Biology subjects

Hoffmann, M.

Publications and source records attributed to Hoffmann, M..

At least 19 recordsLinked to original sources

bioRxiv2026

RnR-ExM: Robust Non-rigid Registration Challenge for Expansion Microscopy Volumes

Expansion Microscopy (ExM) enables nanoscale imaging of biological samples while preserving structural and molecular details. The Robust Non-rigid Registration Challenge for ExM (RnR-ExM) was launched to benchmark 3D registration algorithms on real-world ExM datasets. The challenge released 24 pairs of high-resolution 3D volumes from zebrafish, mouse, and C.~elegans, deliberately selected for their difficulty with standard alignment methods. To evaluate performance, we provided curated segmentation masks of nuclei and blood vessels as landmarks for half of the dataset. To encourage learning-based approaches, we released code for generating synthetic training data reflecting the deformation and appearance of the unlabeled pairs. By submission, 168 participants registered, with six teams submitting results by the deadline; the top three were invited to present at ISBI 2023. Accurate registration of ExM volumes is essential for downstream biological analyses such as multiplexed molecular mapping and cell-type-specific structural profiling. In this paper, we detail the methods and results of these top teams, highlighting current capabilities and future directions for 3D registration in ExM. All datasets and code are available at https://rnr-exm.grand-challenge.org/

neuroscience↗

bioRxiv2026

Epidemiology and virological characteristics of the emerging SARS-CoV-2 variant PJ.2.1

SARS-CoV-2 continues to circulate globally at high levels and to evolve into new variants. Recently, a new saltation variant harbouring a highly mutated spike protein, PJ.2.1, emerged in North America. Here, we provide a brief epidemiological and virological characterization of PJ.2.1 and cocirculating variants. We report that PJ.2.1 is spreading in the USA, Canada, and Spain and mainly infects individuals aged 60 years and older, as do most other variants, with the exception of BA.3.2, which preferentially infects individuals aged 0-9 years. PJ.2.1 was less susceptible to inhibition by an antibody against ACE2 than were the other variants, indicating increased ACE2 binding. In contrast, PJ.2.1 did not show augmented evasion of antibodies from vaccinees who had received the LP.8.1-adapted vaccine compared with most other variants analysed. These results suggest that augmented ACE2 affinity rather than increased antibody evasion might drive the current, rapid spread of PJ.2.1.

microbiology↗

bioRxiv2026

Proteolytic control of the SARS-CoV-2 furin cleavage site defines the phenotypic evolution from the pandemic to endemic state

The successive emergence of SARS-CoV-2 variants with altered tissue tropism has progressively decoupled transmissibility from lower respiratory tract pathogenicity. Omicron lineages transmit exceptionally well whilst limiting severe lung disease. Here, we demonstrate that this phenotype has evolved through two temporally distinct tissue-specific proteolytic controls at the Spike (S) furin cleavage site (FCS). At the virion level, cell-type-dependent furin-mediated FCS hyper-cleavage depletes S in lung but not nasal epithelial cells. At the infected cell membrane during cell-cell spread, TMPRSS2 mediates S FCS cleavage but is negatively regulated in the presence of ACE2. Tissue-specific solute carriers SLC6A19 and SLC6A20 sequester ACE2, thereby relieving inhibition of TMPRSS2 and enabling S FCS cleavage during cell-cell spread. Critically, whilst all SARS-CoV-2 lineages benefit from this latter pathway, Omicron variants have evolved exclusive dependence on it, a strategic consolidation that focuses S proteolytic activation to TMPRSS2 alone. The combined outcomes of S protein regulation across viral and cell membranes reveal how tissue-specific proteolytic optimisation drives Omicron's transmission fitness advantage in the upper respiratory tract but at the cost of heavy attenuation in the lower respiratory tract.

microbiology↗

bioRxiv2026

Reduced DPP4 Binding Confers Resistance to Soluble DPP4 While Preserving MERS-CoV Entry into Cells Expressing High Levels of DPP4

