Talk Title: AI in Action: Elevating The Microscopy Experience

Abstract: This seminar explores the integration of AI in microscopy using Nikon’s NIS.ai suite. Participants will learn how AI tackles challenges like noise reduction, blur correction, and image enhancement, allowing for the identification of features that traditional methods often miss. Through hands-on experience with sample datasets, attendees will see how AI-driven tools optimize image quality and analysis

Workshop Title: Quality Control & Quality Assurance Solutions to Improve
Reproducibility in Fluorescense Microscopy

Abstract: Instrument quality control in fluorescence bio-imaging – Know the bias… to perform reliable measurements. Argolight is a French biotechnology company specializing in the quality control and assurance of fluorescence imaging systems, with the aim of offering reliable and durable solutions, both in terms of hardware and software.

Affiliation: TEMTIA President

Talk Title: Snail and Slug proteins demonstrate cell-specific expression patterns in invasive break cancer subtypes, correlated with proliferation/differentiation status and mixed prognosis

Abstract: Expression pattern of EMT associated transcription factors (EMTaTF) in breast cancer is poorly documented at cellular level. Here, we located Snail/Snai1 and Slug/Snai2 by immunochemistry using validated antibodies in a TMA cohort of 656 invasive breast carcinomas. We implemented digital H-scoring using QuPath software to provide new and unsuspected understanding on the impact of EMTaTF on breast carcinoma progression and recurrence . In Luminal A/B and HER2 breast cancer subtypes, Slug was expressed by almost all basal/myoepithelial cells, but not seen in the invasive component. In triple-negative (TN) tumors, Slug was found in a subpopulation (20-50%) of all invasive tumor cells, but only in 26% of our samples. In addition, Slug was also strongly expressed in fibroblast-like cells in the stroma in most tumors. involving 30% activated fibroblasts (FAP+). In contrast, Snail was frequently expressed by a subpopulation of dispersed tumor cells in all types of invasive breast carcinomas, more prominent in HER2 (57%) and TN (32%) tumors. Few stroma cells were found also to express Snail, mostly endothelial cells. Slug and Snail genes were about never found to be co-expressed in tumor cells. We found that the tumor cell proliferation index (KI67 expression) was strongly correlated to the stroma cell expression of Slug in all tumor types. Using multiplex analysis, we also found that proliferation was mostly restricted to CK8+/Slug- cells in invasive components in LumB samples. By distinguishing tumor subtype and tumor or stroma cell types, we found that aggravated tumor grades could correlate with higher expression levels of Slug in some situations. Survival long-term studies and Invasive disease-free survival studies also showed an unsuspected impact of Slug and/or Snail, with a complex type-specific pattern. Overall, this study, based on a large TMA cohort of invasive breast carcinoma samples, emphasizes new putative roles for Snail and Slug proteins, linked to a clinical impact during breast carcinoma progression and recurrence.

Affiliation: Allen Institute

Talk Title: A human induced pluripotent stem (hiPS) cell model for the holistic study of epithelial to mesenchymal transitions (EMTs)

Abstract: The epithelial to mesenchymal transition (EMT) is a widely studied but poorly defined state change due to the variety of ways in which it has been characterized in cells. There is a need for reproducible cell model systems that enable the integration and comparison of different types of measured observations of cells across many distinct cellular contexts. We present human induced pluripotent stem (hiPS) cells as such a model system by demonstrating its utility through a comparative analysis of hiPS cell-EMT in 2D and 3D cell culture geometries. We developed live-imaging-based assays to directly compare examples of changes in cell function (via migration timing), molecular components (via expression of marker proteins), organization (via reorganization of cell junctions), and environment (via dynamics of basement membrane) in the same experimental system. The EMT-related changes we measured occurred earlier in 2D colonies than in 3D lumenoids, likely due to differences in the basement membrane environments associated with 2D vs. 3D initial hiPS cell culture geometries. We have made the 449 60-hour-long 3D time-lapse movies and the associated tools used for analysis and visualization open-source and easily accessible as a resource for future work in this field.

