bims-gerecp Biomed News
on Gene regulatory networks of epithelial cell plasticity
Issue of 2025–07–20
25 papers selected by
Xiao Qin, University of Oxford
  1. High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer.
  2. Mechanistic Insights into Intestinal Stem Cell Disruption during Infection.
  3. Uncovering Convergent Cell State Dynamics Across Divergent Genetic Perturbations Through Single-Cell High-Content CRISPR Screening.
  4. Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics.
  5. Multiplexed, scalable analog recording of gene regulation dynamics over weeks using intracellular protein tapes.
  6. Developmental Plasticity and Stromal Co-option Shape a Pituitary Neuroendocrine Tumor Transcriptional Continuum.
  7. Recent evolution of the developing human intestine affects metabolic and barrier functions.
  8. Differential cell signaling testing for cell-cell communication inference from single-cell data by dominoSignal.
  9. Oncogenic and tumor-suppressive forces converge on a progenitor-orchestrated niche to shape early tumorigenesis.
  10. A clinical road map for single-cell omics.
  11. Cancer progression through the lens of age-induced metabolic reprogramming.
  12. Mapping cell fate transition in space and time.
  13. The Role of Organoids in Advancing Colorectal Cancer Research: Insights and Future Directions.
  14. Cell barcoding with tandem fluorescent proteins enables high-throughput signaling dynamics analysis.
  15. Cancer research and the mainstream of biology.
  16. The Aging Microenvironment as a Determinant of Immune Exclusion and Metastatic Fate in Pancreatic Cancer.
  17. Bacterial ADP-heptose triggers stem cell regeneration in the intestinal epithelium following injury.
  18. Genetically encoded biosensor for monitoring spatiotemporal dynamics of CCR2 ligands in culture and in vivo.
  19. Tumour tissue: heterogeneous, but not disordered.
  20. Cancer-associated fibroblasts as mediators of tissue microenvironment remodeling in cancer.
  21. Midline assembloids reveal regulators of human axon guidance.
  22. Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context.
  23. Overcoming Barriers in Cancer Biology Research: Current Limitations and Solutions.
  24. Unbiased recording of clonal potency reveals species-specific regulation of mammalian intestine.
  25. Topological velocity inference from spatial transcriptomic data.
  1. bioRxiv. 2025 Jun 15. pii: 2025.06.15.659774. [Epub ahead of print]
    High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer.
    Luke W Koblan, Kathryn E Yost, Pu Zheng, William N Colgan, Matthew G Jones, Dian Yang, Arhan Kumar, Jaspreet Sandhu, Alexandra Schnell, Dawei Sun, Can Ergen, Reuben A Saunders, Xiaowei Zhuang, William E Allen, Nir Yosef, Jonathan S Weissman.
      Charting the spatiotemporal dynamics of cell fate determination in development and disease is a long-standing objective in biology. Here we present the design, development, and extensive validation of PEtracer, a prime editing-based, evolving lineage tracing technology compatible with both single-cell sequencing and multimodal imaging methodologies to jointly profile cell state and lineage in dissociated cells or while preserving cellular context in tissues with high spatial resolution. Using PEtracer coupled with MERFISH spatial transcriptomic profiling in a syngeneic mouse model of tumor metastasis, we reconstruct the growth of individually-seeded tumors in vivo and uncover distinct modules of cell-intrinsic and cell-extrinsic factors that coordinate tumor growth. More generally, PEtracer enables systematic characterization of cell state and lineage relationships in intact tissues over biologically-relevant temporal and spatial scales.
    DOI:  https://doi.org/10.1101/2025.06.15.659774
  2. Am J Physiol Gastrointest Liver Physiol. 2025 Jul 14.
    Mechanistic Insights into Intestinal Stem Cell Disruption during Infection.
    Naomi Chege, Constance A M Finney.
      The intestinal epithelium is in continual flux. It must balance maintaining a healthy microbiota with detecting and destroying intestinal pathogens. Intestinal stem cells (ISCs), which sit in the crypts below the intestinal villi, control this process. Depending on the molecular signals they receive, ISCs rapidly differentiate into the different intestinal epithelial cell subsets, making the intestine a remarkably adaptable organ. However, pathogens can hijack ISC functions to their advantage and establish infections. In this review, we explore the mechanisms used by pathogens to exploit ISCs.
    Keywords:  Hippo, Wnt, Notch; infection; intestinal stem cells; pathogen; signalling
    DOI:  https://doi.org/10.1152/ajpgi.00352.2024
  3. bioRxiv. 2025 May 05. pii: 2025.05.02.651939. [Epub ahead of print]
    Uncovering Convergent Cell State Dynamics Across Divergent Genetic Perturbations Through Single-Cell High-Content CRISPR Screening.
    Zihan Xu, Ziyu Lu, Aileen Ugurbil, Abdulraouf Abdulraouf, Andrew Liao, Jianxiang Zhang, Wei Zhou, Junyue Cao.
