Artificial intelligence-rationalized balanced PPARα/γ dual agonism resets dysregulated macrophage processes in inflammatory bowel disease

A Living Organoid Biobank of Crohn's Disease Patients Reveals Distinct Clinical Correlates of Molecular Subtypes of Disease

Current clinical decision-making lacks reliable preclinical models to predict patient outcomes. Here, we establish patient-derived organoids (PDOs) as predictive tools in Crohn's disease (CD), a complex, heterogeneous disorder. Using a living biobank of adult stem cell-derived colonic-PDOs, we identified two molecular CD subtypes-Immune-Deficient Infectious CD ( IDICD ) and Stress and Senescence-Induced Fibrostenotic CD ( S2FCD )-each with distinct genomic, transcriptomic and functional profiles, along with paired therapeutics. By prospectively linking colonic PDO-derived phenotypes to real-world patient outcomes, we uncovered that while S2FCD associates with severe colonic disease, IDICD associates with severe ileal disease, prior ileocecal surgery, and future disease progression. This approach transforms PDOs from static descriptive models into dynamic tools that capture the past, present, and future of disease behavior and reveals their utility as patient-specific predictive platforms, extending their use beyond oncology to complex inflammatory diseases. Findings also suggest that colonic immune dysfunction may drive ileal-CD, independent of colonic involvement.

GRAPHICAL ABSTRACT

In Brief

In this work, Penrose et al. demonstrate the potential of patient-derived organoids (PDOs) as predictive tools in Crohn's disease (CD) that capture the past, present, and future of disease behavior, thereby advancing PDO-informed precision medicine beyond oncology into complex inflammatory diseases.

HIGHLIGHTS

A living PDO biobank identified two molecular CD subtypes with distinct functional phenotypes.PDO subtyping tracked severity of ileal disease, prior surgery and future disease progression.Colonic immune dysfunction may drive ileal-CD, independent of colonic involvement.Colonic CD-PDOs are dynamic platforms for outcome-deterministic therapeutic testing.

Advancing therapeutic frontiers: a pipeline of novel drugs for luminal and perianal Crohn's disease management

Crohn's disease (CD) is a chronic, complex inflammatory disorder of the gastrointestinal tract that presents significant therapeutic challenges. Despite the availability of a wide range of treatments, many patients experience primary non-response, secondary loss of response, or adverse events, limiting the overall effectiveness of current therapies. Clinical trials often report response rates below 60%, partly due to stringent inclusion criteria. Emerging therapies that target novel pathways offer promise in overcoming these limitations. This review explores the latest investigational drugs in phases I, II, and III clinical trials for treating both luminal and perianal CD. We highlight promising therapies that target known mechanisms, including selective Janus kinase inhibitors, anti-adhesion molecules, tumor necrosis factor inhibitors, and IL-23 selective inhibitors. In addition, we delve into novel therapeutic strategies such as sphingosine-1-phosphate receptor modulators, miR-124 upregulators, anti-fractalkine (CX3CL1), anti-TL1A, peroxisome proliferator-activated receptor gamma agonists, TGFBRI/ALK5 inhibitors, anti-CCR9 agents, and other innovative small molecules, as well as combination therapies. These emerging approaches, by addressing new pathways and mechanisms of action, have the potential to surpass the limitations of existing treatments and significantly improve CD management. However, the path to developing new therapies for inflammatory bowel disease (IBD) is fraught with challenges, including complex trial designs, ethical concerns regarding placebo use, recruitment difficulties, and escalating costs. The landscape of IBD clinical trials is shifting toward greater inclusivity, improved patient diversity, and innovative trial designs, such as adaptive and Bayesian approaches, to address these challenges. By overcoming these obstacles, the drug development pipeline can advance more effective, accessible, and timely treatments for CD.

