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Jinzhi Lei

Publications and source records attributed to Jinzhi Lei.

At least 19 recordsLinked to original sources

Modeling tumor cell heterogeneity and plasticity in adaptive therapy

Adaptive therapy (AT) is designed to postpone the emergence of drug resistance by exploiting evolutionary competition among tumor subclones. Most mathematical models of AT assume a binary population structure of drug-sensitive and drug-resistant cells, which neglects the continuous nature of phenotypic plasticity. In this study, we propose a mathematical model that integrates a continuous drug susceptibility index with a probabilistic inheritance function to describe clonal dynamics under therapy. The resulting integro-differential system generalizes traditional two-type competition models and captures both heterogeneity and plasticity of tumor cells. Analytical and numerical studies show that (i) continuous therapy drives rapid expansion of resistant clones, (ii) adaptive therapy maintains long-term tumor control by dynamically regulating sensitive populations, and (iii) high phenotypic plasticity accelerates phenotype switching, leading to earlier tumor relapse following continuous therapy. These results identify critical parameter regimes where adaptive therapy outperforms fixed regimens and highlight the essential role of plasticity in shaping treatment outcomes. The proposed framework provides a more realistic mathematical foundation for the design of clinically relevant adaptive therapy strategies.

q-bio.PE↗

Combination therapy for colorectal cancer with anti-PD-L1 and cancer vaccine: A multiscale mathematical model of tumor-immune interactions

The tumor-immune system plays a critical role in colorectal cancer progression. Recent preclinical and clinical studies showed that combination therapy with anti-PD-L1 and cancer vaccines improved treatment response. In this study, we developed a multiscale mathematical model of interactions among tumors, immune cells, and cytokines to investigate tumor evolutionary dynamics under different therapeutic strategies. Additionally, we established a computational framework based on approximate Bayesian computation to generate virtual tumor samples and capture inter-individual heterogeneity in treatment response. The results demonstrated that a multiple low-dose regimen significantly reduced advanced tumor burden compared to baseline treatment in anti-PD-L1 therapy. In contrast, the maximum dose therapy yielded superior tumor growth control in cancer vaccine therapy. Furthermore, cytotoxic T cells were identified as a consistent predictive biomarker both before and after treatment initiation. Notably, the cytotoxic T cells-to-regulatory T cells ratio specifically served as a robust pre-treatment predictive biomarker, offering potential clinical utility for patient stratification and therapy personalization.

q-bio.PE↗

Effects of multi-phase control mechanism on fibroblast dynamics: A segmented mathematical modeling approach

Cell size is a fundamental determinant of cellular physiology, influencing processes such as growth, division, and function. In this study, we develop a segmented mathematical framework to investigate how different control mechanisms operating across multiple phases of the cell cycle affect fibroblast population dynamics. Building on our previous work modeling sizer, timer, and adder strategies, we extend the analysis by introducing phase-specific control schemes in the S and G2 phases, incorporating nonlinear growth dynamics and cell death. Using agent-based stochastic simulations, we examine how these mechanisms shape steady-state size distributions and respond to parameter variations. Our results reveal that the steady-state cell size distribution is primarily governed by division kernels and phase-specific control strategies, and appears remarkably robust to cell death modalities. We identify a fundamental trade-off between extrinsic and intrinsic growth feedbacks: while population-density-dependent regulation tightly limits total cell numbers, cell-size-dependent regulation acts as a proportional homeostatic mechanism, suppressing relative size variability. Furthermore, we demonstrate that population recovery is accelerated by the retention of proliferation-competent large cells. This study provides biologically relevant insights into the complex interplay between growth, division, and homeostasis, with implications for understanding tissue repair and disease progression.

q-bio.CB↗

Epigenetic state inheritance drivers drug-tolerant persister-induced resistance in solid tumors: A stochastic agent-based model