Affiliation: Johns Hopkins Medicine

Talk Title: Defining the molecular state basis of metastasis

Abstract: Cancer mortality is driven by metastasis, the process by which cells escape from the tumor and colonize distant organs. We have shown that luminal breast cancer cells can initiate invasion by expressing basal epithelial genes, such as keratin 14 (K14). K14+ luminal breast cancer cells collectively invade and intravasate as adherent clusters. Conversely, triple negative breast cancer (TNBC) cells invade and metastasize in a hybrid EMT state, expressing both E-cadherin and vimentin, with collective spread also favored. In both subtypes, we observe transitions in cell state as the cancer cells expand to form growing metastases in the distant organ. We next sought to understand how intercellular interactions regulated metastasis through deletion of key proteins in the adherens junction (E-cadherin) and tight junction (claudin 7). We demonstrated that E-cadherin acts as an invasion suppressor and a metastasis promoter- when deleted cells invaded more but rapidly died due to anoikis. In contrast, claudin 7 acts as an invasion suppressor and a metastasis suppressor- when we delete claudin 7 we see more invasion in culture, equivalent cell survival, and increased colony formation. We are currently using scRNA-seq to define the molecular states in cancer cells at different stages of metastasis and to describe the extent of their utilization of EMT programs. We then utilize transfer learning to map these cell states in tumors using spatial transcriptomics. Our goal is to identify molecular targets to drive the elimination of metastatic cancer cells, wherever they are located in the body.

Affiliation: University of California, Davis

Talk Title: Dynamic Shifts: Unraveling Cell Adhesion Changes in Neural Crest EMT 

Abstract: Neural crest cells are vertebrate-specific, pluripotent, embryonic stem cells that give rise to more than 30 different adult cell and tissue types including pigment cells, craniofacial bone and cartilage, and the peripheral nervous system. Despite our extensive knowledge of the mechanisms governing neural crest development, which is primarily derived from a limited set of model organisms, there remains a crucial gap in confirming the functional conservation of protein functions across species, encompassing their targets, interactions, and developmental roles. This challenge impedes a comprehensive understanding of neural crest evolution and development. Our research aspires to bridge this gap by identifying both conserved and divergent developmental mechanisms regulating neural crest EMT. We achieve this goal by characterizing the spatiotemporal expression patterns of key regulatory factors governing neural crest cell development and by perturbing these factors in quail (Coturnix japonica) and chick (Gallus gallus) embryos. Our findings reveal intriguing distinctions in the roles played by specific transcription factors, and conservation of post-translational protein trafficking mechanisms, at various developmental stages within closely related organisms. Moving forward, our focus will shift towards unraveling the intricate embryonic microenvironments responsible for shaping these distinct phenotypic outcomes. By investigating the factors influencing neural crest cell development across species, we aim to enrich our understanding of the evolutionary and developmental dynamics underlying this critical biological process. 

Affiliation: The University of Queensland

Talk Title: Tissue mechanics, mechanotransduction and homeostasis 

Abstract: Epithelia constitute many of the principal barriers in metazoan bodies and are also common sites for disease, notably cancer and inflammation. Yet, the incidence of epithelial disease is remarkably low, given their constant exposure to injurious agents. By implication, epithelia must have ways to detect potential disturbances and deal with them. It is now becoming apparent that one basis for such homeostatic response is through tissue mechanics and mechanosensing. Cells constantly exert contractile forces on their neighbours through their cell-cell junctions and possess mechanotransduction pathways at those junctions that detect changes in force. Mechanosensing may then be an early-warning system that allows epithelia to detect, and respond to, homeostatic challenges. Can physiological homeostasis reflect mechanical homeostasis? Conversely, can altered tissue mechanics predispose epithelia to disease? These are ideas that I’ll endeavour to consider in my talk. 

Affiliation: Wesleyan University

Talk Title: Exploring the role of EMT and MET in fluid-solid phase transitions of human airway epithelium

Abstract: Under homeostatic conditions, human airway epithelium is differentiated, stable, and able to withstand insults including pollution, allergens, and pathogens. This epithelial collective is typically stationary but exhibits collective migration in a range of circumstances, including during differentiation, in response to a variety of pathological stimuli, and under disease states such as asthma and COPD. As airway basal cells differentiate and form a stable tissue, they transition from a collectively migratory, fluidized state to a stationary, solid-like state. The fluidized state is characterized by cell elongation and alignment into cooperative migratory flocks, but as the collective solidifies, cells adopt more regular, isotropic, and homogenous shapes, and motion slows. This stationary, differentiated cellular collective can in turn be triggered to undergo a seemingly reverse process, in which the collective fluidizes, and large-scale, coordinated motion emerges. An important question is the extent to which these solidification and fluidization processes rely on the molecular programs that govern mesenchymal-epithelial transitions (MET) and epithelial-mesenchymal transitions (EMT). We find that solidification during differentiation coincides with MET, and that both processes can be accelerated or delayed through inhibition or activation, respectively, of the TGFβ receptor. However, fluidization of the epithelial collective can occur without any evidence of EMT or partial EMT. In particular, we find that cell-cell junctions, apico-basal polarity, and barrier function remain intact and mesenchymal markers of EMT remain unapparent, even as cells elongate and align into cooperative migratory packs. Current work focuses on investigating the relationship between structure and dynamics during solidification and fluidization processes in human airway epithelial collectives.

