A Pilot Basket Study to Evaluate Multi-Analyte Liquid Biopsies for Personalized Treatments in Advanced Refractory Cancers

Prior attempts at personalizing anticancer treatments based on univariate tumor profiling (single gene variant) for selection of monotherapy with targeted agents (single drug) have generally yielded poor response rates. We report findings from the LIQUID IMPACT pilot trial where Multi-analyte Liquid Biopsy (MLB) profiling of circulating tumor analytes in peripheral blood was used to inform selection of personalized combination regimens in advanced refractory cancers. Among the 43 patients evaluable as per study protocol, 34 had targetable pathway activations. Partial Response (PR) was observed in 14 (41.1%) of the 34 patients with signaling pathway activation, including 5 (50%) of 10 cases with mTOR activation, 8 (44.4%) of 18 cases with activation of angiogenesis and 4 (50.0%) of 8 cases with EGFR / ERBB2 activation. PR was not reported among the 9 cases with no detectable pathway activation. Toxicities were manageable and there were no treatment related deaths. The study findings suggest that MLB may be able to inform safe and efficacious combination regimens in patients with advanced refractory cancers.

Meningiomas in dogs

Background: Meningiomas and gliomas are the two most common types of human intracranial tumors. However, meningiomas are not exclusively human tumors and are often seen in dogs and cats. Methods: To present meningioma surgery in dogs and compare the surgical possibilities, tumor location, and to show the differences between human and veterinary approaches to tumor profiling. Eleven dogs with meningiomas were treated surgically for 5 years. All tumors except one were resected radically (Simpson 2). Localization of tumors mirrored that of human meningiomas. Results: Two dogs died in direct relation to surgery. One died 14 months after surgery due to tumor regrowth. Three dogs died of unrelated causes 10–36 months after tumor resection and five dogs are alive and tumor-free 2–42 months after surgery. Conclusion: Radical surgery in dogs is as effective as in humans. Thus, we propose that it should be implemented as first-line treatment. The article is meant to please all those overly curious neurosurgeons in the world.

Germline Biallelic Loss in MBD4 leading to Early Onset AML with Hyper-Mutator Genomic Signature

MBD4, a gene encoding a DNA glycosylase functioning in base excision repair, has recently been described in association with predisposition to early onset acute myeloid leukemia (AML), uveal melanoma and colorectal polyposis. MBD4 is essential for guarding against methylation damage due to spontaneous deamination of 5-methylcytosine and biallelic loss of MBD4 allows CG>TG mutations to accumulate in the genome predisposing to AML (Sanders et al. Blood 2018). Further understanding of the full phenotypic spectrum and mechanisms leading to cancer evolution for this predisposition syndrome is critical for informing early recognition, diagnosis, management, and treatment for these individuals and their at-risk family members with the ultimate goal of improving outcomes. Here we report novel germline mutations in MBD4, expand the spectrum of cancers and describe the mutational signatures associated with this cancer predisposition syndrome. Two siblings (brother and sister) from a non-consanguineous family with strong family history of cancers were diagnosed with early-onset AML and colorectal polyposis in their 30s. Prior to the diagnosis of AML, the brother was diagnosed with colorectal cancer and lymphoma at 24 and 28 years old respectively. He was diagnosed with AML at 30 years old and underwent allogenic hematopoietic stem cell transplant (HSCT) using her sister as donor but subsequently passed away following relapse of his AML. The sister was diagnosed with colorectal polyposis at 33 years old and underwent total colectomy due to numerous (>70) hyperplastic and adenomatous colorectal polyps. At the age of 35 years old she was diagnosed with AML after presenting with progressive peripheral cytopenias, lymphadenopathy and splenomegaly. Her AML was characterized by normal karyotype and absent of NPM1, CEBPA and FLT3 aberrations. Further molecular profiling using targeted myeloid NGS panel identified multiple C>T missense mutations including hotspot DNMT3A mutation c.2644C>T, p.R882C (Table 1). SNP microarray revealed balanced genome but identified copy loss of heterozygosity in chromosome 1p and 1q. She received two cycles of remission induction chemotherapy (7+3 regimen) and achieved remission prior to allogenic HSCT using matched unrelated donor. Her post-transplant course was complicated by chronic graft versus host disease treated with tacrolimus. She currently remains in remission now six years post-transplant. She later developed papillary thyroid carcinoma at the age of 44 for which she underwent total thyroidectomy. Shortly after, she was evaluated with brain MRI due to sensorineural hearing loss, which identified bilateral vestibular schwannoma. Her right schwannoma was resected and the smaller, left schwannoma is being monitored. Tumor profiling on tissue from the right schwannoma detected two C>T truncating mutations in NF2 as well as multiple other C>T missense variants resulting in high tumor mutational burden calculated at 16.8 mutations/MB (Table 1). Tumor profiling performed on tissue from her thyroid carcinoma is pending. Due to concern for germline cancer predisposition syndrome, whole exome sequencing was performed and identified two germline nonsense variants in MBD4 c.1291 C>T, p.Arg431* and c.1688 T>A, p.Leu563* in trans configuration. These truncating variants are located in the glycosylase domain of MBD4 and predicted to abolish the catalytic function of the gene (Figure 1). Both truncating variants (Arg431* and Leu563*) are present in gnomAD with very low allele frequency of 3.18 X 10 -5 and 7.04 X 10 -5 respectively. No additional germline mutations were identified. This case further validates the role of MBD4 as germline predisposition to myeloid malignancies characterized by hyper-mutated genomic signatures. Additionally we expanded the spectrum of cancers associated with this novel cancer predisposition syndrome to include papillary thyroid carcinoma and vestibular schwannomas. Genomic profiling of the normal and affected tissue identified germline bi-allelic loss of function mutation in MBD4 as initiator of methylation defect in key driver genes in tissue specific manner leading to carcinogenesis. This conserved path to mutagenesis is unique to this cancer predisposition syndrome and further biological studies are needed to fully understand the spectrum of cancers associated with this syndrome. Figure 1 Figure 1. Disclosures Majhail: Anthem, Inc: Consultancy; Incyte Corporation: Consultancy.