      High-throughput genomic studies have uncovered associations between diverse genetic alterations and disease phenotypes; however, elucidating how perturbations in functionally disparate genes give rise to convergent cellular states remains challenging. Here, we present PerturbFate, a high-throughput, cost-effective, combinatorial-indexing single-cell platform that enables systematic interrogation of massively parallel CRISPR perturbations across the full spectrum of gene regulation, from chromatin remodeling and nascent transcription to steady-state transcriptomic phenotypes. Using PerturbFate, we profiled over 300,000 cultured melanoma cells to characterize multi-modal phenotypic and gene regulatory responses to perturbations in more than 140 Vemurafenib resistance-associated genes. We uncovered a shared dedifferentiated cell state marked by convergent transcription factor (TF) activity signatures across diverse genetic perturbations. Combined inhibition of cooperative TF hubs effectively reversed cellular adaptation to Vemurafenib treatment. We further dissected phenotypic responses to perturbations in Mediator Complex components, linking module-specific biochemical properties to convergent gene activations. Together, we reveal common regulatory nodes that drive similar phenotypic outcomes across distinct genetic perturbations. We also delineate how perturbations in functionally unrelated genes reshape cell state. PerturbFate thus establishes a versatile platform for identifying key molecular regulators by anchoring multi-modal regulatory dynamics to disease-relevant phenotypes.
    DOI:  https://doi.org/10.1101/2025.05.02.651939
  4. bioRxiv. 2025 Jun 24. pii: 2022.10.02.508492. [Epub ahead of print]
    Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics.
    Inbal Avraham-Davidi, Simon Mages, Johanna Klughammer, Noa Moriel, Shinya Imada, Matan Hofree, Evan Murray, Jonathan Chen, Karin Pelka, Arnav Mehta, Genevieve M Boland, Toni Delorey, Leah Caplan, Danielle Dionne, Robert Strasser, Jana Lalakova, Anezka Niesnerova, Hao Xu, Morgane Rouault, Itay Tirosh, Nir Hacohen, Fei Chen, Omer Yilmaz, Jatin Roper, Orit Rozenblatt-Rosen, Mor Nitzan, Aviv Regev.
      While advances in single cell genomics have helped to chart the cellular components of tumor ecosystems, it has been more challenging to characterize their specific spatial organization and functional interactions. Here, we combine single cell RNA-seq, spatial transcriptomics by Slide-seq, and in situ multiplex RNA analysis, to create a detailed spatial map of healthy and dysplastic colon cellular ecosystems and their association with disease progression. We profiled inducible genetic CRC mouse models that recapitulate key features of human CRC, assigned cell types and epithelial expression programs to spatial tissue locations in tumors, and computationally used them to identify the regional features spanning different cells in the same spatial niche. We find that tumors were organized in cellular neighborhoods, each with a distinct composition of cell subtypes, expression programs, and local cellular interactions. Comparing to scRNA-seq and Slide-seq data from human CRC, we find that both cell composition and layout features were conserved between the species, with mouse neighborhoods correlating with malignancy and clinical outcome in human patient tumors, highlighting the relevance of our findings to human disease. Our work offers a comprehensive framework that is applicable across various tissues, tumors, and disease conditions, with tools for the extrapolation of findings from experimental mouse models to human diseases.
    DOI:  https://doi.org/10.1101/2022.10.02.508492
  5. bioRxiv. 2025 May 10. pii: 2025.05.10.653182. [Epub ahead of print]
    Multiplexed, scalable analog recording of gene regulation dynamics over weeks using intracellular protein tapes.
    Lirong Zheng, Yixiao Yan, Bingxin Zhou, Jormay Lim, Dongqing Shi, Bobae An, BumJin Ko, Emily Klyder, Sethuramasundaram Pitchiaya, Denise J Cai, Edward S Boyden, Donglai Wei, Pietro Lio, Changyang Linghu.
      Gene expression is constantly regulated by gene regulatory networks that consist of multiple regulatory components to mediate cellular functions. An ideal tool for analyzing gene regulation processes would provide simultaneous measurements of the dynamics of many components in the gene regulatory network, but existing methodologies fall short of simultaneously tracking the dynamics of components over long periods of time. Here, we present CytoTape-a genetically encoded, modular, and scalable analog recorder for continuous, multiplexed in situ recording of gene regulation dynamics over multiple days and weeks at single-cell resolution. CytoTape consists of a flexible, thread-like, elongating intracellular protein self-assembly engineered via AI-guided rational design. Gene regulation dynamics, together with timestamps for reconstruction of the continuous time axis, are directly encoded via distinct molecular tags distributed along single CytoTape assemblies in live cells, to be readout at scale after fixation via standard immunofluorescence imaging. CytoTape recorders are modularly designed to record gene expression driven by a variety of activity-dependent promoters. We demonstrated the utility of CytoTape in mammalian embryonic kidney cells, cancer cells, glial cells, and neurons, achieving simultaneous recording of five cell plasticity-associated transcription factor activities and immediate early gene expression levels, namely CREB, c-fos, Arc, Egr1, and Npas4 activities, within single cells in a spatiotemporally scalable manner. CytoTape revealed complex waveforms and nonlinear temporal couplings among these cellular activities, enabling investigations of how gene regulation histories and intrinsic signaling states shape transcriptional logics. We envision CytoTape to have broad applications in both basic and disease-related cell biology research.
