Biology subjects

Waas, M.

Publications and source records attributed to Waas, M..

13 recordsLinked to original sources

bioRxiv2026

Germline BRCA1 Mutation Deregulates Irradiation-Induced Cell Cycle Checkpoints in Human Mammary Luminal Progenitors

Mammary ductal tree comprises two epithelial lineages, basal and luminal, which harbour stem and progenitor cell subsets essential to breast physiology and are cancer-initiating precursors. Dysregulated cellular stress response is an early event in tumorigenesis, yet lineage-rooted study of primary breast epithelium pertinent to familial mutation carriers is limited. Here, we establish a lineage-resolved monolayer culture system that enables propagation of primary human mammary epithelial populations while preserving lineage identity across passages. We identify intrinsically distinct cell cycle response of luminal progenitors and basal cells to irradiation stress where the former engages both G1/S and G2/M checkpoints to achieve cell cycle arrest and the latter relies on the G2/M checkpoint. These lineage distinctions are diminished in germline BRCA1 mutation carriers with an attenuated G1/S checkpoint in luminal progenitors. Paired transcriptomic-proteomic profiling of acute irradiation response uncovers BRCA1+/- luminal progenitor population with sustained AKT-mTOR signaling and compromised cell cycle arrest marking an early deviation in the stress response of these purported cells-of-origin of aggressive breast cancers known to arise in BRCA1 germline mutation carriers. Our study provides a functional framework for determining critical events in the expansion of genomically altered mammary epithelial cells in the high-risk breast to enable future preventive interventions.

cell biology↗

bioRxiv2026

Mapping lineage and functional diversity in the high-risk human mammary epithelium

BackgroundBreast cancer risk is shaped by the vast heterogeneity of mammary epithelial cells, comprising basal, luminal progenitor, and mature luminal populations. While transcriptional variation among these lineages has been extensively studied, protein-level features - particularly in high-risk women - remain underexplored, limiting insight into early cellular and molecular determinants of susceptibility. Moreover, little is known about how clinical covariates influence clonogenic capacity, proteomic states, and epithelial proportions, complicating the design of properly controlled human studies of early breast cancer risk. ResultsWe combined low-input proteomics with functional clonogenic assays to profile mammary epithelial cell subpopulations from a cohort of 21 breast tissues encompassing different germline mutation backgrounds, parity status and age. We quantified over 5,555 proteins and observed marked inter-donor variation in epithelial composition, proteomic programs, and colony-forming capacity. Multivariable modeling revealed that clinical covariates - including age, parity, and germline mutation status - modulate both global proteomic architecture and lineage-specific pathway activity. Parity was associated with reduced basal cell abundance, altered luminal progenitor and mature luminal proteomes, and changes in clonogenicity. Pathway analyses identified both conserved and lineage-restricted responses to shared risk factors. Projection of clonogenic signatures onto METABRIC and TCGA tumors further linked functional programs to tumor subtypes and clinical outcomes. ConclusionsThis study provides the most comprehensive proteomic atlas of cell-type resolved diversity in the high-risk breast to date. By defining how clinical covariates remodel epithelial composition and molecular state, it clarifies key sources of biological variability that challenge controlled study design and offers a resource for improving mechanistic insight, risk assessment, and prevention strategies.

cancer biology↗

bioRxiv2025

Surface proteomics reveals arginine metabolism as a vulnerability in high grade serous ovarian cancer

The significant lethality of high-grade serous ovarian cancer (HGSC) is driven by the lack of long-term efficacy of current treatments, underscoring the need for developing additional therapeutics. Cell surface proteins represent attractive therapeutic targets yet remain underexplored in high-grade serous ovarian cancer. Here, we employed cell surface N-glycoproteomics to elucidate the cell surface proteomes of HGSC cells alongside normal epithelial and cancer-associated stromal cells, uncovering new opportunities for therapeutic intervention. Integration of cell surface N-glycoproteomics and functional screening revealed multiple minimally characterized, HGSC-enriched surface proteins that are critical for HGSC proliferation, most notably, SLC7A1. Multi-omic and functional characterization indicated that SLC7A1 is necessary for HGSC migration, protein synthesis and mitochondrial functions likely linked to its role as an arginine transporter. Finally, we demonstrate that elevated surface expression of SLC7A1 in HGSC reflects dysregulated arginine metabolism, pointing to a putative therapeutic vulnerability. Our work identifies SLC7A1 and arginine metabolism as a previously unrecognized molecular vulnerability in HGSC and provides a framework to guide future therapeutic development.