FORWARD: A Learning Framework for Logical Network Perturbations to Prioritize Targets for Drug Development

Despite advances in artificial intelligence (AI), target-based drug development remains a costly, complex and imprecise process. We introduce F.O.R.W.A.R.D [ Framework for Outcome-based Research and Drug Development ], a network-based target prioritization approach and test its utility in the challenging therapeutic area of Inflammatory Bowel Diseases (IBD), which is a chronic condition of multifactorial origin. F.O.R.W.A.R.D leverages real-world outcomes, using a machine-learning classifier trained on transcriptomic data from seven prospective randomized clinical trials involving four drugs. It establishes a molecular signature of remission as the therapeutic goal and computes, by integrating principles of network connectivity, the likelihood that a drug's action on its target(s) will induce the remission-associated genes. Benchmarking F.O.R.W.A.R.D against 210 completed clinical trials on 52 targets showed a perfect predictive accuracy of 100%. The success of F.O.R.W.A.R.D was achieved despite differences in targets, mechanisms, and trial designs. F.O.R.W.A.R.D-driven in-silico phase '0' trials revealed its potential to inform trial design, justify re-trialing failed drugs, and guide early terminations. With its extendable applications to other therapeutic areas and its iterative refinement with emerging trials, F.O.R.W.A.R.D holds the promise to transform drug discovery by generating foresight from hindsight and impacting research and development as well as human-in-the-loop clinical decision-making.

Exploring the mechanism of enterotoxicity mediated by the microbiome-butyrate-PPAR axis in podophyllotoxin through the toxicological evidence chain (TEC) concept

Podophyllotoxin (PPT) is a lignan derived from the roots and stems of the Podophyllum plant. However, its enterotoxicity restricts its clinical application. The underlying mechanisms by which PPT exerts its action remain largely elusive. This study aimed to evaluate the molecular mechanisms underlying PPT-induced enterotoxicity utilizing the concept of toxicological evidence chain. Changes in body weight, behavior, and histopathological and biochemical markers in rats were observed. Additionally, microbiome, metabolome, and transcriptome analyses were integrated to identify potential microorganisms, metabolic markers, and major pathways using a co-occurrence network. Our findings suggested that PPT induced pathological changes in rats, including weight loss, diarrhea, and inflammation accompanied by increased levels of IFN-γ, IL-5, IL-6, GRO/KC, and IL-12p70. The decrease in butyrate levels in the PPT group may be related to the enrichment of Firmicutes. The reduction of butyrate levels may impair the expression of PPARγ, subsequently promoting Escherichia-Shigella proliferation. Additionally, the suppression of PPARs pathway may result in the increased production of inflammatory factors, contributing to enterotoxicity. This study offers a novel understanding of the molecular mechanisms underlying PPT-induced enterotoxicity, making a significant contribution to developing strategies to mitigate PPT toxicity and prevent associated diseases.

Impact of artificial intelligence on prognosis, shared decision-making, and precision medicine for patients with inflammatory bowel disease: a perspective and expert opinion

INTRODUCTION

Artificial intelligence (AI) is expected to impact all facets of inflammatory bowel disease (IBD) management, including disease assessment, treatment decisions, discovery and development of new biomarkers and therapeutics, as well as clinician-patient communication.

AREAS COVERED

This perspective paper provides an overview of the application of AI in the clinical management of IBD through a review of the currently available AI models that could be potential tools for prognosis, shared decision-making, and precision medicine. This overview covers models that measure treatment response based on statistical or machine-learning methods, or a combination of the two. We briefly discuss a computational model that allows integration of immune/biological system knowledge with mathematical modeling and also involves a 'digital twin', which allows measurement of temporal trends in mucosal inflammatory activity for predicting treatment response. A viewpoint on AI-enabled wearables and nearables and their use to improve IBD management is also included.

EXPERT OPINION

Although challenges regarding data quality, privacy, and security; ethical concerns; technical limitations; and regulatory barriers remain to be fully addressed, a growing body of evidence suggests a tremendous potential for integration of AI into daily clinical practice to enable precision medicine and shared decision-making.

PPARs/macrophages: A bridge between the inflammatory response and lipid metabolism in autoimmune diseases

Autoimmune diseases (AIDs) are a collection of pathologies that arise from autoimmune reactions and lead to the destruction and damage of the body's tissues and cellular components, ultimately resulting in tissue damage and organ dysfunction. The anti-inflammatory effects of the peroxisome proliferator-activated receptor (PPAR), a pivotal regulator of lipid metabolism, are crucial in the context of AIDs. PPAR mitigates AIDs by modulating macrophage polarization and suppressing the inflammatory response. Numerous studies have demonstrated the crucial involvement of lipid metabolism and phenotypic switching in classically activated (M1)/alternatively activated (M2)-like macrophages in the inflammatory pathway of AIDs. However, the precise mechanism by which PPAR, a critical mediator between of lipid metabolism and macrophage polarization, regulates macrophage polarization remains unclear. This review aimed to clarify the role of PPAR and macrophages in the triangular relationship among AIDs, lipid metabolism, and inflammatory response, and aims to summarize the mechanism of the PPAR-mediated macrophage activation and polarization, which impacts the progression and development of AIDs.