The Middle East respiratory syndrome coronavirus uses DPP4/CD26 as receptor for cell entry. Soluble recombinant DPP4 can block MERS-CoV infection in cell culture and in animal models and might hold promise as antiviral. Furthermore, endogenous soluble DPP4 in plasma might reduce MERS-CoV dissemination in infected individuals. Therefore, we addressed whether and how MERS-CoV can acquire resistance against soluble DPP4 (sDPP4), employing a vesicular stomatitis virus (VSV) encoding the MERS-CoV spike (S) protein (VSV-MERS-S). Passaging of VSV-MERS-S in the presence of sDPP4 selected for viral variants with mutations L507I and L507H in the receptor binding domain (RBD) of the S protein. These mutations reduced sDPP4 binding, were compatible with robust entry into cell lines expressing high levels of DPP4 and conferred sDPP4 resistance. In contrast, entry into cell lines expressing low levels of DPP4 was reduced. Furthermore, polymorphisms L507F/R/P, which were detected in MERS-CoV sequences from patients, exhibited an even more pronounced phenotype, with L507R and L507P conferring complete sDPP4 resistance. Collectively, our results show that naturally occurring polymorphisms in the MERS-CoV S protein can confer sDPP4 resistance by reducing sDPP4 binding but might still be compatible with robust viral spread in cells and tissues expressing high levels of DPP4.

microbiology↗

bioRxiv2026

Seasonal variation mediates the importance of species attributes in plant-pollinator interactions

Predicting species interactions remains a major challenge, as multiple species attributes operate simultaneously and their relative importance may vary seasonally and with temporal resolution. Here, we assess how the relative contributions of abundance, trait matching, and phenology to plant-pollinator interactions vary through a flowering season and across temporal resolutions using interaction data from three European botanical gardens. We show that predictive models explain a substantial proportion of variation in visitation patterns, with floral and pollinator abundances consistently explaining most variation across the flowering season. Trait matching between pollinator body size and floral size also contributes to visitation patterns, playing a secondary but persistent role in shaping interactions, while phenology plays a relatively minor role at broader temporal resolutions but becomes more important at finer temporal scales. Additionally, null models accounting for spatio-temporal variation in floral and pollinator abundance reveal consistent patterns of pollinator preference and avoidance, indicating that abundance alone cannot explain the observed interaction patterns. Our results show that seasonal variation and temporal resolution differentially shape the importance of species attributes, highlighting the need for multi-variable approaches that account for temporal dynamics to accurately explain and predict ecological interactions.

ecology↗

bioRxiv2026

The conserved QTQTX motif in the SARS-CoV-2 spike protein is dispensable for cleavage and lung cell entry of the emerging variant BA.3.2

The furin motif in the SARS-CoV-2 spike (S) protein is important for lung cell entry. It is embedded in an extended loop structure and preceded by a highly conserved QTQTX motif that is required for efficient furin cleavage of the SARS-CoV-2 WA-1 S protein. BA.3.2 is an emerging SARS-CoV-2 saltation variant that is spreading globally in April 2026 and encodes for a highly mutated S protein. Here, we analyzed whether the QTQTX motif is also required for spike protein cleavage and lung cell entry of BA.3.2. We report that two patient-derived spike sequences of the BA.3.2 subvariant BA.3.2.2 lack the first QT repeat of the QTQTX motif and show that this motif is largely dispensable for both cleavage and lung cell entry of BA.3.2.2, which we found to depend on TMPRSS2. Our results suggest that the reconfiguration of the BA.3.2 S protein during persistent infection may have significantly altered the determinants of furin cleavage. IMPORTANCEThe furin motif in the SARS-CoV-2 spike (S) protein is unique among sarbecoviruses and constitutes a virulence determinant. A QTQTX motif located immediately upstream of the furin motif is required for furin cleavage of the S protein of the virus that circulated early in the pandemic. Here, we show that the QTQTX motif is largely dispensable for S protein processing and S protein-driven lung cell entry of the emerging saltation variant BA.3.2, which is currently spreading globally. Thus, BA.3.2 evolution within immunocompromised individuals may have relaxed the requirements for furin processing of the spike protein.

microbiology↗

bioRxiv2026

Identifying and ranking species that need urgent management action to achieve Target 4 of the Global Biodiversity Framework

Target 4 of the Kunming-Montreal Global Biodiversity Framework (KMGBF) calls for urgent management actions to halt humaninduced extinctions and enable species recovery. However, most Parties face substantial challenges in determining which species require urgent management actions. Here, we present a transparent, standardised protocol that identifies and ranks species most likely to need urgent management actions at the national level, using globally available data from the IUCN Red List of Threatened Species. The protocol integrates four criteria aligned with Target 4: global extinction risk, rate of decline, population or range restriction, and endemism, to generate a national ranked list of species. Species scoring highly on these four criteria, and therefore most in need of urgent management action, are ranked most highly. We applied this method to all 250 countries and territories listed in the IUCN Red List and pilottested national rankings with participants from eight diverse countries. Across pilots, participants reported that the ranked lists were scientifically robust, timesaving, and valuable starting points for national prioritysetting, while stating the importance of national context, and the need for additional technical and financial support for implementation. Our results demonstrate that a sciencebased approach can meaningfully support Parties in identifying species requiring urgent action under Target 4, in a standardised way. With 2030 approaching rapidly, this protocol provides an immediate, practical tool to accelerate progress toward halting extinctions and advancing species recovery.

