Natural killer (NK) cells are critical components of the innate immune system, renowned for their ability to recognize and eliminate malignant and infected cells without prior sensitization. NK cell immunotherapy encompasses various approaches, including adoptive transfer of ex vivo expanded NK cells, cytokine stimulation to enhance their activity, and genetic modifications to improve persistence and specificity. CREM is a cAMP-responsive transcription factor that modulates gene expression in response to receptor- and cytokine-driven signaling. Recent evidence now shows that IL-15 and CAR stimulation rapidly induce CREM in activated NK cells. Rafei (Nature 643:1076-1086, 2025) further demonstrated in CAR-NK models that CREM functions as a regulatory checkpoint limiting NK cell cytotoxicity and cytokine production, while its relevance in resting/native NK cells remains to be established. The CREM-IL-15 signaling axis has emerged as a pivotal regulator of NK cell biology, influencing their development, activation, and longevity. IL-15 is a critical cytokine for NK cell survival, proliferation, and functional maturation. Understanding this axis is vital, as it offers insights into mechanisms that sustain NK cell activity and those that lead to functional exhaustion, thereby informing strategies to enhance therapeutic efficacy. A central challenge in NK cell immunotherapy is balancing cellular persistence with functional exhaustion. Persistent NK cell activity is desirable for sustained tumor control; however, prolonged activation often results in cellular exhaustion characterized by diminished cytotoxicity and cytokine production. This paradox hampers the long-term success of NK cell-based treatments. The CREM-IL-15 axis plays a complex role in this dynamic, potentially promoting NK cell survival and persistence while also contributing to exhaustion under certain conditions. Deciphering the molecular underpinnings of this paradox is essential for developing interventions that maintain NK cell functionality over time, thereby improving therapeutic outcomes in cancer patients. CREM is a transcription factor induced rapidly by both CAR activation (via immunoreceptor tyrosine-based activation motifs, or ITAMs) and IL-15 signaling. It binds to DNA sites to repress genes involved in cytotoxicity, metabolism, and proliferation. IL-15, a cytokine that promotes NK cell expansion and survival, paradoxically upregulates CREM through the PKA–CREB pathway (cAMP-dependent protein kinase activating CREB, which then drives CREM expression). IL-15 enhances NK persistence initially but triggers CREM-mediated repression, leading to functional decline. Single-cell RNA sequencing (scRNA-seq) and chromatin immunoprecipitation (ChIP-seq) show CREM closes chromatin at key loci (e.g., for MYC targets, MTORC1 signaling, and effector genes like GZMB and IFNG), enriching exhaustion-associated motifs (e.g., ETS family). It integrates signals from CAR ITAMs (STAT-independent) and IL-15 (via JAK–STAT3/5 and PKA). [Image: see text]
Since its inception, synthetic biology has relied on linear genetic modifications to treat living cells as biological counterparts to silicon microchips and computer-aided manufacturing. This paradigm is deeply rooted in the historical frameworks of Turing, Boole, and von Neumann, whose theoretical models remarkably anticipated the computational nature of the central dogma and native genetic operons. However, forcing living cells to strictly conform to the rigid, deterministic constraints of human software ignores a fundamental architectural disconnect: the dynamic, stochastic reality of the cellular cytoplasm and the higher-order 3D organization of the genome, which frequently lead to context-dependent circuit failures. In this Perspective, I argue that forcing living biology to mimic nonliving silicon machinery is neither biologically rational nor practically aspirational. Instead, the true paradigm of cellular programming and engineering lies in steering biological complexity under predictable rules to achieve capabilities that neither wild cells nor digital computers can fulfill alone-such as cancer-destroying circuits, explosive-detecting plants, and inflammation-recording probiotics. Crucially, this programmable oversight can be reinforced by constructing bio-physical hybrid entities that integrate nonliving materials with living cells. This is already manifested in interfacing organisms with semiconductor shells, silicon nanowires, or intracellular polymer hydrogels to create "cyborg cells" with augmented metabolic or synthetic functions. Ultimately, the future of engineering biology relies on treating life's fluid, dynamic architecture not as a design defect, but as a core computational asset. Aligned with this quest to optimize cell programming and engineering, biosafety approaches like biocontainment must be implemented to mitigate the environmental and ethical risks associated with deploying engineered organisms into ecosystems or human hosts.
