Biological Paradigm Research Articles

In vitro gametogenesis: Towards competent oocytes: Limitations and future improvements for generating oocytes from pluripotent stem cells in culture.

Production of oocytes from pluripotent cell cultures in a dish represents a new paradigm in stem cell and developmental biology and has implications for how we think about life. The spark of life for the next generation occurs at fertilization when sperm and oocyte fuse. In animals, gametes are the only cells that transmit their genomes to the next generation. Oocytes contain in addition a large cytoplasm with factors that direct embryonic development. Reconstitution of mouse oocyte and embryonic development in culture provides experimental opportunities and facilitates an unprecedented understanding of molecular mechanisms. However, the application of in vitro gametogenesis to reproductive medicine or infertility treatment remains challenging. One significant concern is the quality of in vitro-derived oocytes. Here, we review the current understanding and identify limitations in generating oocytes in vitro. From this basis, we explore opportunities for future improvements of the in vitro approach to generating high-quality oocytes.

Quality of life and survivorship in patients with low-grade ovarian cancer

ObjectiveHigh-grade (HGOC) and low-grade ovarian carcinoma (LGOC) are distinct malignancies with different biological features, treatment paradigms, and life expectancies. However, differences in quality of life (QOL), sleep, and depressive symptoms have not been examined by grade, and neither have inflammatory profiles associated with these symptoms. We aim to characterize QOL and biomarkers by OC grade. MethodsParticipants included patients with HGOC (N = 578) or LGOC (N = 85). Participants completed baseline assessments of psychosocial factors prior to primary surgery or neoadjuvant chemotherapy and contributed saliva for cortisol and blood for interleukin-6 (IL-6) quantification. Samples were collected intraoperatively to quantify tumor cortisol. General linear models were used to examine differences in biological and psychological variables by grade. ResultsAt baseline, patients with LGOC reported less depression (p = 0.018) and sleep disturbances (p = 0.014), but no significant difference in depressive mood (p = 0.11) or QOL (p = 0.51) compared to patients with HGOC, adjusting for age and disease stage. There were trends towards lower tumor cortisol levels (p = 0.078) in LGOC compared to HGOC. One-year post-diagnosis, we found a significant improvement in QOL and fatigue, and a decrease in vegetative depression and IL-6 levels irrespective of grade. ConclusionsWe present the first characterization of psychosocial experiences of patients with LGOC. Despite having a better disease prognosis, patients with LGOC were just as likely to have mood disturbances as those with HGOC. There was a trend towards differences in tumor cortisol by grade. Our findings highlight the need to address well-being in patients with both low- and high-grade ovarian malignancies.

Leveraging Tunability of Localized-Interfacial Memristors for Efficient Handling of Complex Neural Networks.

A scalable (<130 nm) resistive switching memristor that features both filamentary and interfacial switching aimed at neuromorphic computing is developed in this study. The typically perceived noise or volatility was effectively harnessed as a controlled mechanism for interfacial switching. The multilayer structure for the proposed memristor enhances switching stability by curbing ionic overmigration and mitigating leakage paths. Furthermore, the memristors showcased their reliability by demonstrating more than 15 M cycles in the filamentary mode and 1 M pulses in the interfacial mode. Additionally, retention tests at 85 °C for 104 s confirmed the stability across different states, affirming its reliability as a nonvolatile CMOS-compatible element. While many studies validate performance solely on the MNIST data set, this work also evaluates more complex data sets, demonstrating the robustness of the demonstrated memristor in supervised learning. Specifically, supervised learning simulations on MNIST and fashion MNIST data sets indicated a high learning rate with <4% deviations from numerical training, while offline inference trained on CIFAR-10 and CIFAR-100 data sets revealed <2.5% and <7% deviations caused by programing error accumulation, even with increased memristor counts for these highly complex data sets. Unsupervised learning via spike-timing-dependent plasticity further highlights the potential of the developed memristor in bridging artificial and biological paradigms, offering a significant advance toward efficient and biologically inspired computing architectures.