cancer biology↗

bioRxiv2025

Ancestry-Dependent Immunologic and Prognostic Effects Characterize the Prostate Cancer Urinary Proteome

Urine is an attractive biomarker analyte for non-invasive longitudinal monitoring of health and disease, particularly for diseases of the genitourinary tract, like prostate and bladder cancer. The composition of an individuals urine reflects both genetic and lifestyle characteristics that differ across geographies and populations, like diet, hydration and other socio-economic factors. While men of African ancestry have elevated prostate cancer risk, it is unclear to what extent this influences urinary biomarkers. We therefore quantified the urinary proteomes of 329 localized prostate cancer patients: 135 self-identifying as White and 194 self-identifying as Black. We identified 110 proteins that significantly differed between these groups after controlling for age, PSA, and cISUP. Immune pathways were particularly dysregulated. The urinary proteome of Black patients harboured more features of aggressive cancers than those of grade- and PSA-matched White patients. These observations highlight the importance of controlling for race- and ancestry-associated differences in the development of urinary biomarkers.

cancer biology↗

bioRxiv2025

Progesterone Receptor Expressing Basal Cells and Progesterone Receptor-Primed Progenitors Redefine the Mammary Epithelial Hierarchy

The central role of progesterone in breast biology and cancer is undeniable. Progesterone is a potent mitogen for mammary stem cell expansion and essential for mammopoiesis, yet only a fraction of the luminal epithelium is described to express the progesterone receptor (PR). Progestins in contraceptives and HRT regimens increases breast cancer risk, whilst progesterone inhibition reduces mammary tumorigenesis. Understanding PR within mammary epithelial dynamics is imperative, especially given mammary stem/progenitors cells are the cells-of-origin in breast cancer. Here, we show PR-primed progenitors contribute to both mammary lineages and expose a novel PR+ basal population, challenging current dogma in the field. PR lineage-tracing yields an unprecedented contribution to the luminal and basal compartments. We uncover an asymmetrically dividing PR-primed subpopulation, which has unique bipotent clonogenic capacity and forms TEB-like outgrowths upon transplantation. We enumerate PR+ basal cells and dissect their proteomic landscape, establishing PR+ basal cells as a discrete basal subset, disparate from luminal PR+ cells. Finally, we identify PR+ basal cells in multiple proteomes, scRNAseq datasets and localize PR in clinical breast specimens. This forms a new foundation for comprehending hormone receptor patterning in the breast, not only based on lineage-identity but also the progenitor-progeny hierarchy. Our study shifts the current paradigm of breast biology with implications for breast cancer treatment given the growing interest in anti-progestin based primary prevention strategies.

cell biology↗

bioRxiv2024

Pan-cancer N-glycoproteomic atlas of patient derived xenografts uncovers FAT2 as a therapeutic target for head and neck cancers

Cell surface proteins offer significant cancer therapeutic potential attributable to their accessible membrane localization and central role in cellular signaling. Despite this, their promise remains largely untapped due to the technical challenges inherent to profiling cell surface proteins. Here, we employed N-glycoproteomics to analyze 85 patient-derived xenografts (PDX), constructing Glyco PDXplorer - an in vivo pan-cancer atlas of cancer-derived cell surface proteins. We developed a target discovery pipeline to prioritize proteins with favorable expression profiles for immunotherapeutic targeting and validated FAT2 as a head and neck squamous cancer (HNSC) enriched surface protein with limited expression in normal tissue. Functional studies revealed that FAT2 is essential for HNSC growth and adhesion through regulation of surface architecture and integrin-PI3K signaling. Chimeric antigen receptor (CAR) T cells targeting FAT2 demonstrated potent anti-tumor activity in HNSC models. This work lays the foundation for developing FAT2-targeted therapies and represents a pivotal resource to inform therapeutic target discovery for multiple cancers. HIGHLIGHTSO_LIPan-cancer landscape of cancer-derived cell surface proteins detected in vivo C_LIO_LIDevelopment of a multi-omic discovery pipeline to prioritize proteins with optimal expression profiles as immunotherapy targets C_LIO_LIIdentification and validation of FAT2 as a head and neck squamous cancer enriched surface protein with minimal expression in normal tissues C_LIO_LIFAT2 coordinates cell surface organization, adhesion, growth and survival through the integrin-PI3K-AKT pathway C_LIO_LIFAT2 CAR T cells demonstrate anti-tumour activity in pre-clinical models C_LI