    DOI:  https://doi.org/10.1101/2025.05.10.653182
  6. bioRxiv. 2025 Jun 24. pii: 2025.06.18.659743. [Epub ahead of print]
    Developmental Plasticity and Stromal Co-option Shape a Pituitary Neuroendocrine Tumor Transcriptional Continuum.
    Robert C Osorio, Jun Y Oh, Jangham Jung, Alexander J Ehrenberg, Atul Saha, Meeki Lad, Harmon Khela, Nicole Brennick, Petros Giannikopoulos, William W Seeley, Lea T Grinberg, Aaron Diaz, Manish K Aghi.
      Pituitary neuroendocrine tumors (PitNETs) are common intracranial neoplasms with complex biology underpinned by unresolved cellular origins, molecular heterogeneity, and microenvironment interactions. Here, we employ single-nuclei RNA-sequencing (snRNA-seq) of 419,874 cells from human normal pituitaries and PitNETs with spatial transcriptomics to resolve these challenges. We identify multi-hormonal neuroendocrine cells in both normal and tumor tissues, originating as early pseudotime intermediates from pituitary stem cells, revealing an inherent plasticity that blurs traditional lineage boundaries. PitNETs exhibit a transcriptional continuum across subtypes, challenging their classification into discrete categories. Trajectory analysis uncovers divergent cellular origins: silent gonadotroph adenomas (SGAs), prolactinomas, silent corticotroph adenomas (SCAs), and Cushing's adenomas are closely linked to differentiated neuroendocrine cells, while somatotroph and null cell adenomas (NCAs) appear to derive more directly from adult stem cells. Tumor cells co-opt robust cell-cell communication networks found in normal adult neuroendocrine cells. Spatial profiling further demonstrates that perivascular niches enhance tumorigenicity through angiogenic and epithelial-mesenchymal transition programs. Our work redefines PitNETs as ecosystems shaped by developmental plasticity and microenvironmental crosstalk, offering a roadmap for future therapies targeting lineage fluidity and stromal dependencies.
    DOI:  https://doi.org/10.1101/2025.06.18.659743
  7. Science. 2025 Jul 17. eadr8628
    Recent evolution of the developing human intestine affects metabolic and barrier functions.
    Qianhui Yu, Umut Kilik, Stefano Secchia, Lukas Adam, Yu-Hwai Tsai, Christiana Fauci, Jasper Janssens, Charlie J Childs, Katherine D Walton, Rubén López-Sandoval, Angeline Wu, Marina Almató Bellavista, Sha Huang, Calen A Steiner, Yannick Throm, Michael James Boyle, Zhisong He, Joep Beumer, Barbara Treutlein, Craig B Lowe, Jason R Spence, J Gray Camp.
      Diet, microbiota, and other exposures place the intestinal epithelium as a nexus for evolutionary change; however, little is known about genomic changes associated with adaptation to a uniquely human environment. Here, we interrogate the evolution of cell types in the developing human intestine by comparing tissue and organoids from humans, chimpanzees, and mice. We find that recent changes in primates are associated with immune barrier function and lipid/xenobiotic metabolism, and that human-specific genetic features impact these functions. Enhancer assays, genetic deletion, and in silico mutagenesis resolve evolutionarily significant enhancers of Lactase (LCT) and Insulin-like Growth Factor Binding Protein 2 (IGFBP2). Altogether, we identify the developing human intestinal epithelium as a rapidly evolving system, and show that great ape organoids provide insight into human biology.
    DOI:  https://doi.org/10.1126/science.adr8628
  8. bioRxiv. 2025 May 03. pii: 2025.05.02.651747. [Epub ahead of print]
    Differential cell signaling testing for cell-cell communication inference from single-cell data by dominoSignal.
    Jacob T Mitchell, Orian Stapleton, Kavita Krishnan, Sushma Nagaraj, Dmitrijs Lvovs, Christopher Cherry, Amanda Poissonnier, Wes Horton, Andrew Adey, Varun Rao, Amanda Huff, Jacquelyn W Zimmerman, Luciane T Kagohara, Neeha Zaidi, Lisa M Coussens, Elizabeth M Jaffee, Jeniffer H Elisseeff, Elana J Fertig.