Ubiquitin-specific protease 10 determines colorectal cancer outcome by modulating epidermal growth factor signaling via inositol polyphosphate-4-phosphatase type IIB

Although there have been advances in understanding colorectal cancer (CRC) pathogenesis, significant gaps still exist, highlighting the need for deeper insights. Dysregulated protein homeostasis, including perturbations in the epidermal growth factor receptor (EGFR) pathway, remains a focal point in CRC pathogenesis. Within this context, the roles of ubiquitin ligases and deubiquitinases have attracted attention, but exploration of their precise contributions is still in its early stages. To address this gap, we investigated the involvement of the deubiquitinase USP10 in CRC. Our in vitro and in vivo study reveals a new paradigm in CRC biology and unravels a novel mechanistic axis, demonstrating for the first time the involvement of inositol polyphosphate 4-phosphatase type II B (INPP4B) in USP10-mediated CRC modulation. Specifically, our study demonstrates that the loss of USP10 results in reduced sensitivity to the EGFR tyrosine kinase inhibitors gefitinib and osimertinib. This is accompanied by a decrease in the activation of the AKT1/PKB pathway upon EGF stimulation, which is mediated by INPP4B. Importantly, in vivo xenograft experiments validate these findings and highlight the crucial role of USP10, particularly in conjunction with INPP4B, in driving CRC progression. The findings enhance our understanding of CRC pathobiology and reveal a new regulatory axis involving USP10 and INPP4B in CRC progression. This unique insight identifies USP10 and INPP4B as potential therapeutic targets in CRC.

Weight/height2: Mathematical overview of the world's most widely used adiposity index.

A footnote in Adolphe Quetelet's classic 1835 Treatise on Man described his algebraic analysis of how body weight ( ) varies with height ( ) in adult males and females. Using data on 12 short and 12 tall subjects of each sex, Quetelet established the rule that is approximately proportional ( ) to H2 in adults; that is, when for some constant . Quetelet's Rule ( ), transformed and renamed in the twentieth century to body mass index ( ), is now a globally applied phenotypic descriptor of adiposity at the individual and population level. The journey from footnote to ubiquitous adiposity measure traveled through hundreds of scientific reports and many more lay publications. The recent introduction of highly effective pharmacologic weight loss treatments has heightened scrutiny of BMI's origins and appropriateness as a gateway marker for diagnosing and monitoring people with obesity. This contemporary context prompted the current report that delves into the biological and mathematical paradigms that underlie the simple index . Students and practitioners can improve or gain new insights into their understanding of BMI's historical origins and quantitative underpinning from the provided overview, facilitating informed use of BMI and related indices in research and clinical settings.

CryoSeek: A strategy for bioentity discovery using cryoelectron microscopy

Structural biology is experiencing a paradigm shift from targeted structural determination to structure-guided discovery of previously uncharacterized bioentities. We employed cryoelectron microscopy (cryo-EM) to analyze filtered water samples collected from the Tsinghua Lotus Pond. Here, we report the structural determination and characterization of two highly similar helical fibrils, named TLP-1a and TLP-1b, each approximately 8 nm in diameter with a 15-Å wide tunnel. These fibrils are assembled from a similar protein protomer, whose structure was conveniently automodeled in CryoNet. The protomer structure does not match any available experimental structures, but shares the same fold as many predicted structures of unknown functions. The amino-terminal β strand of protomer n + 4 inserts into a cleft in protomer n to complete an immunoglobulin (Ig)-like domain. This packing mechanism, known as donor-strand exchange (DSE), has been observed in several bacterial pilus assemblies, wherein the donor is protomer n + 1. Despite distinct shape and thickness, this reminiscence suggests that TLP-1a/b fibrils may represent uncharacterized bacterial pili. Our study demonstrates an emerging paradigm in structural biology, where high-resolution structural determination precedes and drives the identification and characterization of completely unknown objects.

G-Protein Signaling in Alzheimer's Disease: Spatial Expression Validation of Semi-Supervised Deep Learning Based Computational Framework.

