bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/152405

Complex polymorphisms in endocytosis genes suggest alpha-cyclodextrin against metastases in breast cancer

Wittkowski, K. M.·Dadurian, C.·Kim, H. S.·Hoshino, A.·Lyden, D.
View original source ↗Export metadata ↓

Abstract

Most breast cancer deaths are caused by metastasis and treatment options beyond radiation and cytotoxic drugs, which have severe side effects, and hormonal treatments, which are or become ineffective for many patients, are urgently needed. This study reanalyzed existing data from three genome-wide association studies (GWAS) using a novel computational biostatistics approach (muGWAS), which had been validated in studies of 600-2000 subjects in epilepsy and autism. MuGWAS jointly analyzes several neighboring single nucleotide polymorphisms while incorporating knowledge about genetics of heritable diseases into the statistical method and about GWAS into the rules for determining adaptive genome-wide significance.\n\nResults from three independent GWAS of 1000-2000 subjects each, which were made available under the National Institute of Healths \"Up For A Challenge\" (U4C) project, not only confirmed cell-cycle control and receptor/AKT signaling, but, for the first time in breast cancer GWAS, also consistently identified many genes involved in endo-/exocytosis (EEC), most of which had already been observed in functional and expression studies of breast cancer. In particular, the findings include genes that translocate (ATP8A1, ATP8B1, ANO4, ABCA1) and metabolize (AGPAT3, AGPAT4, DGKQ, LPPR1) phospholipids entering the phosphatidylinositol cycle, which controls EEC. These novel findings suggest scavenging phospholipids via alpha-cyclodextrins (CD) as a novel intervention to control local spread of cancer, packaging of exosomes (which prepare distant microenvironment for organ-specific metastases), and endocytosis of {beta}1 integrins (which are required for spread of metastatic phenotype and mesenchymal migration of tumor cells).\n\nBeta-cyclodextrins ({beta}CD) have already been shown to be effective in in vitro and animal studies of breast cancer, but exhibits cholesterol-related ototoxicity. The smaller CDs also scavenges phospholipids, but cannot fit cholesterol. An in-vitro study presented here confirms hydroxypropyl (HP)-CD to be twice as effective as HP{beta}CD against migration of human cells of both receptor negative and estrogen-receptor positive breast cancer.\n\nIf the previous successful animal studies with {beta}CDs are replicated with the safer and more effective CDs, clinical trials of adjuvant treatment with CDs are warranted. Ultimately, all breast cancer are expected to benefit from treatment with HPCD, but women with triplenegative breast cancer (TNBC) will benefit most, because they have fewer treatment options and their cancer advances more aggressively.

Source connections

Explore related subjects

cancer biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Wittkowski, K. M., Dadurian, C., Kim, H. S., Hoshino, A., Lyden, D.. 2017-06-20. Complex polymorphisms in endocytosis genes suggest alpha-cyclodextrin against metastases in breast cancer. https://doi.org/10.1101/152405

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Polycomb Marked Promoter Methylation Gains in Aging and Cancer are Independent of Replication

DNA methylation alterations are hallmark features of aging and cancer, occurring early during tumor initiation. Yet how these changes evolve during early tumorigenesis, and whether oncogenic signaling actively drives them, remains poorly understood due to limitations in resolving this at the longitudinal and clonal level. Here we developed a genome-wide DNA methylation profiling method for low DNA amounts and applied it to single stem cell-derived clones from a BRAFV600E -inducible mouse colon organoid model, tracking nucleotide-level methylation heterogeneity over time. BRAFV600E induction produced stepwise methylation divergence consistent with progressive clonal takeover, in contrast to gradual epigenetic drift in uninduced controls. Strikingly, while the specific CpG sites altered differed between BRAFV600E and control lineages, they converged on the same genomic elements. Particularly, Polycomb-marked promoter CpG-island methylation gains were not induced or accelerated by BRAFV600E, challenging models in which oncogenic signaling or cell proliferation actively instructs de novo methylation of Polycomb-targeted promoters. Instead, these gains tracked with "biological aging" independent of replication, which was validated across independent aging, cancer, and cell-line datasets. BRAFV600E -induced clones additionally showed progressive loss of intestinal lineage-specification transcription factor programs, consistent with selection for cells adapted to oncogenic stress. Together, these findings show that epigenetic trajectories during early tumor development, are rooted in baseline, age-dependent drivers of epigenetic alterations, and that oncogenic signaling acts primarily by selecting and expanding clones bearing pre-existing, age-associated epigenetic drift rather than instructing new methylation. Our findings have implications for how promoter methylation is interpreted as a cancer biomarker and for identifying upstream aging-associated processes as targets for early intervention.

cancer biology↗
bioRxiv2026

ORTHOTOPIC TUMOUR INDUCTION PROTOCOL SHAPES TUMOUR MICROENVIRONMENT

Robust preclinical cancer models are essential for studying tumour progression and evaluating therapeutic strategies. Orthotopic implantation of tumour cells into the mammary gland is widely used to model triple-negative breast cancer (TNBC), yet substantial variation exists in the number of cells used to initiate tumours, often without explicit consideration of how this parameter shapes tumour biology. Here, we systematically assess how tumour cell number at implantation influences the tumour microenvironment using the 4T1 orthotopic TNBC model. Mammary tumours initiated with different cell numbers exhibited comparable early growth kinetics and gross size, yet diverged markedly in cellular density, hypoxia, necrosis, proliferation, vascular integrity, and immune cell infiltration. High-density tumours displayed increased HIF-1 staining and necrosis, alongside differences in vascular-associated markers and increased macrophage recruitment. Conversely, low-density tumours remained highly proliferative, less necrotic and exhibited higher PDGFR{beta} staining. Importantly, tumour cells disseminated systemically within days of implantation across all conditions, although differences in colony recovery and ex vivo expansion were not statistically significant. Together, these findings demonstrate that tumour initiating protocols are powerful determinants of tumour state, with potential implications for dissemination frequency and tumour cell fate at distant sites. Rather than representing a source of experimental variability alone, this understanding provides an opportunity to intentionally tailor orthotopic models to investigate specific stages of disease progression and therapeutic response, thereby enhancing cross-study reproducibility and translational relevance.

cancer biology↗
bioRxiv2026

Single-cell characterization of 3D CLL spheroid model that recapitulates lymph node microenvironment-driven phenotypes and in vivo drug responses to ibrutinib

Lymph node (LN) microenvironmental signals promote chronic lymphocytic leukemia (CLL) cell survival, proliferation, and treatment resistance. We previously developed a 3D culture model that recapitulates key features of this protective LN niche. Using single-cell RNA sequencing of ex vivo paired peripheral blood and LN samples, together with matched patient-derived CLL spheroids, we investigated how microenvironmental cues shape CLL phenotypes and their response to ibrutinib. A total of 3 functional CLL states (resting, activated, proliferating) were identified, with expanded populations of activated and proliferating subsets in 3D cultures. After 5 days of in vitro ibrutinib treatment, CLL cells shifted toward a resting phenotype, reflecting published responses in patients at 6 months. Activated CLL cells showed relative resistance to ibrutinib, associated with TLR9-MALT1-MYC pathway activation. The 3D model recapitulated tissue-specific T cell phenotypes observed in patients, and computational analyses predicted several T-to-CLL cell-mediated interactions supporting the LN niche. Collectively, these data reveal distinct ibrutinib responses among CLL subsets and establish the 3D model as a physiologically relevant platform.

cancer biology↗