Outcomes in squamous cell carcinomas (SCCa) of the head and neck, esophagus, and lungs are increasingly linked to the complex interplay between social determinants of health (SDoH) and biological pathways. The emerging field of social genomics provides mechanistic insight into how the environmental and socioeconomic conditions may influence tumor biology through stress-mediated pathways, epigenetic modifications, and altered gene expression. This review explores the role of adverse socioeconomic conditions such as neighborhood deprivation in shaping SCCa outcomes and the potential underlying mechanisms. In response to chronic stress, hypothalamic-pituitary-adrenal (HPA) axis and sympathetic nervous system become activated, leading to dysregulated immune signaling and proinflammatory gene expression pattern collectively known as the Conserved Transcriptional Response to Adversity (CTRA). We discuss epigenetic modifications including DNA methylation (DNAm), histone modification, and micro RNA (miRNA) dysregulation as potential mediators of these stress-related effects. Studies show that SCCa may have distinct race- and neighborhood-specific DNAm patterns including differential methylation of PAX5, HOXA7, and TFPI genes, and altered expression of xenobiotic metabolism genes regulated by Nrf2, a major stress response transcription factor. Therapeutic strategies targeting these biological mediators including β-adrenergic blockers, DNA methyltransferase inhibitors (e.g., azacytidine, decitabine), histone deacetylase inhibitors (e.g., vorinostat), and BET inhibitors have shown variable efficacy in preclinical and clinical SCCa models. Incorporating social context into tumor genomic analysis through geospatial modeling and neighborhood epigenomic profiling may offer a novel opportunity for identifying population-level cancer risk patterns and therapeutic targets. Social genomics provides a deeper understanding of the interaction of socio-environmental exposures with the epigenome and tumor biology influencing disparities in SCCa outcomes. Future research should integrate geospatial and multi-omics data to inform personalized cancer prevention and treatment strategies.
Bone is a multicellular organ that is the site of complex pathophysiological events (such as cancer). 3D confocal and multiphoton microscopy, followed by manual analysis and quantification, allow the identification of molecular, cellular, and tissue mechanisms in their original context, enabling the investigation of spatial biology at subcellular level. The automation of these analyses is becoming increasingly important due to their time-consuming nature, lack of standardization, and inter-subject variability. Deep learning applied to image analysis could overcome current limitations and optimize preclinical research. This includes automatic semantic segmentation of bone cells (osteoblasts, osteoclasts, and blood vessels) and mineral component, followed by parameter extraction and quantification. Accordingly, fluorescence microscopy images were generated, pre-processed, and fed (total 21,395 images: 17,104 for training, 4291 for validation) into a neural network-based architecture named Bo-Net. The fully automatic Bo-Net achieved strong performance across the tested metrics and segmentation accuracy similar to experienced biologists (R = 0.81-0.99 for parameters tested) and improved analysis time from days to seconds in a variety of experimental conditions, confirming its relevance in different biologically relevant contexts. As a result, a fully automated, yet reliable, tool to optimize the analysis of multiparametric fluorescence microscopy images available to the bone research community was generated.
Microenvironment remodelling impacts tumour growth and metastasis, but whether remodelling promotes pre-malignant clonal fitness remains unknown. Here, using single-cell RNA-sequencing of the bone-marrow microenvironment in a mouse model of DNMT3A-mutant clonal haematopoiesis (CH), we identify mesenchymal stromal cells (MSCs) in a molecular state of cellular senescence. Elevated bone-marrow MSC senescence is also observed in humans with CH driven by several common somatic mutations. MSC senescence is induced by mutant haematopoietic cells in a contact-independent manner through production of soluble factors including TNF-α and IL-6. These cytokines activate a Stat3-driven pathway that is necessary and sufficient for MSC senescence induction. Genetic or pharmacological depletion of senescent non-haematopoietic cells reduces the burden of CH and delays progression to myeloid neoplasia. Our findings show that microenvironment remodelling modifies pre-malignant clonal fitness and identifies disruption of the crosstalk between pre-malignant cells and their niche as a cancer prevention strategy.