Systemic study of pathogenic pathways and interrelationships underlying genes associated with Alzheimer's disease (AD) facilitates the identification of new targets for effective treatments. Recently available large-scale multi-omics datasets provide opportunities to use computational approaches for such studies. Here, we devised a novel disease gene identification (digID) computational framework that consists of a semi-supervised deep learning classifier to predict AD-associated genes and a protein-protein interaction (PPI) network-based analysis to prioritize the importance of these predicted genes in AD. digID predicted 1,529 AD-associated genes and revealed potentially new AD molecular mechanisms and therapeutic targets including GNAI1 and GNB1, two G-protein subunits that regulate cell signaling, and KNG1, an upstream modulator of CDC42 small G-protein signaling and mediator of inflammation and candidate coregulator of amyloid precursor protein (APP). Analysis of mRNA expression validated their dysregulation in AD brains but further revealed the significant spatial patterns in different brain regions as well as among different sub-regions of frontal cortex and hippocampi. Super-resolution STochastic Optical Reconstruction Microscopy (STORM) further demonstrated their subcellular co-localization and molecular interactions with APP in a transgenic mouse model of both sexes with AD-like mutations. These studies support the predictions made by digID while highlighting the importance of concurrent biological validation of computationally identified gene clusters as potential new AD therapeutic targets.Significance Statement Powerful computational approaches such as machine learning (ML) can interrogate large-scale multi-omics datasets to predict disease-associated genes unbiasedly via systemic study. This study presents a new disease gene identification (digID) computational framework using semi-supervised deep learning classifier. Empowered by the super-resolution imaging and the spatial biology paradigm, we further revealed that the ML model predicted AD-related G-protein signaling is subject to spatial expression dysregulation. Therefore, computational discoveries require independent biological validation to yield medical insights and our data highlight three novel G-protein genes and their signaling networks to be potential new AD therapeutic targets.

Creating insect neopolyploid lines to study animal polyploid evolution.

Whole-genome duplication (polyploidy) poses many complications but is an important driver for eukaryotic evolution. To experimentally study how many challenges from the cellular (including gene expression) to the life history levels are overcome in polyploid evolution, a system in which polyploidy can be reliably induced and sustained over generations is crucial. Until now, this has not been possible with animals, as polyploidy notoriously causes first-generation lethality. The parasitoid wasp Nasonia vitripennis emerges as a stunningly well-suited model. Polyploidy can be induced in this haplodiploid system through (1) silencing genes in the sex determination cascade and (2) by colchicine injection to induce meiotic segregation failure. Nasonia polyploids produce many generations in a short time, making them a powerful tool for experimental evolution studies. The strong variation observed in Nasonia polyploid phenotypes aids the identification of polyploid mechanisms that are the difference between evolutionary dead ends and successes. Polyploid evolution research benefits from decades of Nasonia research that produced extensive reference-omics data sets, facilitating the advanced studies of polyploid effects on the genome and transcriptome. It is also possible to create both inbred lines (to control for genetic background effects) and outbred lines (to conduct polyploid selection regimes). The option of interspecific crossing further allows to directly contrast autopolyploidy (intraspecific polyploidy) to allopolyploidy (hybrid polyploidy). Nasonia can also be used to investigate the nascent field of using polyploidy in biological control to improve field performance and lower ecological risk. In short, Nasonia polyploids are an exceptional tool for researching various biological paradigms.

Brain-inspired biomimetic robot control: a review.

Complex robotic systems, such as humanoid robot hands, soft robots, and walking robots, pose a challenging control problem due to their high dimensionality and heavy non-linearities. Conventional model-based feedback controllers demonstrate robustness and stability but struggle to cope with the escalating system design and tuning complexity accompanying larger dimensions. In contrast, data-driven methods such as artificial neural networks excel at representing high-dimensional data but lack robustness, generalization, and real-time adaptiveness. In response to these challenges, researchers are directing their focus to biological paradigms, drawing inspiration from the remarkable control capabilities inherent in the human body. This has motivated the exploration of new control methods aimed at closely emulating the motor functions of the brain given the current insights in neuroscience. Recent investigation into these Brain-Inspired control techniques have yielded promising results, notably in tasks involving trajectory tracking and robot locomotion. This paper presents a comprehensive review of the foremost trends in biomimetic brain-inspired control methods to tackle the intricacies associated with controlling complex robotic systems.