The efficacy of anti-cancer therapies is severely limited by the emergence of drug resistance. While genetic drivers are well-characterized, growing evidence suggests that non-genetic mechanisms, particularly those involving drug-tolerant persisters (DTPs), play a pivotal role in solid tumor relapse. To elucidate the evolutionary dynamics of DTP-induced resistance, we develop a stochastic agent-based model (ABM) of solid tumor evolution that couples macroscopic population dynamics with microscopic epigenetic state inheritance during the cell cycle. Our simulations accurately reproduce the temporal progression of relapse observed in experimental studies, capturing the dynamic transition from sensitive cells to DTPs, and ultimately to stable resistant phenotypes under prolonged therapy. By explicitly modeling the epigenetic plasticity of individual cells, our model bridges the gap between cellular heterogeneity and population-level tumor evolution. Furthermore, we performed \textit{in silico} clinical trials using virtual patient cohorts to evaluate therapeutic outcomes, demonstrating that optimized adaptive treatment strategies can significantly delay tumor relapse compared to standard dosing. This study provides a quantitative framework for dissecting DTP-driven resistance mechanisms and designing more effective, biologically informed therapeutic strategies.

q-bio.PE↗

Quantitative cancer-immunity cycle modeling to optimize bevacizumab and atezolizumab combination therapy for advanced renal cell carcinoma

The incidence of advanced renal cell carcinoma(RCC) has been rising, presenting significant challenges due to the limited efficacy and severe side effects of traditional radiotherapy and chemotherapy. While combination immunotherapies show promise, optimizing treatment strategies remains difficult due to individual heterogeneity. To address this, we developed a Quantitative Cancer-Immunity Cycle (QCIC) model that integrates ordinary differential equations with stochastic modelling to quantitatively characterize and predict tumor evolution in patients with advanced RCC. By systematically integrating quantitative systems pharmacology principles with biological mechanistic knowledge, we constructed a virtual patient cohort and calibrated the model parameters using clinical immunohistochemistry data to ensure biological validity. To enhance predictive performance, we coupled the model with pharmacokinetic equations and defined the Tumor Response Index (TRI) as a quantitative metric of efficacy. Systematic analysis of the QCIC model allowed us to determine an optimal treatment regimen for the combination of bevacizumab and atezolizumab and identify tumor biomarkers with clinical predictive value. This study provides a theoretical framework and methodological support for precision medicine in the treatment of advanced RCC.

q-bio.QM↗

Modeling tumor progression in heterogeneous microenvironments: A cellular automata approach

Understanding how microenvironmental heterogeneity influences tumor progression is essential for advancing both cancer biology and therapeutic strategies. In this study, we develop a cellular automata (CA) model to simulate tumor growth under varying microenvironmental conditions and genetic mutation rates, addressing a gap in existing studies that rarely integrate these two factors to explain tumor dynamics. The model explicitly incorporates the cellular heterogeneity of stem and non-stem cells, dynamic cell-cell interactions, and tumor-microenvironment crosstalk. Using computational simulations, we examine the synergistic effects of gene mutation rate, initial tumor burden, and microenvironmental state on tumor progression. Our results demonstrate that lowering the mutation rate significantly mitigates tumor expansion and preserves microenvironmental integrity. Interestingly, the initial tumor burden has a limited impact, whereas the initial condition of the microenvironment critically shapes tumor dynamics. A supportive microenvironment promotes proliferation and spatial invasion, while inhibitory conditions suppress tumor growth. These findings highlight the key role of microenvironmental modulation in tumor evolution and provide computational insights that may inform more effective cancer therapies.

q-bio.CB↗

Mathematical modeling of tumor-immune interactions: methods, applications, and future perspectives