Yes-associated protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ) (YAP/TAZ) are key transcriptional coregulators that govern mammalian cell fate through complex epigenetic mechanisms. As core effectors of the Hippo signaling pathway, they integrate diverse cellular signals-including those mechanical, metabolic, or biochemical in nature-to control lineage specification, organ development, and tissue homeostasis. Although they have been traditionally known for their roles in the control of organ size and tumorigenesis, more recent evidence has revealed their function as important epigenetic modulators that reshape chromatin landscapes to direct cell fate transitions across multiple tissue contexts. Through interactions with chromatin-modifying complexes, the transcriptional machinery, and lineage-specific factors, YAP/TAZ coordinate enhancer activation, superenhancer formation, and chromatin looping to establish transcriptional programs essential for cellular identity. This work reviews the current understanding of YAP/TAZ-mediated epigenetic regulation and examines their tissue-specific roles. We propose a unified mechanistic framework by which the level of YAP/TAZ activity determines enhancer landscapes that favor either differentiated or progenitor-like cellular states, providing a potential basis for applications to regenerative medicine and therapeutic interventions.
Enhancer of zeste homolog 2 (EZH2) is a key epigenetic regulator implicated in tumor progression; however, its expression pattern and subcellular localization across different stages of endometrial carcinogenesis remain incompletely characterized. This study evaluated EZH2 expression in two biologically distinct endometrial carcinoma cell lines (Ishikawa and MFE-319) and in archived human endometrial tissues representing proliferative and secretory endometrium, hyperplasia, and Type I and Type II endometrial carcinomas. Histopathological evaluation was performed using hematoxylin and eosin staining. EZH2 expression was assessed by immunocytochemistry and Western blot analysis in the cell lines and by immunohistochemistry in tissue specimens, while apoptosis was evaluated by TUNEL assay in tissue samples. MFE-319 cells demonstrated significantly higher EZH2 expression than Ishikawa cells (H-score: 352.9 ± 78.9 vs. 137.6 ± 31.5, p < 0.0001), and Western blot analysis confirmed the same direction of change. Among tissue specimens, the highest EZH2 immunoreactivity was observed in Type II endometrial carcinoma (366.0 ± 63.7), with significantly higher expression than proliferative endometrium (231.5 ± 59.3), secretory endometrium (190.5 ± 52.4), and hyperplasia without atypia (261.0 ± 56.9), whereas no significant differences were detected among several intermediate histopathological groups. Nuclear localization of EZH2 became more prominent in atypical hyperplasia and carcinoma tissues. Apoptotic indices were significantly higher in both Type I and Type II carcinomas than in normal endometrium and hyperplasia groups, representing an association with increased EZH2 expression rather than evidence of a direct mechanistic relationship. These findings demonstrate that EZH2 expression differs across histopathological categories of endometrial lesions, with the highest expression observed in Type II endometrial carcinoma. The observed predominance of nuclear EZH2 in atypical hyperplasia and carcinoma further supports its association with aggressive tumor biology, although additional functional and clinicopathological studies are required to establish its clinical and biological significance.
Once regarded solely as an intermediate of the tricarboxylic acid (TCA) cycle involved in energy production, fumarate has now emerged as a pivotal immunometabolite with far-reaching effects on inflammatory signaling and immune cell fate. This review comprehensively delineates the dual nature of fumarate, which functions as a context-dependent rheostat of inflammation. Intracellular fumarate levels are tightly regulated by enzymatic activity, transport systems, and exogenous sources, including the pharmacological agent dimethyl fumarate (DMF). Fumarate can covalently modify critical cysteine residues in proteins through a process known as succination. Importantly, DMF acts at supraphysiological concentrations and may engage mechanisms distinct from those associated with endogenously accumulated fumarate. This unique post-translational modification enables fumarate to directly modulate key signaling pathways, including nuclear factor kappa B (NF-κB), nuclear factor erythroid 2-related factor 2 (NRF2), hypoxia-inducible factor 1-alpha (HIF-1α), Janus kinase/signal transducer and activator of transcription (JAK-STAT), and the NLR family pyrin domain-containing 3 (NLRP3) inflammasome, thereby orchestrating a broad anti-inflammatory program. We further examine how fumarate reshapes the functional phenotypes of macrophages, dendritic cells, T cells, and B cells, ultimately skewing immune responses toward tolerance and resolution. Crucially, this review distinguishes among the physiological roles of endogenous fumarate, the pathological consequences of fumarate accumulation resulting from fumarate hydratase (FH) deficiency, and the pharmacological actions of exogenous fumarate esters. Conversely, dysregulated fumarate metabolism, as observed in conditions such as hereditary leiomyomatosis and renal cell carcinoma (HLRCC) and systemic lupus erythematosus, can paradoxically promote pathological inflammation. The successful clinical translation of fumarate esters, particularly DMF, for the treatment of multiple sclerosis and psoriasis underscores their therapeutic potential. By synthesizing recent advances in fumarate biology, this review not only elucidates its role as a fundamental link between cellular metabolism and immunity but also highlights future directions for targeting fumarate-associated pathways in a broad spectrum of chronic inflammatory diseases.