The migrasome as a developmental learning paradigm in cell biology.

Migrasome is a newly discovered organelle composed of small vesicular structures enclosed in membrane structures. Since its discovery in 2014, migrasome has attracted increasing attention in cell biology due to its critical role in multiple disease processes. Its pivotal role in various disease processes, including cell migration, intercellular communication, removal of damaged mitochondria, embryogenesis localization, immune cell chemotaxis, and virus transmission, underscores its significance in biological systems. With research on migrasome steadily increasing, it becomes a unique resource for undergraduate cell biology education. For deeper understanding of migrasome, we applied a bibliometric approach. Here we conducted a comprehensive analysis of migrasome research by retrieving relevant literature from databases such as Web of Science, Scopus, and PubMed using the keywords "migrasome" or "migrasomes."Employing CiteSpace software and Prism, we analyzed annual publication trends, identified core authors and institutions, assessed national contributions, examined keywords, and scrutinized highly cited literature related to migrasome research. This study presents a comprehensive overview of migrasome research, elucidating its literature characteristics, key contributors, research hotspots, and emerging trends. By shedding light on the current status and future trajectories of migrasome research, we aim to provide valuable insights for teachers in cell biology education. We propose for the integration of migrasome research into undergraduate curricula to enhance the understanding of cell biology among premedical, medical, and biomedical students, thereby fostering a deeper appreciation for the intricate mechanisms governing cellular behavior and disease processes.

A CRISPR activation screen identifies FBXO22 supporting targeted protein degradation.

Targeted protein degradation (TPD) represents a potent chemical biology paradigm that leverages the cellular degradation machinery to pharmacologically eliminate specific proteins of interest. Although multiple E3 ligases have been discovered to facilitate TPD, there exists a compelling requirement to diversify the pool of E3 ligases available for such applications. Here we describe a clustered regularly interspaced short palindromic repeats (CRISPR)-based transcriptional activation screen focused on human E3 ligases, with the goal of identifying E3 ligases that can facilitate heterobifunctional compound-mediated target degradation. Through this approach, we identified a candidate proteolysis-targeting chimera (PROTAC), 22-SLF, that induces the degradation of FK506-binding protein 12 when the transcription of FBXO22 gene is activated. Subsequent mechanistic investigations revealed that 22-SLF interacts with C227 and/or C228 in F-box protein 22 (FBXO22) to achieve target degradation. Lastly, we demonstrated the versatility of FBXO22-based PROTACs by effectively degrading additional endogenous proteins, including bromodomain-containing protein 4 and the echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase fusion protein.

‘A movie about flowers?’ Notes on the ecological turn in adaptation studies

Abstract This article takes up and responds to the recent ecological turn in adaptation studies, exploring the discipline’s widespread interest in the overlap between the notion of adaptation in evolutionary biology and the notion of adaptation in literature, film, and media studies. It argues that in order to develop a historically and ecocritically alert approach to adaptation studies, it is necessary to unpack what is at stake in using biological terms and paradigms to study adaptation in art. Firstly, it offers a survey of several studies that have explored the overlap between adaptation in nature and adaptation in culture, arguing that these have been overly influenced by the notions of neo-Darwinism that were popularized by Richard Dawkins in The Selfish Gene (1976). Secondly, it offers a rereading of the film that has become a primary case study among theorists who have reached for biological metaphors to explain cultural change: Adaptation (2002). It argues that whereas scholars have often tended to use Adaptation as a springboard from which to launch an exploration of the purported homology between adaptation in nature and adaptation in art, in fact, the film’s evolutionary themes are clearly historicizable, tied to a set of values coordinated around ideas of heteronormative reproductivity, dissemination, and growth. Examining those values helps to demonstrate how the film’s evolutionary themes are deployed as part of its representational strategies, thereby challenging the idea that they might be unproblematically used to describe the overlap between adaptation in biology and adaptation in art.