Mathematical oncology is a rapidly evolving interdisciplinary field that uses mathematical models to enhance our understanding of cancer dynamics, including tumor growth, metastasis, and treatment response. Tumor-immune interactions play a crucial role in cancer biology, influencing tumor progression and the effectiveness of immunotherapy and targeted treatments. However, studying tumor dynamics in isolation often fails to capture the complex interplay between cancer cells and the immune system, which is critical to disease progression and therapeutic efficacy. Mathematical models that incorporate tumor-immune interactions offer valuable insights into these processes, providing a framework for analyzing immune escape, treatment response, and resistance mechanisms. In this review, we provide an overview of mathematical models that describe tumor-immune dynamics, highlighting their applications in understanding tumor growth, evaluating treatment strategies, and predicting immune responses. We also discuss the strengths and limitations of current modeling approaches and propose future directions for the development of more comprehensive and predictive models of tumor-immune interactions. We aim to offer a comprehensive guide to the state of mathematical modeling in tumor immunology, emphasizing its potential to inform clinical decision-making and improve cancer therapies.

q-bio.QM↗

A stochastic agent-based model for simulating tumor-immune dynamics and evaluating therapeutic strategies

Tumor-immune interactions are central to cancer progression and treatment outcomes. In this study, we present a stochastic agent-based model that integrates cellular heterogeneity, spatial cell-cell interactions, and drug resistance evolution to simulate tumor growth and immune response in a two-dimensional microenvironment. The model captures dynamic behaviors of four major cell types--tumor cells, cytotoxic T lymphocytes, helper T cells, and regulatory T cells--and incorporates key biological processes such as proliferation, apoptosis, migration, and immune regulation. Using this framework, we simulate tumor progression under different therapeutic interventions, including radiotherapy, targeted therapy, and immune checkpoint blockade. Our simulations reproduce emergent phenomena such as immune privilege and spatial immune exclusion. Quantitative analyses show that all therapies suppress tumor growth to varying degrees and reshape the tumor microenvironment. Notably, combination therapies--especially targeted therapy with immunotherapy--achieve the most effective tumor control and delay the emergence of resistance. Additionally, sensitivity analyses reveal a nonlinear relationship between treatment intensity and therapeutic efficacy, highlighting the existence of optimal dosing thresholds. This work demonstrates the utility of agent-based modeling in capturing complex tumor-immune dynamics and provides a computational platform for optimizing cancer treatment strategies. The model is extensible, biologically interpretable, and well-suited for future integration with experimental or clinical data.

q-bio.TO↗

Quantitative analysis of cell size control mechanisms

Cell size control is crucial for maintaining cellular function and homeostasis. In this study, we develop a first-order partial differential equation model to examine the effects of three key size control mechanisms: the sizer, timer, and adder. Each mechanism is incorporated into the model through distinct boundary conditions. Exact solutions for these mechanisms are derived using the method of characteristics, allowing us to explore how the steady-state size distribution depends on control parameters. Additionally, individual-cell-based stochastic simulations are performed to validate our theoretical findings and investigate the size distribution under various conditions. This study provides new insights into the quantitative dynamics of cell size regulation, highlighting the underlying mechanisms and laying the groundwork for future theoretical and experimental work on size homeostasis in biological systems.

q-bio.CB↗

A tumor-immune model of chronic myeloid leukemia with optimal immunotherapeutic protocols

The interactions between tumor cells and the immune system play a crucial role in cancer evolution. In this study, we explore how these interactions influence cancer progression by modeling the relationships among naive T cells, effector T cells, and chronic myeloid leukemia cells. We examine the existence of equilibria, the asymptotic stability of the positive steady state, and the global stability of the tumor-free equilibrium. Additionally, we develop a partial differential equation to describe the conditions under which the concentration of cancer cells reaches a level that allows for effective control of cancer evolution. Finally, we apply our proposed model to investigate optimal treatment strategies that aim to minimize both the concentration of cancer cells at the end of treatment and the accumulation of tumor burden, as well as the cost associated with treatment during the intervention period. Our study reveals an optimal therapeutic protocol using optimal control theory. We perform numerical simulations to illustrate our theoretical results and to explore the dynamic behavior of the system and optimal therapeutic protocols. The simulations indicate that the optimal treatment strategy can be more effective than a constant treatment approach, even when applying the same treatment interval and total drug input.

q-bio.TO↗

A general mathematical framework for understanding the behavior of heterogeneous stem cell regeneration