ecology↗

bioRxiv2026

Detection of Candidate Circular RNAs to Monitor Anti-Hormonal Response in the Mammary Gland

Anti-hormonal therapies such as selective estrogen receptor modulators like tamoxifen or aromatase inhibitors like letrozole represent a cornerstone for breast cancer prevention and therapy of estrogen receptor-positive breast cancer. Therapeutic monitoring can include blood tests and imaging; however, genetically-based approaches are not yet in practice. Ideally, a test would be able to detect a positive molecular response across different estrogen pathway-suppressive approaches. Circular RNAs are a species of non-coding RNAs detectable in plasma that have been proposed as non-invasive therapeutic biomarkers. To determine whether a set of specific circular RNAs is altered across estrogen-suppressive pathway approaches, we analyzed mammary gland-specific total RNA sequencing data from two individual genetically engineered mouse models (GEMMs) of estrogen pathway-induced breast cancer, with or without exposure to tamoxifen or letrozole. The nf-core/circrna pipeline was used to identify circRNAs that were differentially expressed in response to either tamoxifen or letrozole. We then screened for circRNAs that were differentially regulated by both anti-hormonals. Four up-regulated and 31 down-regulated circRNAs with host genes known to be expressed in human breast epithelial cells were identified as showing reproducible differential regulation in response to anti-hormonal treatment.

cancer biology↗

bioRxiv2026

A Quantum Lens on Molecular Design: A Machine-Learned Energy Function from Interacting Quantum Atoms.

Accurate predictions of the interactions (covalent bonds and non-covalent contacts between atoms) in a molecular system require scalable, accurate, and interpretable energy functions. While classical force fields and knowledge-based energy functions struggle to capture key electronic effects, quantum chemistry approaches such as density functional theory (DFT) provide the necessary accuracy but remain computationally demanding. Furthermore, gaining insight into interactions requires energy decomposition schemes. The Interacting Quantum Atoms (IQA) scheme is exceptionally attractive, offering a chemically intuitive, electron density (ED) topologically based separation into intra- and interatomic contributions, however its high computational cost remains a significant barrier for application to larger systems or tasks like ligand screening in drug discovery. We address these limitations by introducing a novel machine learning (ML) framework to predict accurate energies derived from the IQA scheme together with a comprehensive dataset of molecular systems and their calculated IQA decomposed energies. It enables the rapid and accurate prediction of DFT single point energies and dissects these energies in a physically meaningful and chemically intuitive manner. Our method predicts all intra-atomic energies and inter-atomic interaction energies (covalent and non-covalent) within a defined distance cutoff, providing an energy function that decomposes the total energy into specific atomic contributions. This advance makes the IQA method viable for analyzing interaction energies in applications previously inaccessible due to computational expense, such as elucidating ligand-binding mechanisms and informing rational drug design.

bioinformatics↗

bioRxiv2026

Brain-wide hierarchical and sexually dimorphic tuning for social vocalizations

Vocal repertoires consist of a limited number of call types, even though their sounds can vary continuously in form. Where in the brain receivers partition this variation into discrete types is contested: different accounts place the emergence of categories in the cortex/pallium or already in the midbrain. Because recordings have been limited to isolated regions, it remains unknown whether this partitioning is confined to a single region at all, occurs in parallel across many, or is built up along the pathway. Here we present the first whole-brain, cellular-resolution analysis of how conspecific vocalizations are categorized in a vertebrate, using the glassfish Danionella cerebrum. We find that categorization is neither pallial nor localized. It begins at the first central auditory nuclei, much earlier than previously thought, where a continuous morph between social and non-social sounds evokes an abrupt switch in population activity. The midbrain then sharpens these representations, and the thalamus filters for species-typical pulse rates while splitting call duration into two discrete populations. Only downstream of this shared code do the sexes diverge in forebrain social nuclei. Call type partitioning is thus distributed and hierarchically assembled, rather than read out at any one stage.

neuroscience↗

bioRxiv2026

SATB1 is a targetable modulator of JAK-STAT signaling and cytokines in human Treg and Tconv cells