Charge block-driven liquid-liquid phase separation - mechanism and biological roles.

Liquid-liquid phase separation (LLPS) has increasingly been found to play pivotal roles in a number of intracellular events and reactions, and has introduced a new paradigm in cell biology to explain protein-protein and enzyme-ligand interactions beyond conventional molecular and biochemical theories. LLPS is driven by the cumulative effects of weak and promiscuous interactions, including electrostatic, hydrophobic and cation-π interactions, among polypeptides containing intrinsically disordered regions (IDRs) and describes the macroscopic behaviours of IDR-containing proteins in an intracellular milieu. Recent studies have revealed that interactions between 'charge blocks' - clusters of like charges along the polypeptide chain - strongly induce LLPS and play fundamental roles in its spatiotemporal regulation. Introducing a new parameter, termed 'charge blockiness', into physicochemical models of disordered polypeptides has yielded a better understanding of how the intrinsic amino acid sequence of a polypeptide determines the spatiotemporal occurrence of LLPS within a cell. Charge blockiness might also explain why some post-translational modifications segregate within IDRs and how they regulate LLPS. In this Review, we summarise recent progress towards understanding the mechanism and biological roles of charge block-driven LLPS and discuss how this new characteristic parameter of polypeptides offers new possibilities in the fields of structural biology and cell biology.

Optimized DLP 3D-printed high-resolution nano zirconia-hydroxyapatite scaffold with craniomaxillofacial soft tissue invasion resistance and pro-osteogenic properties via dectin-1/syk inflammatory axis

One major challenge of craniomaxillofacial bone regeneration is the direct contact of subcutaneous fibrous tissue towards bone regenerative region, which results in fast fibroblast invasion and suppression of bone regeneration. Dectin-1, a pattern recognition receptor expressed on activated macrophages, is crucial for directing fibrous invasion. Targeting Dectin-1 and its downstream signaling cascade could be an effective strategy to resist “craniomaxillofacial soft tissue invasion”. Nano zirconia can shelter the essential amino acids of Dectin-1 and was reported to deactivate the inflammation signals. Herein, we succeeded in incorporating nano zirconia into high-resolution 3D hydroxyapatite (HA) scaffolds via modified digital light processing (DLP) technique system. The incorporation of nano zirconia can endow high-resolution HA scaffolds with the capacity of regulating the key structure of extracellular C-type lectin-like domain (CTLD) of dectin-1, proved by computational simulation. This results in inhibiting the dectin-1/syk axis and pro-soft tissue proliferation cytokines production. In vivo experiments further validated the effects of HA/nano zirconia resisting craniomaxillofacial soft tissue invasion and promoting bone regeneration. Our work practices the concept of “soft tissue invasion resisting capacity” via targeting in manipulating dectin-1, which succeeds in attenuating fibrous invasion and craniomaxillofacial bone regeneration. The “soft tissue invasion resisting capacity” could become a valuable biological paradigm of craniomaxillofacial bone biomaterials.

Phenotypic assessment of antiviral activity for spiro-annulated oxepanes and azepenes.

Evolutionary potential of viruses can result in outbreaks of well-known viruses and emergence of novel ones. Pharmacological methods of intervening the reproduction of various less popular, but not less important viruses are not available, as well as the spectrum of antiviral activity for most known compounds. In the framework of chemical biology paradigm, characterization of antiviral activity spectrum of new compounds allows to extend the antiviral chemical space and provides new important structure-activity relationships for data-driven drug discovery. Here we present a primary assessment of antiviral activity of spiro-annulated derivatives of seven-membered heterocycles, oxepane and azepane, in phenotypic assays against viruses with different genomes, virion structures, and genome realization schemes: orthoflavivirus (tick-borne encephalitis virus, TBEV), enteroviruses (poliovirus, enterovirus A71, echovirus 30), adenovirus (human adenovirus C5), hantavirus (Puumala virus). Hit compounds inhibited reproduction of adenovirus C5, the only DNA virus in the studied set, in the yield reduction assay, and did not inhibit reproduction of RNA viruses.

