Biology subjects

Fischer, M. M.

Publications and source records attributed to Fischer, M. M..

7 recordsLinked to original sources

bioRxiv2025

Let there be multifunctionality: Uncovering the criticality zoo of the AC-DCgenetic circuit

Gene regulatory networks (GRNs) govern processes such as cell fate, patterning, and adaptation. While multistability and oscillations are both common GRN dynamics in cell biology, they are typically studied and engineered in isolation. Here, we challenge this separation using the AC-DC circuit, a minimal three- gene network that merges the classical toggle switch and repressilator. Using a thermodynamic formalism and Bayesian inference, we show that even a single-inducer version of the circuit can display diverse mul-tifunctional dynamics, including the coexistence of oscillations and multistability. In addition we explore robustness, classify emergent behaviours, and analyse critical slowing down and regime transitions. Re-markably, the AC-DC circuit can produce more than 30 topologically distinct bifurcation diagrams, chal-lenging the classical view that network topology rigidly constrains dynamical outcomes. This flexibility enables synthetic capabilities that couple hysteresis with oscillations, critical slowing down, and reversibility. By uncovering the hidden potential of minimal genetic circuits and outlining design principles for their implementation, this work opens new directions for harnessing emergent complexity using the basic building blocks of life.

systems biology↗

bioRxiv2023

Vaccination by single dose sporozoite injection of blood stage attenuated malaria parasites

An efficient malaria vaccine remains elusive. As an alternative to malaria subunit vaccines, vaccination approaches are currently explored using live Plasmodium parasites, either attenuated mosquito-derived sporozoites or attenuated blood stage parasites. Both approaches would profit from the availability of attenuated and avirulent parasites with a reduced blood stage multiplication rate. Ideally, such slow growing parasites would proceed normally through the mosquito but cause a self-limiting infection upon transmission. Here we screened gene-deletion mutants of the rodent parasite P. berghei and the human parasite P. falciparum for slow growth. In addition, we tested the P. berghei mutants for avirulence in mice and self-resolving blood stage infections, while preserving sporozoite formation and liver infection. Targeting fifty genes yielded seventeen P. berghei gene-deletion mutants with two mutants causing self-clearing infections in mice while retaining full transmissibility through mosquitoes. For those, infection of mice by a low number of blood stages, infected-mosquito bites or by single injection of sporozoites led to protection from disease after challenge with wild type sporozoites. Two of six generated P. falciparum gene-deletion mutants showed a slow growth rate. Slow growing, avirulent P. falciparum mutants will constitute valuable tools to inform on the induction of immune responses and aid in developing new as well as safeguarding existing attenuated parasite vaccines.

cell biology↗

bioRxiv2023

On minimising tumoural growth under treatment resistance

AO_SCPLOWBSTRACTC_SCPLOWDrug resistance is a major challenge for curative cancer treatment, representing the main reason of death in patients. Evolutionary biology suggests pauses between treatment rounds as a way to delay or even avoid resistance emergence. Indeed, this approach has already shown promising preclinical and early clinical results, and stimulated the development of mathematical models for finding optimal treatment protocols. Due to their complexity, however, these models do not lend themself to a rigorous mathematical analysis, hence so far clinical recommendations generally relied on numerical simulations and ad-hoc heuristics. Here, we derive two mathematical models describing tumour growth under genetic and epigenetic treatment resistance, respectively, which are simple enough for a complete analytical investigation. First, we find key differences in response to treatment protocols between the two modes of resistance. Second, we identify the optimal treatment protocol which leads to the largest possible tumour shrinkage rate. Third, we fit the "epigenetic model" to previously published xenograft experiment data, finding excellent agreement, underscoring the biological validity of our approach. Finally, we use the fitted model to calculate the optimal treatment protocol for this specific experiment, which we demonstrate to cause curative treatment, making it superior to previous approaches which generally aimed at stabilising tumour burden. Overall, our approach underscores the usefulness of simple mathematical models and their analytical examination, and we anticipate our findings to guide future preclinical and, ultimately, clinical research in optimising treatment regimes.