The chromatin organizer SATB1 is indispensable for thymic regulatory T cell (Treg cell) development and T helper cell induction. Several gene loci have been described to be SATB1-controlled, including the transcription factor GATA3 and the cytokine loci IL-4 and IL-17. However, the global effects of SATB1 on fully differentiated human CD4 conventional T cells (Tconv cells) and Treg cells, and thus SATB1s potential as a target for T cell engineering, are poorly understood. We describe SATB1-regulated gene signatures as largely subset-specific, with broader effects on Treg cells. Despite of the distinct gene-regulatory patterns, we observe overarching dysregulated cytokine and JAK-STAT signaling after SATB1 ablation. Functionally, SATB1 KO reduces human Treg cell suppressive capacities but boosts tumor clearance via CD4 CAR T cells in a preclinical, humanized mouse model. Together, Treg destabilization and simultaneous increased activation of CD4 CAR T cells by SATB1 modulation may be an interesting strategy to boost the efficiency of CAR T cell therapies.

immunology↗

bioRxiv2026

Ex vivo drug testing in metastatic biopsies reveals patient-specific vulnerabilities to cancer targeting and immune activating drugs

Biomarker-guided therapies in oncology often fail to induce considerable responses in patients with advanced cancer. As a complementary approach, direct drug testing on individual patient samples is highly attractive yet is currently hampered by the lack of assays that combine (i) fast reporting, (ii) the ability to inform about immune-mediated responses, (iii) robust quantification, and (iv) scalability for parallel assessment of multiple drugs. Here, we introduce our patient-derived ex vivo drug response assay (PEDRA) that fulfills all these requirements. Using malignant pleural effusions (MPEs) from five non-small cell lung cancer (NSCLC) patients with detailed clinical treatment histories, we tested 52 guideline-recommended therapies and eight investigational antibody-drug conjugates (ADCs). In all patients, PEDRA identified treatment options that outperformed the therapies the patients had received. The results reflected clinical observations as well as expectations derived from mutational profiling and disease courses. To extend the applicability of PEDRA beyond MPEs to other metastatic lesions, we generated a protocol starting from core needle biopsies. Owing to its reproducible and quantitative nature, PEDRA may provide a valuable diagnostic tool to guide time-sensitive clinical therapy decisions. Additionally, PEDRA has great potential for preclinical testing of investigational drugs, thereby reducing the need for animal experiments.

cancer biology↗

bioRxiv2026

Common Pitfalls in CircRNA Detection and Quantification

1Circular RNAs have garnered considerable interest, as they have been implicated in numerous biological processes and diseases. Through their stability, they are often considered promising biomarker candidates or therapeutic targets. Due to the lack of a poly(A) tail, circRNAs are best detected in total RNA-seq data after depleting ribosomal RNA. However, we observe that the application of circRNA detection in the vastly more ubiquitous poly(A)-enriched RNA-seq data still occurs. In this study, we systematically compare the detection of circRNAs in two matched poly(A) and ribosomal RNA-depleted data sets. Our results indicate that the comparably few circRNAs detected in poly(A) data are likely false positives. In addition, we demonstrate that the quality of sample processing, as measured by the fraction of ribosomal reads, significantly affects the sensitivity of circRNA detection, leading to a bias in downstream analysis. Our findings establish best practices for circRNA research: total RNA sequencing with effective rRNA depletion is the preferred approach for accurate circRNA profiling, whereas poly(A)-enriched data are unsuitable for comprehensive detection. Employing multiple circRNA detection tools and prioritizing back-splice junctions identified by several algorithms enhances confidence in the selection of candidates. These recommendations, validated across diverse datasets and tissue types, provide generalizable principles for robust circRNA analysis. Key PointsO_LIRibosomal RNA contamination substantially impairs the accuracy of circRNA detection. This technical confounding factor has thus far received limited attention in the field. C_LIO_LITool agreement for circRNA calls is moderate in total RNA-seq but essentially absent in poly(A)-enriched RNA-seq data, underscoring the importance of using multiple tools for circRNA detection. C_LIO_LIBack-splice junctions detected in poly(A)-enriched RNA-seq data are predominantly tool-specific artifacts rather than genuine circRNAs, challenging the validity of circRNA identification in poly(A)-enriched datasets. C_LI

bioinformatics↗

bioRxiv2025

Replication of SARS-CoV-2 Omicron lineages is defined by TMPRSS2 use in environments where ACE2 is complexed with solute carriers SLC6A19 and SLC6A20.