Blood can clot into anomalous, fibrinolysis-resistant forms that arise from prothrombotic seeding areas, including damaged cellular debris and membrane-derived surfaces, giving rise to what we have termed fibrinaloid microclot complexes (colloquially: microclots). Their proteolytic resistance is due in part to the fact that they are amyloid in nature, and they can also entrap inhibitors of proteolysis. They consist of a variety of proteins besides the expected fibrin, and are highly enriched for other amyloidogenic proteins (in contrast to normal clots, whose proteome largely reflects the soluble plasma proteome). They also contain DNA in the form of neutrophil extracellular traps (NETs). Importantly, fibrinaloid microclot complexes are heterogeneous structures comprising multiple phenotypic forms, including those that nucleate and grow on cellular debris such as damaged membranes, microparticles, and immune-derived material. We consider that these debris-associated complexes can act as catalytic scaffolds that recruit fibrin(ogen) and inflammatory molecules, thereby amplifying amyloidogenic transformation and prothrombotic activity. Fibrinaloid microclot complexes have been reported in a widening range of chronic inflammatory and thrombo-inflammatory diseases in which they have been sought, and are highly enriched for amyloidogenic proteins. Additionally, the thrombi extracted from ischaemic stroke also contain proteins in an amyloid form. One mechanism that explains how such macroclots can form and block arteries larger than any leading to them is that this occurs via the accretion of microclots that already contain amyloid. We here show that these microclots exhibit a classical 'apple-green' birefringence when stained with the dye Congo red. It is now important to determine whether inhibiting amyloid-forming clot transitions has therapeutic value.
Red blood cell (RBC) alloimmunization in pregnancy remains a major cause of hemolytic disease of the fetus and newborn (HDFN). Multiple maternal alloantibodies are uncommon and present significant diagnostic, and transfusion challenges. We report a case of a 35-year-old gravida, with anti-D, anti-C, anti-Fya, and anti-M alloantibodies detected at 10 weeks gestation. Initial titers of anti-D and anti-C were low and stable under serial monitoring. Non-invasive fetal genotyping confirmed an RHD-positive fetus. Following routine maternal vaccination against influenza (28 weeks), pertussis (30 weeks), and RSV (32 weeks), a rapid rise in anti-D and anti-C titers was observed at 31-32 weeks, accompanied by increased serologic reactivity of anti-Fya and anti-M. Middle cerebral artery peak systolic velocity (MCA-PSV) rose to 1.7 MoM, indicating fetal anemia. Two intrauterine transfusions with antigen-negative RBCs were performed. The patient delivered at 37 weeks. The neonate required phototherapy, IVIG, and transfusion support but had a favorable outcome. The temporal association between vaccination and antibody escalation raised the question of immune modulation. Although molecular mimicry is unlikely, non-specific polyclonal immune activation with bystander stimulation of memory B cells may represent a biologically plausible mechanism. However, causality cannot be established. This case highlights the dynamic nature of multiple maternal alloimmunizations, the critical role of serial monitoring and logistical challenges of providing antigen-negative blood for IUT.
