Mapping the breast tumor microenvironment: proximity analysis reveals spatial relationships between macrophage subtypes and metastasis-initiating cancer cells

EM Grasset, A Desphande, JW Lee, Y Cho, SM Shin… - bioRxiv, 2024 - biorxiv.org
The development of metastasis, responsible for the majority of cancer-related fatalities, is the
most dangerous aspect of breast cancer, the predominant malignancy affecting women. We …

[HTML][HTML] Exploring Biocomplexity in Cancer: A Comprehensive Review

A Szasz, GP Szigeti - Open Journal of Biophysics, 2024 - scirp.org
Living objects have complex internal and external interactions. The complexity is regulated
and controlled by homeostasis, which is the balance of multiple opposing influences. The …

Temporal tissue dynamics from a single snapshot

S Mannor, U Alon, J Somer - bioRxiv, 2024 - biorxiv.org
Physiological and pathological processes such as inflammation or cancer emerge from the
interactions between cells over time. However, methods to follow cell populations over time …

Explainable Machine Learning Reveals the Role of the Breast Tumor Microenvironment in Neoadjuvant Chemotherapy Outcome

Y Azimzade, M Haugen, X Tekpli, CB Steen… - bioRxiv, 2023 - biorxiv.org
Recent advancements in single-cell RNA sequencing (scRNA-seq) have enabled the
identification of phenotypic diversity within breast tumor tissues. However, the contribution of …

Multiplex imaging of localized prostate tumors reveals changes in mast cell type composition and spatial organization of AR-positive cells in the tumor …

C Ak, Z Sayar, G Thibault, E Burlingame, J Eng… - bioRxiv, 2023 - biorxiv.org
Mapping spatial interactions of cancer, immune and stromal cells present novel
opportunities for patient stratification and for advancing immunotherapy. While single-cell …

Spatial and Compositional Biomarkers in Tumor Microenvironment Predicts Clinical Outcomes in Triple-Negative Breast Cancer

H Mi, R Varadhan, AM Cimino-Mathews, LA Emens… - bioRxiv, 2023 - biorxiv.org
Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with limited
treatment options, which warrants identification of novel therapeutic targets. Deciphering …

Multiplex Single-Cell Bioprinting for Engineering of Heterogeneous Tissue Constructs with Subcellular Spatial Resolution

HR Helms, KA Oyama, JP Ware, SD Ibsen… - bioRxiv, 2024 - biorxiv.org
Tissue development, function, and disease are largely driven by the spatial organization of
individual cells and their cell-cell interactions. Precision engineered tissues with single-cell …

[HTML][HTML] Robust biomarker discovery through multiplatform multiplex image analysis of breast cancer clinical cohorts

J Eng, E Bucher, Z Hu, M Sanders, B Chakravarthy… - bioRxiv, 2023 - ncbi.nlm.nih.gov
Spatial profiling of tissues promises to elucidate tumor-microenvironment interactions and
enable development of spatial biomarkers to predict patient response to immunotherapy and …

G-quadruplex DNA structures mediate non-autonomous instruction of breast tumour microenvironments

P Hunold, MN Hoehne, M Kiljan, O van Ray, J Herter… - bioRxiv, 2023 - biorxiv.org
Breast cancer is characterised by genetic and epigenetic alterations, such as G-quadruplex
(G4) DNA secondary structures. Here, we uncover differentially enriched G4 structure …

Bi-level Graphs for Cellular Pattern Discovery

Z Wang, AS Popel, J Sulam - NeurIPS 2023 AI for Science …, 2023 - openreview.net
The tumor microenvironment is widely recognized for its central role in driving cancer
progression and influencing prognostic outcomes. Despite extensive research efforts …