Stem cell heterogeneity is essential for the homeostasis in tissue development. This paper established a general formulation for understanding the dynamics of stem cell regeneration with cell heterogeneity and random transitions of epigenetic states. The model generalizes the classical G0 cell cycle model, and incorporates the epigenetic states of stem cells that are represented by a continuous multidimensional variable and the kinetic rates of cell behaviors, including proliferation, differentiation, and apoptosis, that are dependent on their epigenetic states. Moreover, the random transition of epigenetic states is represented by an inheritance probability that can be described as a conditional beta distribution. This model can be extended to investigate gene mutation-induced tumor development. The proposed formula is a generalized formula that helps us to understand various dynamic processes of stem cell regeneration, including tissue development, degeneration, and abnormal growth.

q-bio.PE↗

Modelling infectious disease transmission dynamics in conference environments: An individual-based approach

The global public health landscape is perpetually challenged by the looming threat of infectious diseases. Central to addressing this concern is the imperative to prevent and manage disease transmission during pandemics, particularly in unique settings. This study addresses the transmission dynamics of infectious diseases within conference venues, presenting a computational model designed to simulate transmission processes within a condensed timeframe (one day), beginning with sporadic cases. Our model intricately captures the activities of individual attendees within the conference venue, encompassing meetings, rest intervals, and meal breaks. While meetings entail proximity seating, rest and lunch periods allow attendees to interact with diverse individuals. Moreover, the restroom environment poses an additional avenue for potential infection transmission. Employing an individual-based model, we meticulously replicated the transmission dynamics of infectious diseases, with a specific emphasis on close-contact interactions between infected and susceptible individuals. Through comprehensive analysis of model simulations, we elucidated the intricacies of disease transmission dynamics within conference settings and assessed the efficacy of control strategies to curb disease dissemination. Ultimately, our study proffers a numerical framework for assessing the risk of infectious disease transmission during short-duration conferences, furnishing conference organizers with valuable insights to inform the implementation of targeted prevention and control measures.

q-bio.PE↗

A computational scheme connecting gene regulatory network dynamics with heterogeneous stem cell regeneration

Stem cell regeneration is a vital biological process in self-renewing tissues, governing development and tissue homeostasis. Gene regulatory network dynamics are pivotal in controlling stem cell regeneration and cell type transitions. However, integrating the quantitative dynamics of gene regulatory networks at the single-cell level with stem cell regeneration at the population level poses significant challenges. This study presents a computational framework connecting gene regulatory network dynamics with stem cell regeneration through a data-driven formulation of the inheritance function. The inheritance function captures epigenetic state transitions during cell division in heterogeneous stem cell populations. Our scheme allows the derivation of the inheritance function based on a hybrid model of cross-cell-cycle gene regulation network dynamics. The proposed scheme enables us to derive the inheritance function based on the hybrid model of cross-cell-cycle gene regulation network dynamics. By explicitly incorporating gene regulatory network structure, it replicates cross-cell-cycling gene regulation dynamics through individual-cell-based modeling. The numerical scheme holds the potential for extension to diverse gene regulatory networks, facilitating a deeper understanding of the connection between gene regulation dynamics and stem cell regeneration.

q-bio.MN↗

scRDiT: Generating single-cell RNA-seq data by diffusion transformers and accelerating sampling

Motivation: Single-cell RNA sequencing (scRNA-seq) is a groundbreaking technology extensively utilized in biological research, facilitating the examination of gene expression at the individual cell level within a given tissue sample. While numerous tools have been developed for scRNA-seq data analysis, the challenge persists in capturing the distinct features of such data and replicating virtual datasets that share analogous statistical properties. Results: Our study introduces a generative approach termed scRNA-seq Diffusion Transformer (scRDiT). This method generates virtual scRNA-seq data by leveraging a real dataset. The method is a neural network constructed based on Denoising Diffusion Probabilistic Models (DDPMs) and Diffusion Transformers (DiTs). This involves subjecting Gaussian noises to the real dataset through iterative noise-adding steps and ultimately restoring the noises to form scRNA-seq samples. This scheme allows us to learn data features from actual scRNA-seq samples during model training. Our experiments, conducted on two distinct scRNA-seq datasets, demonstrate superior performance. Additionally, the model sampling process is expedited by incorporating Denoising Diffusion Implicit Models (DDIM). scRDiT presents a unified methodology empowering users to train neural network models with their unique scRNA-seq datasets, enabling the generation of numerous high-quality scRNA-seq samples. Availability and implementation: https://github.com/DongShengze/scRDiT