Response to Pazopanib-based Combination Regimen in a Case of FGFR3 Amplified Gastric Adenocarcinoma

We report a case of an advanced refractory Gastric AD which responded favourably to a combination regimen of AGI and other chemotherapy agents which were selected on the basis of multi-analyte tumor profiling. The treatment was well tolerated with transient manageable adverse events and yielded radiological partial response.

Mammary-specific expression of Trim24 establishes a mouse model of human metaplastic breast cancer

Conditional overexpression of histone reader Tripartite motif containing protein 24 (TRIM24) in mouse mammary epithelia (Trim24COE) drives spontaneous development of mammary carcinosarcoma tumors, lacking ER, PR and HER2. Human carcinosarcomas or metaplastic breast cancers (MpBC) are a rare, chemorefractory subclass of triple-negative breast cancers (TNBC). Comparison of Trim24COE metaplastic carcinosarcoma morphology, TRIM24 protein levels and a derived Trim24COE gene signature reveals strong correlation with human MpBC tumors and MpBC patient-derived xenograft (PDX) models. Global and single-cell tumor profiling reveal Met as a direct oncogenic target of TRIM24, leading to aberrant PI3K/mTOR activation. Here, we find that pharmacological inhibition of these pathways in primary Trim24COE tumor cells and TRIM24-PROTAC treatment of MpBC TNBC PDX tumorspheres decreased cellular viability, suggesting potential in therapeutically targeting TRIM24 and its regulated pathways in TRIM24-expressing TNBC.

Germline Whole-Gene Deletion of FH Diagnosed from Tumor Profiling

Hereditary leiomyomatosis and renal cell carcinoma (HL (RCC)) entails cutaneous and uterine leiomyomatosis with aggressive type 2 papillary RCC-like histology. HLRCC is caused by pathogenic variants in the FH gene, which encodes fumarate hydratase (FH). Here, we describe an episode of young-onset RCC caused by a genomic FH deletion that was diagnosed via clinical sequencing. A 35-year-old woman was diagnosed with RCC and multiple metastases: histopathological analyses supported a diagnosis of FH-deficient RCC. Although the patient had neither skin tumors nor a family history of HLRCC, an aggressive clinical course at her age and pathological diagnosis of FH-deficient RCC suggested a germline FH variant. After counseling, the patient provided written informed consent for germline genetic testing. She was simultaneously subjected to paired tumor profiling tests targeting the exome to identify a therapeutic target. Although conventional germline sequencing did not detect FH variants, exome sequencing revealed a heterozygous germline FH deletion. As such, paired tumor profiling, not conventional sequencing, was required to identify this genetic deletion. RCC caused by a germline FH deletion has hitherto not been described in Japan, and the FH deletion detected in this patient was presumed to be of maternal European origin. Although the genotype-phenotype correlation in HLRCC-related tumors is unclear, the patient’s family was advised to undergo genetic counseling to consider additional RCC screening.