      Algorithms for ligand-receptor network inference have emerged as commonly used tools to estimate cell-cell communication from reference single-cell data. Many studies employ these algorithms to compare signaling between conditions and lack methods to statistically identify signals that are significantly different. We previously developed the cell communication inference algorithm Domino, which considers ligand and receptor gene expression in association with downstream transcription factor activity scoring. We developed the dominoSignal software to innovate upon Domino and extend its functionality to test statistically differential cellular signaling. This new functionality includes compilation of active signals as linkages from multiple subjects in a single-cell data set and testing condition-dependent signaling linkage. The software is applicable for analysis of single-cell data sets with multiple subjects as biological replicates as well as with bootstrapped replicates from data sets with few or pooled subjects. We use simulation studies to benchmark the number of subjects in compared groups and cells within an annotated cell type sufficient to accurately identify differential linkages. We demonstrate the application of the Differential Cell Signaling Test (DCST) in the dominoSignal software to investigate consequences of cancer cell phenotypes and immunotherapy on cell-cell communication in tumor microenvironments. These applications in cancer studies demonstrate the ability of differential cell signaling analysis to infer changes to cell communication networks from therapeutic or experimental perturbations, which is broadly applicable across biological systems.
    DOI:  https://doi.org/10.1101/2025.05.02.651747
  9. bioRxiv. 2025 Jun 12. pii: 2025.06.10.656791. [Epub ahead of print]
    Oncogenic and tumor-suppressive forces converge on a progenitor-orchestrated niche to shape early tumorigenesis.
    José Reyes, Isabella Del Priore, Andrea C Chaikovsky, Nikhita Pasnuri, Ahmed M Elhossiny, Tobias Krause, Andrew Moorman, Catherine Snopkowski, Meril Takizawa, Cassandra Burdziak, Nalin Ratnayeke, Ignas Masillioni, Yu-Jui Ho, Ronan Chaligné, Paul B Romesser, Aveline Filliol, Tal Nawy, John P Morris, Zhen Zhao, Marina Pasca Di Magliano, Direna Alonso-Curbelo, Dana Pe'er, Scott W Lowe.
      The transition from benign to malignant growth is a pivotal yet poorly understood step in cancer progression that marks the shift from a pathologically inert condition to a clinically lethal disease. Here, we integrate lineage tracing, single-cell and spatial transcriptomics to visualize the molecular, cellular and tissue-level events that promote or restrain malignancy during the tumor initiation in mouse models of pancreatic ductal adenocarcinoma (PDAC). We identify a discrete progenitor-like population of KRAS -mutant cells that co-activates oncogenic and tumor-suppressive programs-including p53, CDKN2A, and SMAD4-engaging senescence-like responses and remodeling their microenvironment, ultimately assembling a niche that mirrors invasive PDAC. KRAS inhibition depletes progenitor-like cells and dismantles their niche. Conversely, p53 suppression enables progenitor cell expansion, epithelial-mesenchymal reprogramming, and immune-privileged niche formation. These findings position the progenitor-like state as the convergence point of cancer-driving mutations, plasticity, and tissue remodeling-revealing a critical window for intercepting malignancy at its origin.
    DOI:  https://doi.org/10.1101/2025.06.10.656791
  10. Cell. 2025 Jul 10. pii: S0092-8674(25)00676-2. [Epub ahead of print]188(14): 3633-3647
    A clinical road map for single-cell omics.
    Michael A Skinnider, Gregoire Courtine, Jocelyne Bloch, Jordan W Squair.
      In a matter of years, single-cell omics has matured from a pioneering technique employed by just a handful of specialized laboratories to become a ubiquitous feature of biological research and a key driver of scientific discovery. The widespread adoption and development of single-cell omic assays has sparked mounting enthusiasm that these technologies are poised to also enhance the precision of diagnosis, the monitoring of disease progression, and the personalization of therapeutic strategies. Despite initial forays into clinical settings, however, single-cell technologies are not yet routinely used to inform medical or surgical decision-making. Here, we identify and categorize key experimental, computational, and conceptual barriers that currently hinder the clinical deployment of single-cell omics. We focus on the potential for single-cell transcriptomics to guide clinical decision-making through the development of combinatorial biomarkers that simultaneously quantify multiple cell-type-specific pathophysiological processes. We articulate a framework to identify patient subpopulations that stand to benefit from such biomarkers, and we outline the experimental and computational requirements to derive reproducible and actionable clinical readouts from single-cell omics.
    Keywords:  machine learning; patient cohorts; personalized medicine; single-cell; spatial transcriptomics
    DOI:  https://doi.org/10.1016/j.cell.2025.06.009
  11. Nat Rev Cancer. 2025 Jul 11.
    Cancer progression through the lens of age-induced metabolic reprogramming.
    Felicia Lazure, Ana P Gomes.