cancer biology↗

bioRxiv2023

FABP7 Progenitors are a Targetable Metabolic Root in the BRCA1 Breast

It has been nearly 3 decades since the discovery of the BRCA1/2 genes and their link to breast cancer risk, with prophylactic mastectomy remaining the primary management option for these high-risk mutation carriers. The current paucity of interception strategies is due to undefined, targetable cancer precursor populations in the high-risk breast. Despite known cellular alterations in the BRCA1 breast, epithelial populations at the root of unwarranted cell state transitions remain unresolved. Here, we identify a root progenitor population that is dysregulated in BRCA1 carriers stemming from the metabolic role of BRCA1. This fatty-acid binding protein 7 (FABP7) expressing luminal progenitor population is spatially confined to the mammary ducts, has enhanced clonogenic capacity, and is the predicted origin of mixed basal-luminal differentiation in the BRCA1 but not BRCA2 breast. We show global H3K27 acetylation is reduced within ductal FABP7 cells in BRCA1 carriers in situ, linking to a non-canonical metabolic role of BRCA1 in regulating acetyl-CoA pools and de novo fatty acid synthesis. We demonstrate FABP7 progenitor capacity is preferentially ablated in BRCA1 carriers through inhibition of fatty acid metabolism using an FDA-approved fatty acid synthase (FASN) inhibitor. This study lays the foundation for metabolic control of breast progenitor dynamics to mitigate breast cancer risk in the BRCA1 breast.

cell biology↗

bioRxiv2023

Droplet based low input proteomic platform for rare cell populations

Deep proteomic profiling of rare cell populations has been constrained by sample input requirements. Here, we present DROPPS, an accessible low-input platform that generates high-fidelity proteomic profiles of 100 - 2,500 cells. By applying DROPPS within the mammary epithelium, we elucidated the connection between mitochondrial activity and clonogenicity, discovering and validating CD36 as a marker of progenitor capacity in the basal cell compartment. We anticipate DROPPS will accelerate biology-driven proteomic research for a multitude of rare cell populations.

biochemistry↗

bioRxiv2023

Prostate Cancer Reshapes the Secreted and Extracellular Vesicle Urinary Proteomes

Urine is a complex biofluid that reflects both overall physiologic state and the state of the genitourinary tissues through which it passes. It contains both secreted proteins and proteins encapsulated in tissue-derived extracellular vesicles (EVs). To understand the population variability and clinical utility of urine, we quantified the secreted and EV proteomes from 190 men, including a subset with prostate cancer. We demonstrate that a simple protocol enriches prostatic proteins in urine. Secreted and EV proteins arise from different subcellular compartments. Urinary EVs are faithful surrogates of tissue proteomes, but secreted proteins in urine or cell line EVs are not. The urinary proteome is longitudinally stable over several years. It can accurately and non-invasively distinguish malignant from benign prostatic lesions, and can risk-stratify prostate tumors. This resource quantifies the complexity of the urinary proteome, and reveals the synergistic value of secreted and EV proteomes for translational and biomarker studies.

systems biology↗

bioRxiv2020

CIRFESS: An interactive resource for querying the set of theoretically detectable peptides for cell surface and extracellular enrichment proteomic studies

Cell surface transmembrane, extracellular, and secreted proteins are high value targets for immunophenotyping, drug development, and studies related to intercellular communication in health and disease. As the number of specific and validated affinity reagents that target this subproteome are limited, mass spectrometry (MS)-based approaches will continue to play a critical role in enabling discovery and quantitation of these molecules. Given the technical considerations that make MS-based cell surface proteome studies uniquely challenging, it can be difficult to select an appropriate experimental approach. To this end, we have integrated multiple prediction strategies and annotations into a single online resource, Compiled Interactive Resource for Extracellular and Surface Studies (CIRFESS). CIRFESS enables rapid interrogation of the human proteome to reveal the cell surface proteome theoretically detectable by current approaches and highlights where current prediction strategies provide concordant and discordant information. We applied CIRFESS to identify the percentage of various subsets of the proteome which are expected to be captured by targeted enrichment strategies, including two established methods and one that is possible but not yet demonstrated. These results will inform the selection of available proteomic strategies and development of new strategies to enhance coverage of the cell surface and extracellular proteome. CIRFESS is available at www.cellsurfer.net/cirfess.