Machine learning identifies signatures of macrophage reactivity and tolerance that predict disease outcomes

BACKGROUND

Single-cell transcriptomic studies have greatly improved organ-specific insights into macrophage polarization states are essential for the initiation and resolution of inflammation in all tissues; however, such insights are yet to translate into therapies that can predictably alter macrophage fate.

METHOD

Using machine learning algorithms on human macrophages, here we reveal the continuum of polarization states that is shared across diverse contexts. A path, comprised of 338 genes accurately identified both physiologic and pathologic spectra of "reactivity" and "tolerance", and remained relevant across tissues, organs, species, and immune cells (>12,500 diverse datasets).

FINDINGS

This 338-gene signature identified macrophage polarization states at single-cell resolution, in physiology and across diverse human diseases, and in murine pre-clinical disease models. The signature consistently outperformed conventional signatures in the degree of transcriptome-proteome overlap, and in detecting disease states; it also prognosticated outcomes across diverse acute and chronic diseases, e.g., sepsis, liver fibrosis, aging, and cancers. Crowd-sourced genetic and pharmacologic studies confirmed that model-rationalized interventions trigger predictable macrophage fates.

INTERPRETATION

These findings provide a formal and universally relevant definition of macrophage states and a predictive framework (http://hegemon.ucsd.edu/SMaRT) for the scientific community to develop macrophage-targeted precision diagnostics and therapeutics.

FUNDING

This work was supported by the National Institutes for Health (NIH) grant R01-AI155696 (to P.G, D.S and S.D). Other sources of support include: R01-GM138385 (to D.S), R01-AI141630 (to P.G), R01-DK107585 (to S.D), and UG3TR003355 (to D.S, S.D, and P.G). D.S was also supported by two Padres Pedal the Cause awards (Padres Pedal the Cause/RADY #PTC2017 and San Diego NCI Cancer Centers Council (C3) #PTC2017). S.S, G.D.K, and D.D were supported through The American Association of Immunologists (AAI) Intersect Fellowship Program for Computational Scientists and Immunologists. We also acknowledge support from the Padres Pedal the Cause #PTC2021 and the Torey Coast Foundation, La Jolla (P.G and D.S). D.S, P.G, and S.D were also supported by the Leona M. and Harry B. Helmsley Charitable Trust.

Peroxisome Proliferator-Activated Receptor-Targeted Therapies: Challenges upon Infectious Diseases

Peroxisome proliferator-activated receptors (PPARs) α, β, and γ are nuclear receptors that orchestrate the transcriptional regulation of genes involved in a variety of biological responses, such as energy metabolism and homeostasis, regulation of inflammation, cellular development, and differentiation. The many roles played by the PPAR signaling pathways indicate that PPARs may be useful targets for various human diseases, including metabolic and inflammatory conditions and tumors. Accumulating evidence suggests that each PPAR plays prominent but different roles in viral, bacterial, and parasitic infectious disease development. In this review, we discuss recent PPAR research works that are focused on how PPARs control various infections and immune responses. In addition, we describe the current and potential therapeutic uses of PPAR agonists/antagonists in the context of infectious diseases. A more comprehensive understanding of the roles played by PPARs in terms of host-pathogen interactions will yield potential adjunctive personalized therapies employing PPAR-modulating agents.

The role of cholesterol and mitochondrial bioenergetics in activation of the inflammasome in IBD