Extracellular vesicles (EVs) originating from bacteria and gut microbiota have recently been recognized as pivotal agents in the communication between host and microbes, exhibiting considerable promise as innovative biomarkers and therapeutic instruments in the realm of oncology. These nanoscale vesicles encapsulate a heterogeneous array of molecular constituents, including metabolites, proteins, nucleic acids, and toxins, which possess the capacity to influence tumor proliferation, apoptosis, immune responses, and metastasis. Recent investigations underscore their bifunctional nature: specific bacterial EVs can facilitate oncogenesis by altering signaling cascades such as BRCA1/EXO1/TP53BP1 or TGF-β1/Smad, while others may suppress tumor growth through the induction of oxidative stress, mitophagy, or the activation of antitumor immunity via STING or cGAS pathways. The metabolomic and molecular characterizations of bacterial and fecal EVs afford a distinctive, non-invasive perspective into tumor biology and the interactions between host and microbiome. Sophisticated diagnostic methodologies, encompassing targeted metabolomics, high-throughput sequencing, and flow cytometry-based characterization of EVs, have enabled the discovery of EV-derived cancer biomarkers with exceptional specificity and sensitivity. Moreover, engineered EVs that transport therapeutic agents, including prodrugs, microRNAs, or photosensitizers, exhibit significant anticancer efficacy in preclinical experimental models. This review consolidates contemporary understanding regarding the molecular mechanisms, diagnostic capabilities, and therapeutic implications of bacterial and gut microbiota-derived EVs in the context of cancer.
Computational simulations of tumor evolution are increasingly used to infer the rules underlying cancer growth. To make reliable inferences, such models must be able to reflect the properties of real tumors. Recent work has shown that lung tumors undergo frequent and late subclonal expansions, which are associated with poor prognosis. This paper tests three candidate simulations of three-dimensional tumor growth, which make different assumptions about the nature of competition between cells, for their ability to replicate these late expansions. The study identifies a computationally-efficient model which can produce multi-region sequencing data realistic to lung tumors. This model assumes two distinct stages of growth, with the second stage involving local competition for space and resources within and between small tissue areas in a fixed-size tumor. When inferring the model-specific fitness effect of driver mutations in a large cohort of lung cancers, the study finds that inference pipelines based on a two-stage model imply much larger selection effects than those based on single-stage models, driven by model-specific assumptions about the practical consequences of selection strength. This work emphasizes the importance of model assumptions to the results of tumor-specific, simulation-based inferences.
MicroRNAs (miRNAs) are small non-coding RNA molecules essential for growth and development in eukaryotes. In plants, the master gene DICER-LIKE 1 (DCL1) catalyzes the biogenesis of miRNAs by processing double-stranded precursors that give rise to mature miRNAs. We sought to understand the function and evolution of microRNAs using Marchantia polymorpha, a model bryophyte that allows comparative approaches to infer characteristics of the ancestral land plant. We functionally characterized loss-of-function mutants of MpDCL1 a generated by means of CRISPR-Cas9-mediated genomic edition and the miR166/CLASS III HD-ZIP regulatory circuit in Marchantia polymorpha. We report that MpDCL1a is required for the biogenesis of miRNAs and uncovered a central role for miR166/Homeodomain Zipper Class III-regulated auxin synthesis in the specification of cell identity, patterning, meristem function, laminar expansion, and the development of the body in the last common ancestor of the bryophytes and vascular plants. Our findings indicate that DCL1, Class III HD-ZIP, miR166, and auxin functioned in the development of the body of the last common ancestor of extant land plants and provide a novel working framework to interrogate the basic principles of cell specification and patterning in plants.
A library of N6-modified adenosine derivatives (compounds 7-36) was synthesized via a one-step reaction of 6-chloro- or 2-amino-6-chloro-(β-D-ribofuranosyl)-9H-purine with primary or secondary amines. The structures of selected compounds (14, 31, 34) were confirmed by single-crystal X-ray diffraction, revealing diverse crystal packing motifs and hydrogen-bonding networks. Biological evaluation demonstrated a broad range of cytotoxic activities across a panel of cancer and non-cancer cell lines, ranging from highly potent to non-toxic derivatives. Structure-activity relationship analysis revealed that the biological properties of the synthesized compounds were strongly influenced by the nature of the N6 substituent, with distinct structural features governing anticancer and antiviral activities. Several compounds (21, 22, 28, 30, and 32) markedly reduced cancer cell viability, with compound 28 exhibiting the highest potency across multiple solid tumor models. Importantly, compound 28 induced apoptosis, suppressed proliferation, and rapidly decreased cell viability in both HCT116 and HCT116 p53-/- colorectal carcinoma cells, indicating p53-independent activity. In contrast, cladribine displayed pronounced p53 dependence, promoting apoptosis primarily in p53-proficient cells and inducing a senescence-like phenotype rather than rapid cell death. Antiviral screening identified compounds 22, 25, and 35 as promising inhibitors of human parainfluenza virus type 3 (HPIV-3), whereas compound 12 exhibited the highest activity and selectivity against human adenovirus type 5 (AdV5). Collectively, these findings identify N6-modified adenosines as a promising class of compounds for developing anticancer agents with p53-independent activity and reveal several derivatives as attractive scaffolds for further optimization toward antiviral agents targeting respiratory viruses.