Epigenetic marks uniquely tune the material properties of HP1α condensates

Biomolecular condensates have emerged as a powerful new paradigm in cell biology with broad implications to human health and disease, particularly in the nucleus where phase separation is thought to underly elements of chromatin organization and regulation. Specifically, it has been recently reported that phase separation of heterochromatin protein 1alpha (HP1α) with DNA contributes to the formation of condensed chromatin states. HP1α localization to heterochromatic regions is mediated by its binding to specific repressive marks on the tail of histone H3, such as trimethylated lysine 9 on histone H3 (H3K9me3). However, whether epigenetic marks play an active role in modulating the material properties of HP1α and dictating emergent functions of its condensates remains to be understood. Here, we leverage a reductionist system, composed of modified and unmodified histone H3 peptides, HP1α, and DNA, to examine the contribution of specific epigenetic marks to phase behavior of HP1α. We show that the presence of histone peptides bearing the repressive H3K9me3 is compatible with HP1α condensates, whereas peptides containing unmodified residues or bearing the transcriptional activation mark H3K4me3 are incompatible with HP1α phase separation. Using fluorescence microscopy and rheological approaches, we further demonstrate that H3K9me3 histone peptides modulate the dynamics and viscoelastic network properties of HP1α condensates in a concentration-dependent manner. Additionally, in cells exposed to uniaxial strain, we find there to be a decreased ratio of nuclear H3K9me3 to HP1α. These data suggest that HP1α-DNA condensates are viscoelastic materials, whose properties may provide an explanation for the dynamic behavior of heterochromatin in cells and in response to mechanostimulation.

The emergence of theoretical biology: Two fundamental works of Ervin Bauer (1890–1938) in English translation

Ervin Bauer (1890–1938) outlined the paradigm of theoretical biology from the perspective of biophysics and bioenergetics. His molecular-based biological theory is centered on the principle of sustainable non-equilibrium, which is continuously produced and maintained by all biological systems throughout their life. Ervin Bauer became the victim of Stalin's Great Terror. Here we present two of the fundamental works of Ervin Bauer in English translation: the paper “The definition of living beings on the basis of their thermodynamic properties, and the fundamental biological principles that follow from it” published in Naturwissenschaften (1920) and the excerpts from his magnum opus “Theoretical Biology” (1935). These works became a bibliographical rarity. A complete English translation of “Theoretical Biology” is an important task for the future.

Abstract 7368: Sentinel omics signatures: Comparative clinical and blood sample analysis from canine mammary tumor patients and their human guardian

Abstract Breast cancer remains a leading cause of morbidity and mortality worldwide, necessitating innovative approaches for early detection and intervention. This study leverages the comparative biology paradigm, exploring the shared oncological pathways between humans and canines through a unique multi-omics approach. We have gathered a diverse cohort comprising healthy dogs, canine mammary tumor patients, and their respective human guardians, collecting comprehensive clinical data alongside blood samples. Employing RNA-seq, MBD-seq, and LCMS, we aim to construct a detailed transcriptomic, methylomic, and proteomic landscape to elucidate potential sentinel biomarkers indicative of an oncogenic environment shared between species. While results are forthcoming, the premise of our research rests on the hypothesis that environmental factors contributing to mammary cancer may manifest systemically, potentially affecting both canines and humans. By delineating these interspecies molecular signatures, we hope to advance the field of precision medicine, offering insights into early detection and the systemic nature of cancer pathobiology. This abstract presents the foundation and direction of our ongoing investigation, with a commitment to providing a comprehensive update, inclusive of significant findings, at the conference. Citation Format: Keun Hong Son, A-Reum Nam, Hyoung-Min Park, HuiSu Kim, Jeong-Woon Lee, Je-Yoel Cho. Sentinel omics signatures: Comparative clinical and blood sample analysis from canine mammary tumor patients and their human guardian [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7368.