Affiliation: Instituto de Neurosciencias, CSIC-UMH

Talk Title: EMT trajectories in development, fibrosis and cancer 

Abstract: Epithelial homeostasis is crucial for maintaining tissue architecture and must therefore be tightly regulated in the adult. In contrast, embryonic cells show a high degree of epithelial plasticity necessary for proper morphogenesis and, in particular, for the massive cell movements that occur during gastrulation and neural crest delamination, among other processes. We have studied cell movements, plasticity, and epithelial-to-mesenchymal transitions (EMTs) in different contexts. Lineage tracing and single-cell transcriptomics have allowed us to reveal how EMT programs are implemented along cellular plasticity trajectories in three different settings, namely neural crest, renal fibrosis and breast cancer. For breast cancer, our data unveil a new role for the EMT in orchestrating an additional layer of intratumour heterogeneity, driving the distribution of functions associated with either inflammation or cancer cell dissemination towards metastasis. 

Affiliation: University of Cambridge, California Institute of Technology

Talk Title: Decoupling principles of embryonic development

Abstract: Early mammalian development is characterized by a series of critical transitions, including embryo implantation and subsequent dramatic remodeling. During these early stages, the germ layers emerge, laying the foundation for the body’s structure and organs. Understanding these processes is essential to elucidate the mechanisms underlying normal development, developmental anomalies, and potential strategies for tissue and organ repair. The inherent challenge in studying these stages is their occurrence within the maternal environment, rendering direct observation difficult. Recently developed platforms for ex utero culture of human embryos through early post-implantation stages have partially addressed this limitation. However, the use of human embryos in research is fraught with ethical controversies, and the limited availability of embryos donated for research further restricts experimental investigation. To circumvent these challenges, we have developed multiple stem cell-based models of mammalian embryos. These models provide a manipulable system to study the fundamental aspects of human embryo development. They facilitate the exploration of how changes in tissue architecture are directed through transitions in distinct stem cell potency states at successive steps of differentiation. They allow us to understand how embryonic and extraembryonic tissues interact to create new tissues and organs. These stem cell-based models offer significant potential to improve outcomes in assisted reproductive technologies, elucidate the causes of early pregnancy failure, and provide insights into the developmental origins of diseases.

Affiliation: University of Pittsburgh

Talk Title: Data-driven mechanistic modeling of EMT regulation 

Abstract: High-throughput techniques, especially at the single cell level, have greatly expanded our knowledge of cellular processes. With the increasing availability of data, a fundamental question arises: how can we leverage this data to gain mechanistic insights? Unlike static data typically targeted by statistics-based machine learning approaches, single cell data are snapshots from the dynamical state space of a cell having interacting components that dictate the temporal evolution of the system. Consequently, we witness a growing convergence of two disciplines: data science and systems biology. The latter seeks to unravel qualitative and quantitative causal relationships among cellular components, as well as their functions within the broader context of cell regulatory networks, all through the lens of dynamical systems theory, towards a goal of engineering and controlling cell state transition dynamics. I will briefly summarize some of our recent efforts on analyzing single cell data through the lens of systems biology. Specifically, I will present our recent efforts of applying single cell snapshot and live cell imaging data analyses on EMT regulation. 

Affiliation: Indian Institute of Science, Bangalore

Talk Title: Epigenetic memory acquired during long-term EMT induction governs the recovery to the epithelial state 

Abstract: Epithelial-mesenchymal transition (EMT) and its reverse mesenchymal-epithelial transition (MET) are critical during embryonic development, wound healing and cancer metastasis. While phenotypic changes during short-term EMT induction are reversible, long-term EMT induction has been often associated with irreversibility. Here, we show that phenotypic changes seen in MCF10A cells upon long-term EMT induction by TGFβ need not be irreversible, but have relatively longer time scales of reversibility than those seen in short-term induction. Next, using a phenomenological mathematical model to account for the chromatin-mediated epigenetic silencing of the miR-200 family by ZEB family, we highlight how the epigenetic memory gained during long-term EMT induction can slow the recovery to the epithelial state post-TGFβ withdrawal. Our results suggest that epigenetic modifiers can govern the extent and time scale of EMT reversibility and advise caution against labelling phenotypic changes seen in long-term EMT induction as ‘irreversible’. 