bioinformatics↗

bioRxiv2019

Reference glycan structure libraries of primary human cardiomyocytes and pluripotent stem cell-derived cardiomyocytes reveal cell-type and culture stage-specific glycan phenotypes

Cell surface glycoproteins play critical roles in maintaining cardiac structure and function in health and disease and the glycan-moiety attached to the protein is critical for proper protein folding, stability and signaling. However, despite mounting evidence that glycan structures are key modulators of heart function and must be considered when developing cardiac biomarkers, we currently do not have a comprehensive view of the glycans present in the normal human heart. In the current study, we used porous graphitized carbon liquid chromatography interfaced with mass spectrometry (PGC-LC-MS) to generate glycan structure libraries for primary human heart tissue homogenate, cardiomyocytes (CM) enriched from human heart tissue, and human induced pluripotent stem cell derived CM (hiPSC-CM). Altogether, we established the first reference structure libraries of the cardiac glycome containing 265 N- and O-glycans. Comparing the N-glycome of CM enriched from primary heart tissue to that of heart tissue homogenate, 21 structures significantly differed, and the high mannose class is increased in enriched CM. Moreover, by comparing primary CM to hiPSC-CM collected during 20-100 days of differentiation, dynamic changes in the glycan profile throughout in vitro differentiation were observed and differences between primary and hiPSC-CM were revealed. Namely, >30% of the N-glycome significantly changed across these time-points of differentiation and only 23% of the N-glycan structures were shared between hiPSC-CM and primary CM. These observations are an important complement to current genomic, transcriptomic, and proteomic profiling and reveal new considerations for the use and interpretation of hiPSC-CM models for studies of human development, disease, and drug testing. Finally, these data are expected to support future regenerative medicine efforts by informing targets for evaluating the immunogenic potential of hiPSC-CM and harnessing differences between immature, proliferative hiPSC-CM and adult primary CM.

biochemistry↗

bioRxiv2019

SurfaceGenie: A web-based application for integrating predictive and experimental data for rational candidate surface marker prioritization

MotivationCell-type specific surface proteins can be exploited as valuable markers for a range of applications including immunophenotyping live cells, targeted drug delivery, and in vivo imaging. Despite their utility and relevance, the unique combination of molecules present at the cell surface are not yet described for most cell types. A significant challenge in analyzing omic discovery datasets is the selection of candidate markers that are most applicable for downstream applications. ResultsHere, we developed GenieScore, a prioritization metric that integrates a consensus-based prediction of cell surface localization with user-input data to rank-order candidate cell-type specific surface markers. In this report, we demonstrate the utility of GenieScore for analyzing human and rodent data from proteomic and transcriptomic experiments in the areas of cancer, stem cell, and islet biology. We also demonstrate that permutations of GenieScore, termed IsoGenieScore and OmniGenieScore, can efficiently prioritize co-expressed and intracellular cell-type specific markers, respectively. Availability and ImplementationCalculation of GenieScores and lookup of SPC scores is made freely accessible via the SurfaceGenie web-application: www.cellsurfer.net/surfacegenie.

systems biology↗

bioRxiv2018

Are these cardiomyocytes? Protocol development reveals impact of sample preparation on the accuracy of identifying cardiomyocytes by flow cytometry

Modern differentiation protocols enable efficient, yet imperfect, differentiation of human pluripotent stem cells into cardiomyocytes (hPSC-CM). As the number of laboratories and studies implementing this technology expands, the accurate assessment of cell identity in differentiation cultures is paramount to well-defined studies that can be replicated among laboratories. While flow cytometry is apt for routine assessment, a standardized protocol for assessing cardiomyocyte identity in hPSC-CM cultures has not yet been established. To address this gap, the current study leveraged targeted mass spectrometry to confirm the presence of troponin proteins in hPSC-CM and systematically evaluated multiple anti-troponin antibodies and sample preparation protocols for their suitability in assessing cardiomyocyte identity. Results demonstrate challenges of interpreting data generated by published methods and informed the development of a robust protocol for routine assessment of hPSC-CM. Overall, the new data, workflow for evaluating fit-for-purpose use of antibodies, and standardized protocol described here should benefit investigators new to this field as well as those with expertise in hPSC-CM differentiation.

developmental biology↗