The Omicron variant of SARS-CoV-2 emerged in late 2021 and since then Omicron subvariants have continued to evolve and dominate globally. The viral S protein evolved towards highly efficient antibody evasion and replicative capacity in the upper respiratory tract resulting in high transmissibility. At the same time, the mutations acquired in the S protein diminish infection of the lung epithelium and pathogenic potential. The changing entry requirements for Omicron sub-lineages that lead to this shift in tropism remain poorly understood. We resolve the changing replication requirements of SARS-CoV-2 to be related to two distinct pools of ACE2. The first pool relates to ACE2s role in the renin angiotensin system (RAS) and this pool can complex with TMPRSS2 (RAS-ACE2). The second pool relates to ACE2s role as a protein solute carrier chaperone than cannot complex with TMPRSS2 (Chaperone ACE2). Here, we demonstrate that pre-Omicron lineages replicate in a TMPRSS2 dependent manner across both ACE2 pools, whilst Omicron lineages can only spread and replicate using chaperone ACE2. This provides a mechanistic basis for the evolving infectivity requirements of SARS-CoV-2 and furthermore provides approaches to track and monitor ACE2 utilizing coronaviruses. Graphical AbstractMechanistic basis for shift in SARS-CoV-2 tropism with the arrival of Omicron. A. Chaperone ACE2 is defined structurally as a heterodimer of dimers with a solute carrier protein-SLC6A19 or SLC6A20. Here this ACE2 structure can exist uncomplexed from TMPRSS2 and enables TMPRSS2 use by both pre-Omicron and Omicron lineages. B. Renin Angiotensin ACE2 is defined by ACE2 with an exposed collectrin-like domain (CLD), which enables binding of TMPRSS2 or ADAM-17. Here ACE2 can form a complex with TMPRSS2 in a manner that allows pre-Omicron but not Omicron lineages to utilize TMPRSS2 to facilitate infection. Here Omicron lineages are heavily attenuated as they cannot use TMPRSS2 to spread. C. to E. Based on single cell profiles, ACE2 can exist as a chaperone with SLC6A20 in C. the Nasal Cavity or D. primarily as RAS-ACE2 in the lung to respond to acute lung injury. E. The largest pool of ACE2 in our body resides within the small intestine on enterocytes and this further facilitates replication in this tissue by pre-Omicron and Omicron lineages. O_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC="FIGDIR/small/663433v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@172aa47org.highwire.dtl.DTLVardef@109285eorg.highwire.dtl.DTLVardef@394f8corg.highwire.dtl.DTLVardef@958e31_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Proteolytic processing of the Marburg virus glycoprotein depends on Sec616β and is required for cell entry

Ebola and Marburg virus (EBOV, MARV) cause severe disease and therapeutic options are urgently needed. The Sec61 translocon facilitates ER import of viral glycoproteins (GPs) and may represent a therapeutic target. Here, we report that the Sec61 subunit Sec61{beta}, although dispensable for GP expression, is required for proteolytic cleavage of MARV- but not EBOV-GP and that an intact furin motif is essential for robust cell entry of Marburg- but not Ebolaviruses. Further, MARV- but not EBOV-GP was cleaved by the furin-related enzyme SKI-1, for which a cleavage motif was identified in silico, and cleavage by SKI-1 was impaired in SEC61B-KO cells. In addition, Sec61{beta} was required for normal N-glycosylation of MARV-GP and mutation of a sequon (N563D) abrogated cleavage. Finally, the absence of Sec61{beta} modestly, and blockade of Sec61 via apratoxin S4 markedly, inhibited EBOV and MARV infection. These results reveal a differential protease dependence of MARV and EBOV and identify Sec61 as a potential therapeutic target. Author summaryThe filoviruses Ebola virus (EBOV) and Marburg virus (MARV) spread from animals to humans and can cause deadly outbreaks. These viruses rely on a surface glycoprotein (GP) for infection, which is processed by the enzyme furin in infected human cells. Cleavage of EBOV-GP was thought to be non-essential for infection. However, using lab models for filovirus entry into cells, we discovered that MARV, unlike EBOV, needs this cleavage step to infect cells efficiently. We also found that the host cell protein Sec61{beta} is necessary for proteolytic processing and glycosylation of MARV-GP but not EBOV-GP. In addition, we showed that another cellular enzyme, SKI-1, can process MARV- but not EBOV-GP. Finally, we found that removing Sec61{beta} or blocking Sec61 activity reduced infection by both viruses. These findings show key differences in how the two viruses interact with host cells and suggest that targeting Sec61 could be a promising new strategy to fight Ebola and Marburg virus infections.

