Erica Pimenta

Cancer frequently clusters in families due to shared environment and genetics. However, many familial cancer cases lack a clinically recognized pathogenic germline variant (PGV). We analyzed germline genomes and family history from 2,726 individuals without a PGV in the All of Us Research Program, including 1,496 cases across 18 cancer types with extensive family history and 1,230 family history-negative, cancer-free controls. We identified allelic series of rare structural variants inactivating MSH2 in individuals with phenotypes consistent with Lynch syndrome and BRCA1 in breast cancer. Cancer polygenic risk scores were enriched in cases and correlated with patterns of cancer diagnoses within families. Exome-wide rare variant analyses nominated six candidate predisposition genes, including TSTD2 and BRAT1 in thyroid and breast cancer, respectively. Overall, polygenic risk and rare variants impacting known genes explained a median of 5% of unexplained familial cancers, increasing to 11% when including newly nominated risk factors.

Transcriptional programs in renal cell carcinoma (RCC) have been linked to tumor heterogeneity and clinical outcomes, but analogous efforts to define chromatin programs shaping disease biology have been limited. Here, we generated single-cell ATAC-seq profiles from patients with RCC and integrated them with three previously published datasets to identify chromatin programs in tumor cells. We identified an interferon response program enriched in BAP1 -mutant tumors, and, in bulk ATAC-seq cohorts with linked clinical data, this program was associated with poor prognosis. Mechanistic analyses in isogenic models suggested that BAP1 loss induces a tumor-intrinsic interferon response, with dysregulated endogenous retroviruses as a potential upstream trigger. We further characterized the BAP1 mutation–associated tumor microenvironment across single-cell, bulk, and multiplex immunofluorescence data, identifying features of both inflammation and immune evasion. Together, our findings nominate tumor-intrinsic interferon signaling as a candidate driver of BAP1 -associated aggressiveness in RCC and highlight immune evasion pathways as potential therapeutic targets.

Sarcomas are rare cancers thought to arise from aberrant mesenchymal stem cell (MSC) differentiation. Liposarcoma (LPS) is among the most commonly diagnosed sarcomas and provides insights into dysfunctional differentiation through its well- and dedifferentiated subtypes (WDLPS and DDLPS). Despite differences in histology and clinical behavior, the molecular pathways underlying each subtype remain poorly defined, leaving patients with DDLPS reliant on empiric chemotherapies. We applied single-nucleus multiome sequencing and spatial profiling to human normal adipose, WDLPS, and DDLPS tissues and identified lineage-specific blocks in differentiation within LPS. We found that DDLPS is characterized by loss of insulin-like growth factor 1 (IGF1) signaling and activation of early mesenchymal and glucagon-like peptide-1 (GLP-1)–associated programs. IGF1 signaling loss was restricted to the DDLPS component within mixed histology tumors and correlated with poor survival in patients with LPS. In normal adipocytes, IGF1 drives differentiation through peroxisome proliferator–activated receptor gamma 2 (PPARG2). We found that DDLPS cells lack PPARG2, causing a barrier to differentiation. This defect rendered DDLPS cells unresponsive to exogenous proadipogenic signals. Restoration of PPARG2 expression alone was sufficient to reenable adipogenesis, pinpointing PPARG2 as the key molecular determinant of lineage fate. Last, IGF1 deficiency in DDLPS was associated with up-regulation of the IGF1 receptor (IGF1R), creating a selective vulnerability to IGF1R-targeted antibody-drug conjugates. In summary, we identified lineage-specific defects in DDLPS, with PPARG2 as the molecular mediator of differentiation state in LPS. More broadly, our findings demonstrate how defining lineage-specific mechanisms of tumor state can inform the development of nonchemotherapeutic treatment approaches.

Renal cell carcinoma (RCC) is characterized by recurrent somatic mutations in epigenetic regulators, which stratify patients into clinically significant subgroups with distinct prognoses and treatment responses. However, the cell type-specific epigenetic landscape of RCC—broadly and in the context of these mutations—is incompletely understood. To investigate these open questions, we integrated single nucleus ATAC sequencing data from RCC tumors across four independent cohorts. In clear cell RCC tumors, we identified four shared malignant epigenetic programs related to angiogenesis, proximal tubule-like features, interferon (IFN) signaling, and one that lacked distinct genomic regions with increased accessibility. Among the mutated epigenetic regulators, BAP1 mutation exhibited the most significant impact on chromatin accessibility in tumor cells, and the associated epigenetic changes were linked to IFN response. We identify multiple potential sources of elevated IFN signaling in these lesions, such as increased immune infiltration and increased accessibility and expression of an IFN-associated ERV, ERV3-16A3_LTR. We find that the expression of ERV3-16A3_LTR may itself be a negative prognostic biomarker in ccRCC. Our findings highlight the convergence of malignant epigenetic programs across ccRCC tumors and suggest that BAP1 loss, potentially through ERV3-16A3_LTR dysregulation, is associated with an IFN response-high epigenetic program.