Affiliation: University of California, San Francisco

Talk Title: Spatially controlled RNA decay drives a developmental EMT program 

Abstract: The epithelial-mesenchymal transition (EMT) drives cellular movements during development to create specialized tissues and structures in the vertebrate embryo. Neural crest cells, a multipotent stem cell population, undergo a tightly regulated EMT to delaminate from the neural tube and initiate migration. We have shown that avian neural crest development is controlled by a transient pulse of Draxin, which acts as a molecular rheostat of canonical Wnt signaling. Tight spatiotemporal regulation of Draxin expression is essential for proper neural crest development, and its rapid downregulation is a hallmark of EMT. However, precisely how Draxin transcripts are regulated to ensure their rapid removal has been unclear. To tackle this question, we adapted in vivo reporters and a live RNA imaging approach and found that the rapid degradation of Draxin mRNA is mediated post-transcriptionally via its 3’-untranslated region (3’-UTR). Hybridization chain reaction (HCR) and immunolabeling combined with in situ super-resolution imaging revealed that endogenous Draxin transcripts are targeted to cytoplasmic processing bodies (P-bodies), which are membrane-less sites of RNA processing and decay. Through time-lapse imaging, we found Draxin mRNA not only co-localizes with a fluorescently-tagged P-body component (DCP1a), but is also rapidly dissolved within P-bodies in migrating neural crest cells. Furthermore, knockdown of the RNA helicase DDX6 via CRISPR/Cas9, known to dissolve P-bodies, disrupted compartmentalization of Draxin mRNA to P-bodies. Importantly, disruption of P-bodies via DDX6 knockdown inhibited endogenous Draxin mRNA degradation and impeded neural crest EMT in vivo. This is consistent with observations in human patients who display defects in P-body assembly and often present with craniofacial abnormalities, a hallmark of neural crest dysfunction. This work provides the first description of P-bodies in vertebrate neural crest through super-resolution imaging and an adapted RNA live imaging approach, and identifies an mRNA that is targeted to and degraded within P-bodies. Together, our data highlight a novel and important role for spatial regulation of gene expression during development— playing an essential role in neural crest EMT via targeted RNA decay. 

Affiliation: The University of Sheffield

Talk Title: Drosophila midgut morphogenesis – a simplified model for studying the cellular and molecular mechanisms underlying mesenchymal-to-epithelial transitions

Abstract: Mesenchymal-to-epithelial transitions (METs) convert cells from migratory mesenchymal to polarised epithelial states. Despite its importance for both normal and pathological processes, very little is known about the regulation of MET in vivo. We have established the embryonic Drosophila midgut as a powerful model for studying MET. During morphogenesis, midgut cells undergo an epithelial-to-mesenchymal transition (EMT), enabling their collective migration through the embryo, before then undertaking a reverse MET, re-epithelialising to form the embryonic midgut epithelium. Experimentally, the midgut is highly accessible, amenable to genetic manipulation, and we have developed methods to image these cells at subcellular resolution and track them in 4D throughout the whole process of EMT-migration-MET. We have shown that while down-regulation of the EMT-TF Serpent is required for MET, it is not sufficient, and that highly specific interactions with surrounding environment are also required. Upon down-regulation of the EMT-TF Serpent, midgut cells repolarize in response to the tissue-specific secretion of the laminin trimer containing the vertebrate α1,2 laminin homologue, wing blister (wb) from the neighboring visceral mesoderm. This demonstrates, in an in vivo context, that the down-regulation of an EMT-TF and MET are genetically separable events. I will discuss our recent results from work which has been focused on understanding how midgut cells epithelialise downstream of contact with lamininW. I hope to bring my excitement and enthusiasm for using diverse developmental model systems to study epithelial-to-mesenchymal plasticity to the society. As always, I am eager to discuss and exchange ideas with cancer biologists, to further understand how findings in development may relate to tumour progression.

Affiliation: MRC-Laboratory of Molecular Biology

Talk Title: Mechanisms of human renal mesenchymal-to-epithelial transition 

Abstract: During embryogenesis, organs form through the transformation of simple groups of cells into complex 3D structures. This remarkable feat is accomplished through the collective and controlled changes in the shapes and arrangements of a large number of cells. The central aim of my group is to understand how genetic programmes drive morphological changes in individual cells, and how those shape changes are coordinated through cell-cell interactions across an entire epithelium to sculpt a nascent tissue. Because organ shape is critical for organ function, defects in morphogenesis lead to severe diseases including spina bifida or polycystic kidney disease. We use human renal organoids derived from iPSCs to understand how de novo epithelial polarisation, or mesenchymal-to-epithelial transition, occurs in the context of nephron tube morphogenesis, what transcriptional blueprint is required to kick-start the process and what molecular players drive the cell biological changes. I will discuss our recent findings addressing these questions. 

Affiliation: Memorial Sloan Kettering Cancer Center

Talk Title: Building the endoderm through widespread intercalation 

Abstract: TBA