microbiology↗

bioRxiv2025

Q1020R in the spike proteins of MERS-CoV from Arabian camels and recent human cases confers resistance against soluble human DPP4

The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is a pre-pandemic coronavirus that is transmitted from camels, the natural reservoir, to humans and can cause severe disease. MERS cases have been documented in Arabia but not Africa, although the virus is circulating in both Arabian and African camels. Further, evidence has been provided that viruses in African camels might have a reduced capacity to cause disease. However, the underlying determinants are incompletely understood. Here, employing pseudotyped particles as model systems for MERS-CoV entry into cells, we compared cell entry of viruses from African and Arabian camels and its inhibition. We show that viruses found in Arabian camels and recent human cases are less susceptible to inhibition by human soluble DPP4 (sDPP4) than viruses from African camels, although both enter human cells efficiently and are comparably sensitive to inhibition by IFITM proteins and neutralizing antibodies. Furthermore, relative resistance to soluble DPP4 was linked to mutation Q1020R, present in the spike proteins of recent Arabian but not African viruses. These results support the concept that soluble DPP4 might constitute a natural barrier against human infection that is more efficiently overcome by viruses currently circulating in Arabian camels than those in African camels. IMPORTANCEMERS-CoV is an emerging virus that can cause severe lung disease, MERS, and is transmitted from camels to humans. Although MERS-CoV infects camels in both Africa and Arabia, MERS cases have only been documented in Arabia for reasons that remain incompletely understood. Here, we provide evidence that viruses recently circulating in Arabian camels and causing human infections are less susceptible to inhibition by human sDPP4 - a secreted version of the viral receptor that is present in various bodily fluids. Furthermore, we link sDPP4 resistance to mutation Q1020R in the spike protein of these viruses. These results suggest that viruses currently circulating in Arabian camels are better equipped to overcome a natural barrier to infection, sDPP4, than those circulating in African camels.

microbiology↗

bioRxiv2025

POMT-dependent O-mannosylation regulates integrin β1 maturation via N-glycan processing

Withdrawal StatementThe authors have withdrawn this manuscript because following a careful internal review conducted in the course of manuscript revision, the authors identified that parts of the presented data could not be reliably traced back to the corresponding original datasets in their current form. While the general biological interpretation is not necessarily invalidated by this finding, the integrity of the present data representation no longer meets the standard required for publication. For this reason, the authors have decided to withdraw this preprint and will refrain from pursuing publication until the underlying data situation has been fully clarified and, if possible, reconstructed. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author. The authors regret any inconvenience caused to the scientific community.

cell biology↗

bioRxiv2025

Plastimos: a live cell imaging-based framework to study dynamics of EMT-mediated cellular plasticity in breast cancer

Cancer cell plasticity, primarily mediated by the process of epithelial-mesenchymal transition (EMT), plays a critical role in promoting therapeutic resistance, tumor heterogeneity, and metastasis. EMT-mediated plasticity enables cancer cells to undergo molecular and phenotypic changes, which alter their invasiveness and resistance to treatments. This study aims to develop a quantitative, high-throughput system to assess EMT-mediated plasticity, which can inform therapeutic strategies for metastatic cancers. To accomplish this, we developed Plastimos, a semi-automated imaging analysis pipeline. This framework utilizes time-series images to track live cells through deep learning-based segmentation and employs a greedy algorithm to map cell trajectories, enabling the extraction of cellular phenotypic features. These features are used to study the EMT-mediated plasticity state of cells in response to the well-known EMT-inducing factors EGF and TGF-{beta}1. We selected two breast cancer cell lines, MCF7 and MDA-MB-231, representing classical epithelial-like and mesenchymal-like cell. The pipeline assigns a Plasticity Index based on various parameters, including motility, morphology, and proliferation, thus providing a quantitative estimate for the plasticity of deviating from the epithelial state. Our results indicate that epithelial-like cells respond to EMT-inducing factors at both molecular and phenotypic levels, while mesenchymal-like cells responses are only seen phenotypically. The Plasticity Index classifies cells along the EMT spectrum, converting to a Plasticity Score that reflects mesenchymal proportions. Availability and implementationThe pipeline implementation and the source code of Plastimos can be found at: https://github.com/Durdam/Plastimos.git

bioinformatics↗