cancer biology↗

bioRxiv2022

On tumoural growth and treatment under cellular dedifferentiation

Differentiated cancer cells may regain stem cell characteristics; however, the effects of such a cellular dedifferentiation on tumoural growth and treatment are currently understudied. Thus, we here extend a mathematical model of cancer stem cell (CSC) driven tumour growth to also include dedifferentiation. We show that dedifferentiation increases the likelihood of tumorigenenis and the speed of tumoural growth, both modulated by the proliferative potential of the non-stem cancer cells (NSCCs). We demonstrate that dedifferentiation also may lead to treatment evasion, especially when a treatment solely targets CSCs. Conversely, targeting both CSCs and NSCCs in parallel is shown to be more robust to dedifferentiation. Despite dedifferentiation, perturbing CSC-related parameters continues to exert the largest relative effect on tumoural growth; however, we show the existence of synergies between specific CSC- and NSCC-directed treatments which cause superadditive reductions of tumoural growth. Overall, our study demonstrates various effects of dedifferentiation on growth and treatment of tumoural lesions, and we anticipate our results to be helpful in guiding future molecular and clinical research on limiting tumoural growth in vivo.

cancer biology↗

bioRxiv2022

Oncogenic signalling is coupled to colorectal cancer cell differentiation state

Colorectal cancer progression is intrinsically linked to stepwise deregulation of the intestinal differentiation trajectory. In this process, sequential mutations of APC/Wnt, KRAS, TP53 and SMAD4 stepwisely enable an oncogenic signalling network. Here, we developed a novel mass cytometry antibody panel to analyse colorectal cancer cell differentiation and signalling in human isogenic colorectal cancer organoids and in patient-derived cultures. We define a differentiation axis following EphrinB2 abundance in all tumour progression states from normal to cancer. We show that during colorectal cancer progression, oncogenes decrease dependence on external factors and shape distribution of cells along the differentiation axis. In this regard, subsequent mutations can have stem cell-promoting or restricting effects. Individual nodes of the signalling network remain coupled to the differentiation state, regardless of the presence of oncogenic signals. Our work underscores the key role of cell plasticity as a hallmark of cancer that is gradually unlocked during colorectal cancer progression.

cancer biology↗

bioRxiv2021

Maintaining and escaping feedback control in hierarchically organised tissue: a case study of the intestinal epithelium

The intestinal epithelium is one of the fastest renewing tissues in mammals. It shows a hierarchical organisation, where intestinal stem cells at the base of crypts give rise to rapidly dividing transit amplifying cells that in turn renew the pool of short-lived differentiated cells. Upon injury and stem-cell loss, cells can also dedifferentiate. Tissue homeostasis require a tightly regulated balance of differentiation and stem cell proliferation, and failure can lead to tissue extinction or to unbounded growth and cancerous lesions. Here, we present a two-compartment mathematical model of intestinal epithelium population dynamics that includes a known feedback inhibition of stem cell differentiation by differentiated cells. The model shows that feedback regulation stabilises the number of differentiated cells as these become invariant to changes in their apoptosis rate. Stability of the system is largely independent of feedback strength and shape, but specific thresholds exist after unbounded growth occurs. When dedifferentiation is added to the model, we find that the system can recover more gracefully after certain external perturbations. However, dedifferentiation makes the system more prone to loosing homoeostasis. Taken together, our mathematical model shows how a feedback-controlled hierarchical tissue can maintain homeostasis and can be robust to many external perturbations.

cancer biology↗

bioRxiv2019

Hospital use of antibiotics as the main driver of infections with antibiotic-resistant bacteria - a reanalysis of recent data from the European Union

Antimicrobial resistance in bacteria causes significant morbidity worldwide. The development and acquisition of resistance to antibiotics is believed to primarily develop under the selective pressure of widespread antibiotic use in humans, however antimicrobial usage in livestock has been proposed as additional, if not principal, driver of antibiotic resistance. In this work, we correlate recent data from the European Union on antibiotic resistance rates with data on antibiotic usage in the primary care and hospital sector and data on veterinary antimicrobial consumption across the individual member states. We quantify the strength of these different potential drivers of antimicrobial resistance in order to compare their biological importance. We found that the correlation between antibiotic use in the hospital sector and antibiotic resistance rates is significantly higher than the correlation between resistance rates and any of the other two predictors. This suggests increased antibiotic use in hospitals as the main driver of the development of antibiotic resistances and necessitates further research on and a re-evaluation of the risks associated with antibiotic use in human and veterinary medicine.

microbiology↗