Biology subjects

Bacchiocchi, A.

Publications and source records attributed to Bacchiocchi, A..

4 recordsLinked to original sources

bioRxiv2026

HaloPROTAC-mediated degradation reveals SOX10-dependent gene expression changes in melanoma cells

The transcription factor SOX10 is required for melanoma cell proliferation. However, SOX10 expression in single cells is heterogeneous, and low SOX10-expressing cells exhibit a dormant-invasive phenotype associated with drug resistance and metastasis. Despite longstanding interest in SOX10 as a diagnostic marker and potential therapeutic target in melanoma, the molecular mechanism and targets of SOX10 remain incompletely understood. New tools for the study and perturbation of SOX10 in cancer-relevant systems are needed to address these gaps in our knowledge. In this study, we engineered a patient-derived WW165 melanoma cell line for programmable SOX10 targeted proteolysis. We achieved this by replacing the endogenous copies of SOX10 with a SOX10-HaloTag transgene that supports cell growth, but can be rapidly degraded by the ubiquitin-proteasome system upon with a commercially available HaloPROTAC3 degrader molecule. We demonstrate that inducible degradation of SOX10-HaloTag faithfully recapitulates the known SOX10 transcriptional program, while also enabling discovery of SOX10 target genes previously undetected with standard genetic silencing approaches. We validated NAV2 and NCKAP5 as novel genes that are directly bound by SOX10 and coregulated with SOX10 expression in a patient cohort. This study demonstrates that new biological insights into the function of SOX10 can be enabled by targeted degradation and suggests that analogous approaches could prove powerful in the study of other transcription factors. We further suggest that the SOX10-HaloTag expressing melanoma cell line developed in this study could find further applications in investigating the consequences of SOX10 targeted degradation in vitro and in vivo.

biochemistry↗

bioRxiv2025

Perturbational single-cell profiling of patient tumors defines lineage- and context-specific programs of innate immune resistance

AbstractDespite promise in preclinical models, most immuno-oncology drug candidates fail in clinical trials. These failures reflect limitations in our ability to directly model the response of human tumor and immune cells to immunotherapies. To address this gap and test the effect of innate immune agonists, we developed PERCEPT, an approach that uses ex vivo perturbational single-cell RNA sequencing to compare the response of immunomodulatory treatments with unstimulated controls directly in patient samples. Using PERCEPT, we tested cytokines and innate immune agonists in melanoma and Merkel cell carcinoma (MCC) and identified the dsRNA mimetic, RIG-I agonist, Stem Loop RNA (SLR) 14 as a powerful inducer of anti-viral states and enhancer of T cell activation. We compared transcriptional responder and non-responder patient samples and identified midkine (MDK), a multifunctional cytokine, as a potent repressor of IFN signaling in both tumor and immune cells. MDK expression dampened MHC-I presentation in human tumor cells and reduced activation of antigen-presenting cells, disrupting tumor immunity at multiple levels. In contrast to prior studies, we identified MDK as specifically enriched in neuroendocrine cancers such as MCC and small cell lung cancer compared with melanoma, suggesting the importance of lineage- and context-specific targeting. Our results demonstrate the utility of high-dimensional controlled perturbation of patient samples to identify mechanisms of innate immune response and resistance and demonstrate an actionable path towards clinical development of MDK-inhibiting therapies including FDA-approved ALK inhibitors in neuroendocrine cancers.

cancer biology↗

bioRxiv2024

Clonal determinants of organotropism and survival in metastatic uveal melanoma

Uveal melanoma (UM), the most common intraocular primary cancer in adults, demonstrates a unique proclivity for liver metastasis. To understand the molecular underpinnings of this organotropism, we analyzed the genomic features of liver and extrahepatic UM metastases, identifying distinct molecular signatures that mirror the clonal diversity in primary UM tumors. Liver metastases were enriched in BAP1 mutations and exhibited a higher prevalence of monosomy 3 compared to extrahepatic metastases. Analysis of the tumor-liver microenvironment crosstalk at the single-cell level underscored a significant role for hepatic stellate cells in facilitating UM growth and establishment in the liver. Notably, within the primary tumor, clones that demonstrated a high affinity for the liver, compared to those with low liver affinity, exhibited a distinct transcriptional profile characterized by the upregulation of pathways that activate hepatic stellate cells, specifically involving TGF-{beta} signaling, cytokine signaling, extracellular matrix remodeling, and angiogenesis. Liver-tropic clones displayed not only an increased affinity for liver colonization but were also associated with worse survival outcomes, underscoring the adverse prognostic significance of hepatic metastases in UM. Our findings demonstrate that trajectories of metastatic dissemination and patient survival in UM are established early in the primary tumors evolution, opening pathways for the development of targeted therapeutic interventions to improve patient outcomes.

cancer biology↗

bioRxiv2021

Integrative molecular and clinical profiling of acral melanoma identifies LZTR1 as a key tumor promoter and therapeutic target

Acral melanoma, the most common melanoma subtype among non-Caucasian individuals, is associated with poor prognosis. However, its key molecular drivers remain obscure. Here, we performed integrative genomic and clinical profiling of acral melanomas from a cohort of 104 patients treated in North America or China. We found that recurrent, late-arising amplifications of cytoband chr22q11.21 are a leading determinant of inferior survival, strongly associated with metastasis, and linked to downregulation of immunomodulatory genes associated with response to immune checkpoint blockade. Unexpectedly, LZTR1 - a known tumor suppressor in other cancers - is a key candidate oncogene in this cytoband. Silencing of LZTR1 in melanoma cell lines caused apoptotic cell death independent of major hotspot mutations or melanoma subtypes. Conversely, overexpression of LZTR1 in normal human melanocytes initiated processes associated with metastasis, including anchorage-independent growth, formation of spheroids, and increased levels of MAPK and SRC activities. Our results provide new insights into the etiology of acral melanoma and implicate LZTR1 as a key tumor promoter and therapeutic target.

cancer biology↗