      Ageing is an important risk factor for cancer incidence and augments cancer progression. A shared hallmark of ageing and cancer is metabolic reprogramming, which has been suggested to be not only a cause but also a consequence of ageing. Strikingly, many age-regulated pathways are known to also drive tumour progression, suggesting that metabolic reprogramming connects ageing and tumorigenic processes and shapes whether malignant phenotypes manifest, thrive and evolve. With the rising average age of the world population, understanding how age-related changes in the body influence cancer progression is of paramount importance. In this Perspective, we discuss the metabolic changes that occur with ageing and their potential links with tumour initiation and progression and the development of metastatic disease. Finally, we discuss age-induced metabolic divergences that cause racial disparities and their consequences for the tumorigenic process.
    DOI:  https://doi.org/10.1038/s41568-025-00845-4
  12. Nat Biotechnol. 2025 Jul 16.
    Mapping cell fate transition in space and time.
      
    DOI:  https://doi.org/10.1038/s41587-025-02704-x
  13. Cancers (Basel). 2025 Jun 25. pii: 2129. [Epub ahead of print]17(13):
    The Role of Organoids in Advancing Colorectal Cancer Research: Insights and Future Directions.
    Zahra Heydari, Rex Devasahayam Arokia Balaya, Gobinda Sarkar, Lisa Boardman.
      Organoids are three-dimensional (3D) structures that mimic the architecture and functionality of human organs, providing a novel approach to study diseases such as colorectal cancer (CRC). This review aims to explore the impact of organoids on understanding CRC and their potential use in exploring therapeutic outcomes. Colorectal cancer, characterized by the transformation of colonic epithelial cells into adenomas and carcinomas, remains one of the top causes of cancer-related morbidity and mortality worldwide. Traditional two-dimensional (2D) cell cultures fail to replicate the tumor microenvironment in an effective manner, which highlights the need for advanced 3D models. Organoids preserve the genetic and phenotypic properties of the original tumors, allowing for improved disease modeling, drug screening, and personalized medicine applications. When using patient-derived organoids (PDOs), researchers can gain insights into CRC initiation, progression, and treatment outcome. Ultimately, organoids represent an encouraging platform for improving therapeutic strategies for CRC, potentially leading to better patient outcomes through tailored treatment approaches.
    Keywords:  3D models; colorectal cancer; organoids; patient-derived organoids; personalized medicine
    DOI:  https://doi.org/10.3390/cancers17132129
  14. bioRxiv. 2025 Jun 20. pii: 2025.06.17.660155. [Epub ahead of print]
    Cell barcoding with tandem fluorescent proteins enables high-throughput signaling dynamics analysis.
    Jhen-Wei Wu, Jr-Ming Yang, Suyang Wang, Yun Chen, Chuan-Hsiang Huang.
      Cell barcodes are essential for a wide array of experimental applications, including lineage tracing, genetic screening, and single-cell analysis. An optimal barcode library would provide high diversity, live-cell compatible identification, and simple readout. In this work, we introduce single chain tandem fluorescent protein (sctFP) barcodes, constructed by linking different fluorescent proteins (FPs) into a single polypeptide chain with varied copy numbers. We found that the fluorescence signal intensity ratio at different wavelengths can reliably differentiate sctFPs generated using cnidarian FPs, but not prokaryotic FPs that require exogenous cofactors. The sctFPs enable the multiplexing of genetically encoded fluorescent biosensors, enhancing current biosensor multiplexing methods through a simplified imaging and analysis pipeline that support high-throughput applications. Their robust spectral profiles are compatible with a broad range of biosensor types. Using sctFPs, we demonstrate simultaneous tracking of various signaling activities with biosensors of different spectral properties. Together, this strategy provides a robust and scalable method for barcoding cells across diverse experimental contexts.
    DOI:  https://doi.org/10.1101/2025.06.17.660155
  15. Front Cell Dev Biol. 2025 ;13 1623849
    Cancer research and the mainstream of biology.
    Toivo Maimets.
      John Cairns, a British molecular biologist, has pointed out that biology and cancer research have always developed together, and cancer theories have followed "whatever branch of biology happens at the time to be fashionable and exciting". Indeed, following the long historical development of biological thought confirms this observation. However, tumour theories have never been merely a "fellow runner" to more modern biology theories. Cancer is an exceptionally large medical and economic problem, and the practical results of cancer research are carefully followed and critically analysed by the community. If the expected results do not arrive and the scientific data do not fit into the old theory, then the theory must be corrected. In other words, tumour theories not only derive from the prevailing biological worldview, but they also influence and, if necessary, actively change it. That is exactly what we are witnessing today-the ruling reductionist Somatic Mutations Theory (SMT) does not explain many new experimental findings and extensive research over the last 50 years has not brought major breakthroughs in cancer treatment. This century brings back the attention to developmental biology (embryology) in connection with the epigenetic revolution in biology, and the causes of tumours are searched for in the disorders of differentiation of cells/tissues and communication between them in the organism.
    Keywords:  cancer; development; oncogenes; reductionism; somatic mutation theory
    DOI:  https://doi.org/10.3389/fcell.2025.1623849
  16. bioRxiv. 2025 May 10. pii: 2025.05.08.652966. [Epub ahead of print]
    The Aging Microenvironment as a Determinant of Immune Exclusion and Metastatic Fate in Pancreatic Cancer.