Inflammatory Bowel Disease (IBD) is characterized by a loss of intestinal barrier function caused by an aberrant interaction between the immune response and the gut microbiota. In IBD, imbalance in cholesterol homeostasis and mitochondrial bioenergetics have been identified as essential events for activating the inflammasome-mediated response. Mitochondrial alterations, such as reduced respiratory complex activities and reduced production of tricarboxylic acid (TCA) cycle intermediates (e.g., citric acid, fumarate, isocitric acid, malate, pyruvate, and succinate) have been described in in vitro and clinical studies. Under inflammatory conditions, mitochondrial architecture in intestinal epithelial cells is dysmorphic, with cristae destruction and high dynamin-related protein 1 (DRP1)-dependent fission. Likewise, these alterations in mitochondrial morphology and bioenergetics promote metabolic shifts towards glycolysis and down-regulation of antioxidant Nuclear erythroid 2-related factor 2 (Nrf2)/Peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α) signaling. Although the mechanisms underlying the mitochondrial dysfunction during mucosal inflammation are not fully understood at present, metabolic intermediates and cholesterol may act as signals activating the NLRP3 inflammasome in IBD. Notably, dietary phytochemicals exhibit protective effects against cholesterol imbalance and mitochondrial function alterations to maintain gastrointestinal mucosal renewal in vitro and in vivo conditions. Here, we discuss the role of cholesterol and mitochondrial metabolism in IBD, highlighting the therapeutic potential of dietary phytochemicals, restoring intestinal metabolism and function.

The PPARα Regulation of the Gut Physiology in Regard to Interaction with Microbiota, Intestinal Immunity, Metabolism, and Permeability

Peroxisome proliferator-activated receptor alpha (PPARα) is expressed throughout the mammalian gut: in epithelial cells, in the villi of enterocytes and in Paneth cells of intestinal crypts, as well as in some immune cells (e.g., lamina propria macrophages, dendritic cells) of the mucosa. This review examines the reciprocal interaction between PPARα activation and intestinal microbiota. We refer to the published data confirming that microbiota products can influence PPARα signaling and, on the other hand, PPARα activation is able to affect microbiota profile, viability, and diversity. PPARα impact on the broad spectrum of events connected to metabolism, signaling (e.g., NO production), immunological tolerance to dietary antigens, immunity and permeability of the gut are also discussed. We believe that the phenomena described here play a prominent role in gut homeostasis. Therefore, in conclusion we propose future directions for research, including the application of synthetic activators and natural endogenous ligands of PPARα (i.e., endocannabinoids) as therapeutics for intestinal pathologies and systemic diseases assumed to be related to gut dysbiosis.

Partial Synthetic PPARƳ Derivative Ameliorates Aorta Injury in Experimental Diabetic Rats Mediated by Activation of miR-126-5p Pi3k/AKT/PDK 1/mTOR Expression

Type 2 diabetes mellitus (T2D) is a world wild health care issue marked by insulin resistance, a risk factor for the metabolic disorder that exaggerates endothelial dysfunction, increasing the risk of cardiovascular complications. Peroxisome proliferator-activated receptor PPAR) agonists have therapeutically mitigated hyperlipidemia and hyperglycemia in T2D patients. Therefore, we aimed to experimentally investigate the efficacy of newly designed synthetic PPARα/Ƴ partial agonists on a High-Fat Diet (HFD)/streptozotocin (STZ)-induced T2D. Female Wistar rats (200 ± 25 g body weight) were divided into four groups. The experimental groups were fed the HFD for three consecutive weeks before STZ injection (45 mg/kg/i.p) to induce T2D. Standard reference PPARƳ agonist pioglitazone and the partial synthetic PPARƳ (PIO; 20 mg/kg/BW, orally) were administered orally for 2 weeks after 72 h of STZ injection. The aorta tissue was isolated for biological ELISA, qRT-PCR, and Western blotting investigations for vascular inflammatory endothelial mediators endothelin-1 (ET-1), intracellular adhesion molecule 1 (ICAM-1), E-selectin, and anti-inflammatory vasoactive intestinal polypeptide (VIP), as well as microRNA126-5p and p-AKT/p-Pi3k/p-PDK-1/p-mTOR, endothelial Nitric Oxide Synthase (eNOS) immunohistochemical staining all are coupled with and histopathological examination. Our results revealed that HFD/STZ-induced T2D increased fasting blood glucose, ET-1, ICAM-1, E-selectin, and VIP levels, while decreasing the expression of both microRNA126-5p and p-AKT/p-Pi3k/p-PDK-1/p-mTOR phosphorylation. In contrast, the partial synthetic PPARƳ derivative evidenced a vascular alteration significantly more than reference PIO via decreasing (ET-1), ICAM-1, E-selectin, and VIP, along with increased expression of microRNA126-5p and p-AKT/p-Pi3k/p-PDK-1/p-mTOR. In conclusion, the partial synthetic PPARƳ derivative significantly affected HFD/STZ-induced T2D with vascular complications in the rat aorta.