Biology subjects

Schueddig, E.

Publications and source records attributed to Schueddig, E..

3 recordsLinked to original sources

bioRxiv2026

Cellular stemness identifies high-risk ductal carcinoma in situ and offers a therapeutic interception opportunity

Ductal carcinoma in situ (DCIS) exhibits substantial heterogeneity in its risk of progression to invasive breast cancer, yet the cellular and molecular determinants of high-risk lesions remain incompletely defined. Using spatially resolved single-cell transcriptomic and epigenomic profiling of 43 patient-derived DCIS and DCIS/invasive ductal carcinoma (IDC) samples, we delineate cellular programs, spatial organization, and epigenetic regulatory mechanisms associated with invasive potential. We identify an epithelial population with stemness features within luminal hormone-responsive (LumHR) cells that progressively expands from benign tissue to DCIS and IDC, and is strongly associated with invasive progression and recurrence-linked transcriptional programs. Spatial mapping reveals discrete DCIS niches enriched for stem-like LumHR cells, characterized by elevated CEACAM6 expression and enhanced ligand-receptor interactions, including CEACAM6-EGFR signaling between epithelial and stromal compartments, including cancer-associated fibroblasts, macrophages (APOC1-positive) and perivascular cells. These niches define a microenvironmental context that supports stemness and invasive potential. Epigenomic analyses implicate FOXA1 as a key regulator of these stem-like transcriptional states. Pharmacologic disruption of FOXA1-regulatory network using LSD1 inhibition suppresses stemness-associated transcriptional programs in vitro and significantly restrains tumor growth in vivo. Collectively, these findings define high-risk DCIS as a stemness-driven disease embedded within specialized microenvironments, and identify associated regulatory networks as candidate biomarkers and therapeutic vulnerabilities.

cancer biology↗

bioRxiv2026

Integrative modeling of read depth and B-allele frequency improves single-cell copy number calling from targeted DNA sequencing panels

Copy number variations (CNVs) drive cancer initiation and progression, but resolving them at single-cell resolution from targeted DNA sequencing panels remains challenging. The Mission Bio Tapestri platform generates two complementary signals for CNV inference: sequencing depth and B-allele frequency (BAF) from heterozygous variants; however, existing methods such as karyotapR rely primarily on read depth, potentially missing allele-specific events invisible to depth-only approaches. Here we introduce scPloidyR, a hidden Markov model (HMM) that jointly models read depth and BAF at amplicon resolution for single-cell copy number calling from Tapestri data. scPloidyR fits independent per-chromosome Markov chains with copy number states as hidden variables, factorizes emission probabilities into depth and BAF likelihoods, and learns parameters via Baum-Welch expectation-maximization with Viterbi decoding. We compared scPloidyR with the established karyotapR Gaussian Mixture Model (GMM) through two simulation studies that evaluates BAF noise, variant density, amplicon density, sample size, and heterozygosity rate, and through application to a public Tapestri five-cell-line mixture dataset. In simulations, scPloidyR substantially outperformed karyotapR on class-balanced metrics (macro-F1: 0.472 vs. 0.264; alteration F1: 0.902 vs. 0.383 in simulation study 1) when allelic information was available. Adding just one heterozygous variant per amplicon increased scPloidyR accuracy from 0.548 to 0.899 for copy number gains. However, when BAF information was absent, karyotapR outperformed scPloidyR, and high BAF noise substantially degraded joint-model performance. On real data, scPloidyR produced more spatially coherent and biologically plausible copy number profiles. These results establish that joint depth-BAF modeling provides a clear advantage for single-cell CNV calling when allelic information is available, while depth-only methods remain preferable when such information is absent. Author SummaryCancer cells frequently gain or lose copies of DNA segments, and detecting these changes in individual cells is critical for understanding how tumors evolve and resist treatment. A technology called Tapestri sequences DNA from thousands of single cells and produces two types of signals: how much DNA is present (read depth) and which version of each gene a cell carries (allele information). Existing tools mainly use the first signal, potentially missing important changes that only the second signal can reveal. We developed scPloidyR, a statistical method that combines both signals to more accurately identify DNA copy number changes in single cells. Through simulations and analysis of real cancer cell data, we found that using both signals together substantially improves detection when allele information is available -- even a small amount of allele data makes a meaningful difference. However, when allele information is absent, the simpler depth-only approach performs better. Our work provides researchers with a new tool and practical guidance on when each approach is most effective for studying cancer at single-cell resolution.

bioinformatics↗

bioRxiv2025

Proton FLASH Exposure Preserves Gut Commensal Microbiomes and Spares Intestinal Stem Cells

Emerging evidence shows Proton FLASH radiotherapy can spare normal tissues while maintaining anti-tumor efficacy. However, its impact on intestinal stem cell (ISC) populations and the gut microbiome remains unclear. This is critical, as the gut microbiome influences ISC radiosensitivity. In a mouse model of radiation-induced gastrointestinal syndrome, FLASH-irradiated mice exhibited better survival and less crypt-villus damage compared to mice exposed to conventional proton irradiation. Using scRNA-sequencing, we demonstrated that proton FLASH exposure using pulsed pencil beam scanning spares two distinct ISC populations--Lgr5+ CBCs and a Clu+, Mif+, Fabp2+, Anxa2+ revival stem cell (revSC) population--by modulating oxidative stress and cell cycle progression. Analysis of alpha and beta diversity demonstrated that FLASH modulates gut microbiota composition without compromising overall species richness. Notably, FLASH-irradiated mice had higher abundances of Alistipes sp. and Akkermensia sp., both known for protective effects on ISCs and the intestinal mucosa. The critical role of microbiome in FLASH-mediated sparing effect against radiation toxicity was further confirmed by fecal microbiota transplantation, where FLASH-donor microbiota demonstrated reduced lethality in recipients exposed to proton irradiation with conventional dose rate. Our findings highlight the crucial role of the microbiome in the FLASH-mediated sparing of the mucosal epithelium.

bioengineering↗