Morphological and structural characteristics of the elytra reduce impact damage to ladybird beetles

Beetle elytra act as natural protective covers and effectively shield their flexible abdomens and fragile hindwings from damage. The existing studies have attributed this contribution of the elytra to its honeycomb structures. In this combined experimental and theoretical study, we used the seven-spotted ladybird beetle to demonstrate that both biological morphology and the hollow structure of the dome-like elytra combined to reduce damage during falling. The falling ladybird beetles had a high probability (59.52%) of hitting the ground with the costal edge of the elytra. This strategy could assist with converting the translational energy into rotational kinetic energy, resulting in the reduction of the impulse during falling. In addition, the hollow structures on the elytra could further absorb the residual impact energy. In the future, this biological paradigm could be used as a basis for the development of falling/landing techniques for advanced robots.

Abstract B106: Spatially-constrained optimal transport interaction analysis reveals therapy-associated remodeling in the pancreatic cancer microenvironment

Abstract Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies with a five-year overall survival of only 11%. Treatment failure is ubiquitous, driven by genetic and phenotypic heterogeneity combined with a highly desmoplastic and immunosuppressive microenvironment. Identifying novel therapeutic targets in the tumor microenvironment (TME) is critical to improving patient outcomes and can be advanced through understanding the cell intrinsic states and cell-cell interactions driving clinically-relevant properties. Recent applications of single-cell and spatial proteo-transcriptomic technologies to PDAC have enhanced our understanding of intratumoral heterogeneity, cell state plasticity, and neighborhood composition. However, prior studies were unable to provide high-plex molecular information while preserving in situ spatial relationships at single-cell resolution, limiting detailed analyses of cell-cell interactions and potential therapeutic avenues. Advances in spatial technology have enabled subcellular resolution while profiling up to several thousand transcripts. We performed spatial molecular profiling (SMI; NanoString CosMx) on 13 patient-derived PDAC tumors using a 990-plex mRNA panel, which yielded 753,133 high confidence single-cell profiles. We then developed a novel method for inferring multicellular interactions—Spatially Constrained Optimal Transport Interaction Analysis (SCOTIA), an optimal transport model with a cost function that includes both spatial distance and ligand–receptor (LR) gene expression. We used SCOTIA to dissect the remodeled TME in response to neoadjuvant FOLFIRINOX and chemoradiotherapy. Our results uncovered a marked change in LR interactions between cancer-associated fibroblasts and malignant cells in response to treatment, which was supported by results from experiments using a murine tumoroid co-culture system. We observed in treated specimens a lower abundance of myofibroblastic CAFs (myCAFs) and higher prevalence of inflammatory CAFs (iCAFs), which express high levels of IL6 family cytokines and spatially co-localize with cancer cell subtypes previously associated with therapeutic resistance (i.e., neural-like, basal/mesenchymal). Two of the most consistent treatment-enriched LR interactions between CAFs and cancer cells were CLCF1-CNTFR and LIF-IL6ST, members of the IL6 cytokine family. While CAF-derived IL6 family ligands and downstream JAK/STAT3 and MAPK activation have been linked to induction of a mesenchymal cancer cell phenotype in several malignancies as well as neuroendocrine differentiation in prostate cancer, an association with the neural-like malignant cell state in pancreatic cancer has not been previously established. Overall, this study demonstrates that characterization of the TME using high-plex single-cell spatial transcriptomics allows for identification of molecular interactions that may play a role in the emergence of chemoresistance and establishes a translational spatial biology paradigm that can be broadly applied to other malignancies, diseases, and treatments. Citation Format: Alexander T.F. Bell, Jacob T. Mitchell, Ashley L. Kiemen, Melissa Lyman, Kohei Fujikura, Jae W. Lee, Erin Coyne, Sarah M. Shin, Pei-Hsun Wu, Jacquelyn W. Zimmerman, Denis Wirtz, Won J. Ho, Neeha Zaidi, Elizabeth Thompson, Elizabeth M. Jaffee, Laura D. Wood, Elana J. Fertig, Luciane T. Kagohara. Spatially-constrained optimal transport interaction analysis reveals therapy-associated remodeling in the pancreatic cancer microenvironment [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr B106.