Biology subjects

McMahon-Skates, T.

Publications and source records attributed to McMahon-Skates, T..

2 recordsLinked to original sources

bioRxiv2024

Harmonizing terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) with multiplexed iterative immunofluorescence enriches spatial contextualization of cell death

Terminal deoxynucleotidyl transferase dUTP Nick End Labeling (TUNEL) is an essential tool for the detection of cell death in tissues. Although TUNEL is not known to be compatible with multiplexed spatial proteomic methods, harmonizing TUNEL with such methods offers the opportunity to delineate cell-type specific cell death labeling and precise spatial contextualization of cell death in complex tissues. Here we evaluated variations of the TUNEL assay for their compatibility with a multiplexed immunofluorescence method, multiple iterative labeling by antibody neodeposition (MILAN), in two different tissues and injury models for cell death, acetaminophen-induced hepatocyte necrosis and dexamethasone-induced adrenocortical apoptosis. Using a commercial Click-iT-based assay as a standard, TUNEL signal could be reliably produced independent of antigen-retrieval method, with tissue-specific minor differences in signal-to-noise. In contrast, proteinase K treatment consistently reduced or even abrogated protein antigenicity, while pressure cooker treatment consistently enhanced protein antigenicity for the targets tested. Antibody-based TUNEL protocols using pressure-cooker antigen retrieval were MILAN erasure-compatible thus enabling harmonization of TUNEL with MILAN. As many as four staining cycles could be performed without loss of subsequent TUNEL signal, while first-round TUNEL did not influence protein antigenicity in subsequent rounds. We conclude this harmonized assay performs comparably to an established commercial assay, but preserves protein antigenicity, thus enabling versatile integration with multiplexed immunofluorescence using MILAN. We anticipate this harmonized protocol will enable broad and flexible integration of TUNEL into multiplexed spatial proteomic assays, thus vastly enhancing the spatial contextualization of cell death in complex tissues.

pathology↗

bioRxiv2023

Chronic metabolic stress drives developmental programs and loss of tissue functions in non-transformed liver that mirror tumor states and stratify survival

Under chronic stress, cells must balance competing demands between cellular survival and tissue function. In metabolic dysfunction-associated steatotic liver disease (MASLD, formerly NAFLD/NASH), hepatocytes cooperate with structural and immune cells to perform crucial metabolic, synthetic, and detoxification functions despite nutrient imbalances. While prior work has emphasized stress-induced drivers of cell death, the dynamic adaptations of surviving cells and their functional repercussions remain unclear. Namely, we do not know which pathways and programs define cellular responses, what regulatory factors mediate (mal)adaptations, and how this aberrant activity connects to tissue-scale dysfunction and long-term disease outcomes. Here, by applying longitudinal single-cell multi-omics to a mouse model of chronic metabolic stress and extending to human cohorts, we show that stress drives survival-linked tradeoffs and metabolic rewiring, manifesting as shifts towards development-associated states in non-transformed hepatocytes with accompanying decreases in their professional functionality. Diet-induced adaptations occur significantly prior to tumorigenesis but parallel tumorigenesis-induced phenotypes and predict worsened human cancer survival. Through the development of a multi-omic computational gene regulatory inference framework and human in vitro and mouse in vivo genetic perturbations, we validate transcriptional (RELB, SOX4) and metabolic (HMGCS2) mediators that co-regulate and couple the balance between developmental state and hepatocyte functional identity programming. Our work defines cellular features of liver adaptation to chronic stress as well as their links to long-term disease outcomes and cancer hallmarks, unifying diverse axes of cellular dysfunction around core causal mechanisms.

systems biology↗