A hybrid agent-based model of the developing mammary terminal end bud

Agent-based approaches for biological modeling in oncology: A literature review

CONTEXT

Computational modeling involves the use of computer simulations and models to study and understand real-world phenomena. Its application is particularly relevant in the study of potential interactions between biological elements. It is a promising approach to understand complex biological processes and predict their behavior under various conditions.

METHODOLOGY

This paper is a review of the recent literature on computational modeling of biological systems. Our study focuses on the field of oncology and the use of artificial intelligence (AI) and, in particular, agent-based modeling (ABM), between 2010 and May 2023.

RESULTS

Most of the articles studied focus on improving the diagnosis and understanding the behaviors of biological entities, with metaheuristic algorithms being the models most used. Several challenges are highlighted regarding increasing and structuring knowledge about biological systems, developing holistic models that capture multiple scales and levels of organization, reproducing emergent behaviors of biological systems, validating models with experimental data, improving computational performance of models and algorithms, and ensuring privacy and personal data protection are discussed.

Lysine stimulates the development of the murine mammary gland at puberty via PI3K/AKT/mTOR signalling axis

Lysine is one of the essential amino acids. The effect of lysine on milk protein and milk fat anabolism has been reported, but the effect on mammary glands development has not been studied in detail. The normal development of the mammary glands at puberty is crucial to lactation of mammals. In this study, to explore the effect of lysine on mammary glands development, we fed different concentrations of lysine (0.025%, 0.05%, 0.1%) to pubertal mice and found that the addition of 0.1% lysine to drinking water significantly promoted mammary glands development. Furthermore, we treated mMECs (mouse mammary epithelial cells) with different concentrations of lysine (0, 0.2, 0.4, 0.6, 0.8 and 1 mM) to explore the underlying mechanism, and found that lysine promoted the proliferation of mMECs and development of mammary glands through PI3K/AKT/mTOR signalling pathway in pubertal mice. Overall, the results of this study revealed that lysine activated the PI3K/AKT/mTOR signal axis, elevated protein concentrations of cell proliferation markers, such as PCNA, Cyclin D1 and D3, and enhanced the proliferation of mMECs, finally promoted the murine mammary glands development at puberty.

Dedifferentiation-mediated stem cell niche maintenance in early-stage ductal carcinoma in situ progression: insights from a multiscale modeling study

We present a multiscale agent-based model of ductal carcinoma in situ (DCIS) to study how key phenotypic and signaling pathways are involved in the early stages of disease progression. The model includes a phenotypic hierarchy, and key endocrine and paracrine signaling pathways, and simulates cancer ductal growth in a 3D lattice-free domain. In particular, by considering stochastic cell dedifferentiation plasticity, the model allows for study of how dedifferentiation to a more stem-like phenotype plays key roles in the maintenance of cancer stem cell populations and disease progression. Through extensive parameter perturbation studies, we have quantified and ranked how DCIS is sensitive to perturbations in several key mechanisms that are instrumental to early disease development. Our studies reveal that long-term maintenance of multipotent stem-like cell niches within the tumor are dependent on cell dedifferentiation plasticity, and that disease progression will become arrested due to dilution of the multipotent stem-like population in the absence of dedifferentiation. We have identified dedifferentiation rates necessary to maintain biologically relevant multipotent cell populations, and also explored quantitative relationships between dedifferentiation rates and disease progression rates, which may potentially help to optimize the efficacy of emerging anti-cancer stem cell therapeutics.

Long Intergenic Non-Coding RNAs in the Mammary Parenchyma and Fat Pad of Pre-Weaning Heifer Calves: Identification and Functional Analysis

Enhanced plane of nutrition at pre-weaning stage can promote the development of mammary gland especially heifer calves. Although several genes are involved in this process, long intergenic non-coding RNAs (lincRNAs) are regarded as key regulators in the regulated network and are still largely unknown. We identified and characterized 534 putative lincRNAs based on the published RNA-seq data, including heifer calves in two groups: fed enhanced milk replacer (EH, 1.13 kg/day, including 28% crude protein, 25% fat) group and fed restricted milk replacer (R, 0.45 kg/day, including 20% crude protein, 20% fat) group. Sub-samples from the mammary parenchyma (PAR) and mammary fat pad (MFP) were harvested from heifer calves. According to the information of these lincRNAs' quantitative trait loci (QTLs), the neighboring and co-expression genes were used to predict their function. By comparing EH vs R, 79 lincRNAs (61 upregulated, 18 downregulated) and 86 lincRNAs (54 upregulated, 32 downregulated) were differentially expressed in MFP and PAR, respectively. In MFP, some differentially expressed lincRNAs (DELs) are involved in lipid metabolism pathways, while, in PAR, among of DELs are involved in cell proliferation pathways. Taken together, this study explored the potential regulatory mechanism of lincRNAs in the mammary gland development of calves under different planes of nutrition.