    Priyanka Gupta, Rabi Murad, Lily Ling, Yijuan Zhang, Karen Duong-Polk, Swetha Maganti, Cheska Galapate, Cosimo Commisso.
      Aging is a critical yet understudied determinant in pancreatic ductal adenocarcinoma (PDAC). Despite a strong epidemiological association with age, conventional PDAC preclinical models fail to capture the histopathological and stromal complexities that emerge in older organisms. Using an age-relevant syngeneic orthotopic model, we demonstrate that organismal aging accelerates PDAC progression and metastasis. Through transcriptomic profiling, we identify a conserved extracellular matrix gene signature enriched in cancer-associated fibroblasts (CAFs) from aged tumors, consistent with an augmented fibrotic landscape that supports immunosuppression, metastatic tropism, and poor prognosis. To directly test the functional impact of stromal aging, we employed heterochronic co-implantation models, revealing that revitalizing the aged tumor stroma with young CAFs restores immune infiltration and attenuates metastasis in older hosts. Conversely, aged CAFs, while immunosuppressive, fail to enhance metastasis in young hosts, suggesting that a youthful microenvironment exerts dominant regulatory control over disease progression. These findings demonstrate that stromal age is a critical modulator of both immune exclusion and metastatic behavior in PDAC. Importantly, our work establishes a new conceptual framework for understanding how aging shapes the tumor microenvironment in PDAC and opens a fertile avenue of investigation into age-specific stromal regulation. Moreover, this work raises compelling questions about the underlying molecular mechanisms-questions now accessible through our models-and lays the foundation for future efforts to therapeutically target stromal aging in PDAC.
    Statement of Significance: Our study links aging, stromal remodeling, and PDAC aggressiveness, highlighting how age-dependent stromal changes drive progression and suggesting that rejuvenating the aged microenvironment may improve outcomes in older patients.
    DOI:  https://doi.org/10.1101/2025.05.08.652966
  17. Cell Stem Cell. 2025 Jul 04. pii: S1934-5909(25)00231-0. [Epub ahead of print]
    Bacterial ADP-heptose triggers stem cell regeneration in the intestinal epithelium following injury.
    Shawn Goyal, Cynthia X Guo, Ojas Singh, Adrienne Ranger, Caitlin F Harrigan, Justin Meade, Alexander Luchak, Derek K Tsang, Herbert Y Gaisano, Nan Gao, Scott A Yuzwa, Jeffrey L Wrana, Dana J Philpott, Scott D Gray-Owen, Stephen E Girardin.
      ADP-heptose (ADP-Hep), a metabolite produced by gram-negative bacteria, is detected in the host cytosol by the kinase ALPK1, which engages TIFA-dependent innate immune responses. However, the function of ALPK1-TIFA signaling in primary cells and in physiological settings remains poorly understood. Here, we showed that, in the intestinal epithelium, ALPK1 and TIFA were mainly expressed by the intestinal stem cell (ISC) pool, where they controlled the replacement of homeostatic ISCs by new revival stem cells (revSCs) following injury. Mechanistically, ADP-Hep triggered pro-inflammatory nuclear factor κB (NF-κB) signaling and tumor necrosis factor (TNF)-dependent ISC apoptosis, which initiated a transforming growth factor β (TGF-β)- and YAP-dependent revSC program. Single-cell transcriptomics and lineage-tracing experiments identified Paneth cells as a cell of origin for revSC induction in response to ADP-Hep. In vivo, revSC emergence following irradiation or dextran-sodium-sulfate-induced injury was blunted in Tifa-/- mice. Together, our work reveals that ALPK1-TIFA signaling contributes to ISC turnover in response to bacterial detection in the intestine.
    Keywords:  Alpk1; CLU; Tifa; innate immunity; intestine; regeneration; revival stem cell
    DOI:  https://doi.org/10.1016/j.stem.2025.06.009
  18. Nat Methods. 2025 Jul 15.
    Genetically encoded biosensor for monitoring spatiotemporal dynamics of CCR2 ligands in culture and in vivo.
    Xian Xiao, Chenyu Wang, Xun Guo, Fengxue Xi, Qiuling Qian, Guoteng Liang, Ming Chen, Xiaoting Sun, Balint Szabo, Miao Jing, Kiryl D Piatkevich.
      Chemokines regulate immune cell migration in development, homeostasis and inflammation, but the precise spatiotemporal pattern of chemokine release in vivo remains elusive due to the constraints of existing detection methodologies. Here, we report the engineering and characterization of a genetically encoded green fluorescent chemokine sensor, named CRAFi-CCR2, which utilizes the CCR2 receptor as a sensing moiety. In astrocytes, hCRAFi-CCR2, derived from the human CCR2B receptor, exhibited ~300% increase in fluorescence in response to mCCL2, with nanomolar affinity (2.5 nM). Activation of hCRAFi-CCR2 did not affect downstream signaling pathways, such as calcium mobilization and receptor internalization. Using this sensor, we performed 17-20 h of real-time imaging to observe endogenous mCCL2 release under inflammatory conditions, both in cell culture and in mice. In mouse brain, we observed spatial heterogeneity of CCL2 signal response on a scale of about 20-50 µm, highlighting the complexity of the immune system's spatiotemporal signaling.