Polycaprolactone (PCL) has emerged as a promising biomaterial for artificial heart applications due to its biodegradability and mechanical properties. However, its hydrophobic nature and limited biocompatibility pose challenges for cardiovascular applications, requiring optimal cell-material interactions. This study investigates the surface modification of silk fibroin-derived peptide/PCL coatings to enhance biocompatibility and cellular response for potential artificial heart applications. PCL substrates were blended with varying concentrations of silk fibroin-derived peptide (0.2%, 0.5%, and 1% w/v). Surface characterization was performed using water contact angle measurements, Fourier transform infrared spectroscopy (FTIR), and scanning electron microscopy. Biocompatibility was evaluated through cell viability assays and CD31 expression analysis. Silk fibroin-derived peptide incorporation significantly improved surface hydrophilicity, with contact angles decreasing from 78° (bare PCL) to 62° (1% silk fibroin-derived peptide). FTIR analysis confirmed successful incorporation of silk fibroin-derived peptides, showing characteristic PCL ester C=O absorption at ∼1720 cm-1 and concentration-dependent amide I contributions at ∼1630-1670 cm-1. Cell viability studies demonstrated enhanced cellular response with increasing silk fibroin-derived peptide concentration, particularly evident at day 7. CD31 expression analysis revealed improved endothelial marker expression, with the highest levels observed on 1% silk fibroin-derived peptide-incorporated substrates. The results demonstrate that silk fibroin blended to PCL significantly enhances biocompatibility through improved hydrophilicity and cellular interactions. Taken together, these preliminary results indicate that silk fibroin-derived peptide-incorporated PCL could represent a promising biomaterial platform for artificial heart applications, with the potential to improve endothelial compatibility and support endothelialization.
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Intratumoral microbiota, an important component of the tumor microenvironment (TME), have attracted increasing attention in cancer immunotherapy. Emerging evidence links intratumoral microbiota to tumor immune microenvironment (TIME) remodeling, immune cell infiltration, and heterogeneous responses to immune checkpoint inhibitors (ICIs). However, the overall research landscape, knowledge base, and hotspot evolution in this field remain insufficiently characterized. This study aimed to systematically map this field through bibliometric and visualization analyses. Publications up to November 8, 2025, were retrieved from the Web of Science Core Collection, Scopus, and PubMed. After screening, deduplication, and data standardization, bibliometric analyses were performed using R, VOSviewer, CiteSpace, and Scimago Graphica to examine publication trends, collaboration networks, knowledge bases, and keyword evolution. A total of 245 publications were included, comprising 141 original articles and 104 reviews. Since the first publication appeared in 2017, the field has grown exponentially, with a compound annual growth rate (CAGR) of 63.1% from 2017 to 2024. China ranked first in publication output, followed by the United States, while the United States occupied a more central position in total citations and international collaboration. Frontiers in Immunology was the most productive journal, whereas Science, Cell, and Nature constituted the major co-cited knowledge base, with 1,172, 729, and 670 co-citations, respectively. Keyword analysis showed that "intratumoral microbiota" was the most frequent term (90 occurrences), with excellent clustering quality (modularity Q = 0.6963; silhouette S = 0.9351). Research hotspots have gradually shifted from early explorations of gut microbiota, CD8+ T cells, and immune mechanisms toward immunotherapy resistance, microbial biomarkers, and microbiota-targeted interventions, including engineered bacteria, extracellular vesicles, and fecal microbiota transplantation. Research on intratumoral microbiota in cancer immunotherapy has rapidly developed into a distinct interdisciplinary field. Current hotspots are moving from mechanistic exploration toward response prediction and translational intervention. Future studies should prioritize standardized detection, spatial and multi-omics validation, and multicenter prospective evaluation to support the clinical translation of microbiota-based biomarkers and therapeutic strategies.