An Intravital Microscopy Toolbox to Study Mammary Gland Dynamics from Cellular Level to Organ Scale

The architecture of the mouse mammary gland is highly dynamic and constantly remodeled during pubertal development and estrous cycle-driven sprouting and regression of alveolar side branches. During each of these developmental stages, turnover is driven by distinct subsets of mammary epithelial cells. Extensive previous research has shed light on the unique morphological and cell biological characteristics of each stage. However, technological shortcomings failed to capture the dynamics and single-cell contributions to mammary remodeling. Here, we developed in vivo imaging strategies to follow the same mammary ducts over time and quantify the dynamics of mammary gland growth and remodeling from single-cell level to organ scale. Using a combination of intravital microscopy and genetic reporter systems we show how proliferative heterogeneity drives ductal morphogenesis during different developmental stages. To visualize pubertal growth at the cellular level, we performed long-term time-lapse imaging of extending terminal end buds through a mammary imaging window. We show that single-cells within the terminal end buds are extremely motile and continuously exchange position whilst the duct is elongating. To visualize short-term remodeling in the adult mammary gland at the single cell level, we performed multi-day intravital imaging in photoconvertible Kikume Green-Red mice and fluorescent ubiquitination-based cell cycle indicator mice. We demonstrate that the contribution of single-cells to estrous-driven remodeling is highly variable between cells in the same micro-environment. To assess the effects of this dynamic proliferative contribution on the long-term stability of tissue architecture, we developed a repeated skin flap method to assess mammary gland morphology by intravital microscopy over extended time spans for up to six months. Interestingly, in contrast to the short-term dynamic remodeling, the long-term morphology of the mammary gland remains remarkably stable. Together, our tool box of imaging strategies allows to identify and map transient and continuing dynamics of single cells to the architecture of the mammary gland.

A Multiscale Agent-Based Model of Ductal Carcinoma In Situ

OBJECTIVE

we present a multiscale agent-based model of Ductal Carcinoma in Situ (DCIS) in order to gain a detailed understanding of the cell-scale population dynamics, phenotypic distributions, and the associated interplay of important molecular signaling pathways that are involved in DCIS ductal invasion into the duct cavity (a process we refer to as duct advance rate here).

METHODS

DCIS is modeled mathematically through a hybridized discrete cell-scale model and a continuum molecular scale model, which are explicitly linked through a bidirectional feedback mechanism.

RESULTS

we find that duct advance rates occur in two distinct phases, characterized by an early exponential population expansion, followed by a long-term steady linear phase of population expansion, a result that is consistent with other modeling work. We further found that the rates were influenced most strongly by endocrine and paracrine signaling intensity, as well as by the effects of cell density induced quiescence within the DCIS population.

CONCLUSION

our model analysis identified a complex interplay between phenotypic diversity that may provide a tumor adaptation mechanism to overcome proliferation limiting conditions, allowing for dynamic shifts in phenotypic populations in response to variation in molecular signaling intensity. Further, sensitivity analysis determined DCIS axial advance rates and calcification rates were most sensitive to cell cycle time variation.

SIGNIFICANCE

this model may serve as a useful tool to study the cell-scale dynamics involved in DCIS initiation and intraductal invasion, and may provide insights into promising areas of future experimental research.

Pubertal mammary development as a "susceptibility window" for breast cancer disparity

Factors such as socioeconomic status, age at menarche and childbearing patterns are components that have been shown to influence mammary gland development and establish breast cancer disparity. Pubertal mammary gland development is selected as the focus of this review, as it is identified as a "window of susceptibility" for breast cancer risk and disparity. Here we recognize non-Hispanic White, African American, and Asian American women as the focus of breast cancer disparity, in conjunction with diets associated with changes in breast cancer risk. Diets consisting of high fat, N-3 polyunsaturated fatty acids, N-6 polyunsaturated fatty acids, as well as obesity and the Western diet have shown to lead to changes in pubertal mammary gland development in mammalian models, therefore increasing the risk of breast cancer and breast cancer disparity. While limited intervention strategies are offered to adolescents to mitigate development changes and breast cancer risk, the prominent solution to closing the disparity among the selected population is to foster lifestyle changes that avoid the deleterious effects of unhealthy diets.

Understanding Ductal Carcinoma In Situ Invasion using a Multiscale Agent-Based Model

Ductal carcinoma in situ (DCIS) is commonly treated clinically through surgical resection. Although surgical options exist for resection, it is unclear which is optimal to reduce the likelihood of future invasive disease. This is further complicated by challenges in determining correct surgical margins from disease diagnostics, with mammographic imaging misidentifying surgical margins by as much as 2 cm vs. histological examination. We have implemented a threedimensional, hybrid multiscale model of DCIS to study disease initiation and progression. In order to shed new light on current biological questions and clinical challenges surrounding the disease, we present here an improved version of this model, with more biologically relevant molecular signaling pathways, cell phenotype hierarchies, and duct architecture variation. In particular, a cell necrosis, lysis and calcification pathway has been incorporated into the model to help better understand the relationship between diagnostic imaging and the true extent of disease invasion. We observe that deficiencies in availability of molecular signaling molecules that upregulate cell proliferation may be overcome by dynamic shifts in phenotypic distributions within the disease mass. Hypoxia, necrosis, and calcification together functioned as a hypoxia relief mechanism, and were observed to maintain a consistent distance between the DCIS leading edge and the site of necrosis onset, providing insights for improving surgical margins.