    DOI:  https://doi.org/10.1038/s41592-025-02742-y
  19. Nat Rev Cancer. 2025 Jul 14.
    Tumour tissue: heterogeneous, but not disordered.
    Barbara T Grünwald, Rama Khokha.
      
    DOI:  https://doi.org/10.1038/s41568-025-00852-5
  20. Curr Opin Cell Biol. 2025 Jul 14. pii: S0955-0674(25)00105-X. [Epub ahead of print]96 102567
    Cancer-associated fibroblasts as mediators of tissue microenvironment remodeling in cancer.
    Fernanda G Kugeratski, Emily J Kay, Sara Zanivan.
      Cancer-associated fibroblasts (CAFs) are a multifunctional cell population of solid tumors that substantially remodel the tumor microenvironment (TME). The combination of single-cell and spatial technologies with elegant mouse models and analysis of patient samples is enabling unprecedented advances in the characterization of CAF origins, heterogeneity, and functions within the TME. As such, the field is now evolving to delineate tissue-specific subpopulations of CAFs, their markers, and the biological context in which each subset presents with a tumor-promoting or a tumor-restraining function. In this timely review, we discuss recent advances in CAF biology in the context of emerging areas of interest in the field of anticancer therapy: immunotherapy, metabolism, and extracellular vesicles. We also highlight the substantial role of CAFs in modulating the immune microenvironment and the recent advances in targeting CAFs for cancer treatment.
    DOI:  https://doi.org/10.1016/j.ceb.2025.102567
  21. Science. 2025 Jul 17. 389(6757): 282-289
    Midline assembloids reveal regulators of human axon guidance.
    Massimo M Onesto, Neal D Amin, Chenjie Pan, Xiaoyu Chen, Ji-Il Kim, Noah Reis, Sabina Kanton, Alfredo M Valencia, Zuzana Hudacova, James P McQueen, Marc Tessier-Lavigne, Sergiu P Pașca.
      Organizers orchestrate cell patterning and axon guidance in the developing nervous system. Although nonhuman models have led to fundamental discoveries about floor plate (FP)-mediated midline organization, an experimental model of the human FP would enable insights into human neurodevelopment and midline connectivity. Here, we developed organoids resembling human FP (hFpOs) and assembled them with human spinal cord organoids (hSpOs) to generate midline assembloids (hMAs). We demonstrate that hFpOs promote ventral patterning, commissural axon guidance, and bilateral connectivity. To investigate midline regulators, we profiled the hFpO secretome, identifying 27 human-enriched genes compared with mouse. In an arrayed CRISPR screen of hMAs, we discovered that loss of GALNT2 and PLD3 impaired FP-mediated guidance of axons. This platform holds promise for revealing aspects of human-specific neurobiology and disease.
    DOI:  https://doi.org/10.1126/science.adq7934
  22. bioRxiv. 2025 Jul 09. pii: 2025.07.07.663560. [Epub ahead of print]
    Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context.
    Zhou Zhou, Albert Li, Junke Zhang, Haiyuan Yu, Abdullah Ozer, John T Lis.
      Enhancers are gene-distal cis -regulatory elements that drive cell type-specific gene expression. While significant progress has been made in identifying enhancers and characterizing their epigenomic features, much less effort has been devoted to elucidating mechanistic interactions among clusters of functionally linked regulatory elements within their endogenous chromatin contexts. Here, we developed a novel recombinase-mediated genome rewriting platform and applied our divergent transcription architectural model to understand how a long-range human enhancer confers a remarkable 10,000-fold activation to its target gene, NMU, at its native locus. Our systematic dissection reveals transcription factor synergy at this enhancer and highlights the interplay between a divergently transcribed core enhancer unit and emerging new types of cis -regulatory elements-notably, intrinsically inactive facilitators that augment and buffer core enhancer activity, and an adjacent retroviral long terminal repeat promoter that represses enhancer activity. We discuss the broader implications of our focused study on enhancer mechanisms and regulation genome-wide.
    DOI:  https://doi.org/10.1101/2025.07.07.663560
  23. Cancers (Basel). 2025 Jun 23. pii: 2102. [Epub ahead of print]17(13):
    Overcoming Barriers in Cancer Biology Research: Current Limitations and Solutions.
    Giovanni Colonna.