cs.LG↗

Mathematical modeling of heterogeneous stem cell regeneration: from cell division to Waddington's epigenetic landscape

Stem cell regeneration is a crucial biological process for most self-renewing tissues during the development and maintenance of tissue homeostasis. In developing the mathematical models of stem cell regeneration and tissue development, cell division is the core process connecting different scale biological processes and leading to changes in cell population number and the epigenetic state of cells. This chapter focuses on the primary strategies for modeling cell division in biological systems. The Lagrange coordinate modeling approach considers gene network dynamics within each cell and random changes in cell states and model parameters during cell division. In contrast, the Euler coordinate modeling approach formulates the evolution of cell population numbers with the same epigenetic state via a differential-integral equation. These strategies focus on different scale dynamics, respectively, and result in two methods of modeling Waddington's epigenetic landscape: the Fokker-Planck equation and the differential-integral equation approaches. The differential-integral equation approach formulates the evolution of cell population density based on simple assumptions in cell proliferation, apoptosis, differentiation, and epigenetic state transitions during cell division. Moreover, machine learning methods can establish low-dimensional macroscopic measurements of a cell based on single-cell RNA sequencing data. The low dimensional measurements can quantify the epigenetic state of cells and become connections between static single-cell RNA sequencing data with dynamic equations for tissue development processes. The differential-integral equation presented in this chapter provides a reasonable approach to understanding the complex biological processes of tissue development and tumor progression.

q-bio.QM↗

Algebraic Multiplicity and the Poincaré Problem

In this paper we derive an upper bound for the degree of the strict invariant algebraic curve of a polynomial system in the complex project plane under generic condition. The results are obtained through the algebraic multiplicities of the system at the singular points. A method for computing the algebraic multiplicity using Newton polygon is also presented.

math.CA↗

Dynamics of cell-type transition mediated by epigenetic modifications

Maintaining tissue homeostasis requires appropriate regulation of stem cell differentiation. The Waddington landscape posits that gene circuits in a cell form a potential landscape of different cell types, wherein cells follow attractors of the probability landscape to develop into distinct cell types. However, how adult stem cells achieve a delicate balance between self-renewal and differentiation remains unclear. We propose that random inheritance of epigenetic states plays a pivotal role in stem cell differentiation and present a hybrid model of stem cell differentiation induced by epigenetic modifications. Our comprehensive model integrates gene regulation networks, epigenetic state inheritance, and cell regeneration, encompassing multi-scale dynamics ranging from transcription regulation to cell population. Through model simulations, we demonstrate that random inheritance of epigenetic states during cell divisions can spontaneously induce cell differentiation, dedifferentiation, and transdifferentiation. Furthermore, we investigate the influences of interfering with epigenetic modifications and introducing additional transcription factors on the probabilities of dedifferentiation and transdifferentiation, revealing the underlying mechanism of cell reprogramming. This \textit{in silico} model provides valuable insights into the intricate mechanism governing stem cell differentiation and cell reprogramming and offers a promising path to enhance the field of regenerative medicine.

q-bio.QM↗

Power law dependence in a random differential equation

This paper studies a random differential equation with random switch perturbations. We explore how the maximum displacement from the equilibrium state depends on the statistical properties of time series of {the} random switches. We show a power law dependence between the upper bound of displacement and the frequency of random perturbation switches, and the slope of power law dependence is dependent on the specific distribution of the intervals between switching times. This result {suggests} a quantitative connection between frequency modulation and amplitude modulation under random perturbations.

math-ph↗