broaden the way in vivo studies are designed and executed and to reshape drug discovery programs. However, acquisition of patient-derived samples, and propagation, annotation and distribution of PDXs are complex processes that require a high degree of coordination among clinic, surgery and laboratory personnel, and are fraught with challenges that are administrative, procedural and technical. Here, we examine in detail the major aspects of this complex process and relate our experience in establishing a PDX Core Laboratory within a large academic institution.