      Cancer research faces significant biological, technological, and systemic limitations that hinder the development of effective therapies and improved patient outcomes. Traditional preclinical models, such as 2D and 3D cell cultures, murine xenografts, and organoids, often fail to reflect the complexity of human tumor architecture, microenvironment, and immune interactions. This discrepancy results in promising laboratory findings not always translating effectively into clinical success. A core obstacle is tumor heterogeneity, characterized by diverse genetic, epigenetic, and phenotypic variations within tumors, which complicates treatment strategies and contributes to drug resistance. Hereditary malignancies and cancer stem cells contribute strongly to generating this complex panorama. Current early detection technologies lack sufficient sensitivity and specificity, impeding timely diagnosis. The tumor microenvironment, with its intricate interactions and resistance-promoting factors, further promotes treatment failure. Additionally, we only partially understand the biological processes driving metastasis, limiting therapeutic advances. Overcoming these barriers involves not only the use of new methodological approaches and advanced technologies, but also requires a cultural effort by researchers. Many cancer studies are still essentially observational. While acknowledging their significance, it is crucial to recognize the shift from deterministic to indeterministic paradigms in biomedicine over the past two to three decades, a transition facilitated by systems biology. It has opened the doors of deep metabolism where the functional processes that control and regulate cancer progression operate. Beyond biological barriers, systemic challenges include limited funding, regulatory complexities, and disparities in cancer care access across different populations. These socio-economic factors exacerbate research stagnation and hinder the translation of scientific innovations into clinical practice. Overcoming these obstacles requires multidisciplinary collaborations, advanced modeling techniques that better emulate human cancer, and innovative technologies for early detection and targeted therapy. Strategic policy initiatives must address systemic barriers, promoting health equity and sustainable research funding. While the complexity of cancer biology and systemic challenges are formidable, ongoing scientific progress and collaborative efforts inspire hope for breakthroughs that can transform cancer diagnosis, treatment, and survival outcomes worldwide.
    Keywords:  advanced approaches for cancer progression; cancer; cancer stem cells; deep molecular mechanisms in cancer; determinism and indeterminism in cancer; drug resistance; epigenetic heterogeneity; hereditary malignancies; novel approaches in studying cancer; tumor heterogeneity; tumor microenvironment
    DOI:  https://doi.org/10.3390/cancers17132102
  24. bioRxiv. 2025 Jun 12. pii: 2025.06.10.658707. [Epub ahead of print]
    Unbiased recording of clonal potency reveals species-specific regulation of mammalian intestine.
    Mirazul Islam, Matthew E Bechard, Yilin Yang, Alan J Simmons, Yanwen Xu, James N Higginbotham, Ping Zhao, Zheng Cao, Naila Tasneem, Sarah E Glass, Nicholas O Markham, Frank Revetta, Marisol A Ramirez-Solano, Qi Liu, Jeffrey L Franklin, Ken S Lau, Robert J Coffey.
      The mammalian intestine regenerates rapidly after damage, yet the clonal dynamics and species-specific regulation of different populations remain poorly understood. Here we used synthetic or naturally occurring DNA alterations to reconstruct clonal histories of the mouse and human intestinal epithelium at single-cell resolution. In mice, we uncovered the clonal architecture of different cell types and their roles in regeneration, supporting a hierarchical regenerative response model. We identified a rare embryonic precursor population that persisted in the adult and was crucial for regeneration after irradiation. This population was marked by Tob2, which is required for nuclear transport of Ascl2. A parallel clonal analysis of 65 human colonic biopsies revealed secretory lineage bias and an age-associated decline in clonal diversity in the distal colon. Unlike highly proliferative murine Lgr5+ stem cells, human LGR5+ cells were found largely quiescent, revealing species-specific difference in clonal potency, and suggesting a distinct regulation of intestinal stemness.
    DOI:  https://doi.org/10.1101/2025.06.10.658707
  25. Nat Biotechnol. 2025 Jul 16.
    Topological velocity inference from spatial transcriptomic data.
    Yichen Gu, Jialin Liu, Kun H Lee, Chen Li, Lu Lu, Jaimee Moline, Renxiang Guan, Joshua D Welch.
      Incorporating space and time into models of cell fate transition will be a key step toward characterizing how interactions among neighboring cells, local niche factors and cell migration contribute to tissue development. Here we propose Topological Velocity Inference (TopoVelo), a model for jointly inferring spatial and temporal dynamics of cell fate transition from spatial transcriptomic data. TopoVelo extends the RNA velocity framework to model single-cell gene expression dynamics of an entire tissue with spatially coupled differential equations. TopoVelo estimates cell velocity from developing mouse cerebral cortex, learns interpretable spatial cell state dependencies that correlate with the expression of ligand-receptor genes and reveals spatial signatures of mouse neural tube closure. Finally, we generate Slide-seq data from an in vitro model of human development and use TopoVelo to study the spatial patterns of early differentiation. Our work introduces a new dimension into the study of cell fate transitions and lays a foundation for modeling the collective dynamics of cells comprising an entire tissue.
    DOI:  https://doi.org/10.1038/s41587-025-02688-8
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