The promise of TFEB has never been in doubt. The transcription factor controls the expression of hundreds of genes involved in lysosomal biogenesis and autophagy, the twin processes by which cells build new recycling machinery and degrade damaged components. When TFEB is active, it migrates into the nucleus and switches on the genetic program that keeps cellular clearance running. Boosting TFEB activity, researchers reasoned, could help cells cope with the buildup of toxic material that characterizes many diseases. The idea has attracted enormous attention: nearly 3,000 scientific publications now focus on TFEB, more than 90 percent of them appearing in the last decade alone. Experimental studies have explored TFEB activation as a strategy in lysosomal storage disorders, Parkinson’s disease, obesity and cancer, and the protein ranks among the priority targets of the Michael J. Fox Foundation’s Targets to Therapies initiative for Parkinson’s disease.

Yet a stubborn obstacle has kept TFEB from the clinic. Transcription factors as a class are notoriously difficult to target with drugs. They operate inside the nucleus, lack the well-defined enzymatic pockets that medicinal chemists prefer to bind, and are embedded in dense regulatory networks that are hard to manipulate selectively. No therapy specifically designed to activate TFEB has reached patients, despite years of effort. What was missing, essentially, was a handle: an upstream control point that could be pharmacologically tuned to dial TFEB activity up or down. The new study, coordinated by Gennaro Napolitano at TIGEM, provides exactly that. Rather than attacking TFEB itself, the researchers mapped the molecular machinery that senses lysosomal stress and switches TFEB on, revealing several proteins along the way that are far more amenable to drug development.

The scientific lineage of the work runs through Andrea Ballabio, former scientific director of TIGEM, whose research in 2009 first established TFEB as the master regulator of lysosomal function and cellular clearance. That discovery transformed lysosomal biology, recasting the lysosome from a static waste bin into a dynamically regulated system with its own genetic control hub. But one fundamental question remained open: how do cells actually detect that their lysosomes are malfunctioning, and how do they translate that signal into TFEB activation? The sensing step, the molecular bridge between lysosomal perturbation and the nuclear response, had never been fully described. Closing that gap was the central achievement of the new research, which involved collaborators at the University of Fribourg in Switzerland, UC Berkeley in the United States, the University of Rome Tor Vergata in Italy and the German Cancer Research Center (DKFZ) in Germany, with primary support from Fondazione Telethon and Fondazione AIRC.

The answer the team uncovered is a signaling cascade that begins at the lysosome itself. When lysosomal function is disturbed, the lysosomal proton pump known as v-ATPase, a molecular machine that acidifies the organelle’s interior, initiates the response. The stress signal is then transmitted through the adaptor protein TAX1BP1 to two enzymes, TBK1 and ULK1, which become activated. Once switched on, these kinases modify a protein called FNIP1, and this modification sets off a chain of events that releases TFEB to move from the cytoplasm into the nucleus. There, TFEB activates the genes that drive cellular recycling and lysosomal biogenesis. In effect, the cell possesses a dedicated alarm system for lysosomal trouble, wired through TBK1 and ULK1, and TFEB is the responder that answers the call.

“Researchers have known for years that TFEB plays a fundamental role in helping cells maintain their recycling machinery and adapt to stress,” says Alessandra Esposito, first author of the study. “What remained unclear was how cells sense lysosomal dysfunction and translate that signal into TFEB activation. Our work identifies the molecular players involved in this process and reveals a signaling pathway that had never been described before.” The identification of this axis, running from v-ATPase through TAX1BP1 and the TBK1 and ULK1 kinases to FNIP1 and finally TFEB, gives researchers a complete wiring diagram of the lysosomal stress response, and every component in that diagram is a potential point of pharmacological intervention.

The discovery is not only about boosting cellular recycling. The researchers also examined the pathway in the context of follicular lymphoma, a blood cancer in which mutations affecting ATP6V1B2, a component of the v-ATPase proton pump, are relatively common. They showed that these mutations cause persistent activation of TFEB, which in turn helps tumor cells survive and proliferate in nutrient-poor environments, a hallmark of the tumor microenvironment in lymphoma. In this setting, the newly mapped pathway works against the patient: cancer cells exploit the lysosomal stress response to adapt to scarcity and keep growing. That finding suggests a second therapeutic strategy, one of inhibition rather than activation. Drugs that block the TBK1-ULK1 signaling axis might deprive such tumors of their survival advantage, opening a potential avenue for treating follicular lymphoma and possibly other malignancies that depend on lysosomal reprogramming.

“Rather than targeting TFEB itself, our study identifies molecular regulators that control its activation,” Esposito explains. “This provides new entry points for the development of therapeutic strategies aimed at harnessing TFEB activity in disease.” The distinction matters enormously for drug development. Kinases such as TBK1 and ULK1 are enzymes with well-characterized active sites, and potent inhibitors of both already exist in the chemical biology toolkit. A pathway made of kinases and adaptor proteins is, from a medicinal chemistry standpoint, a far more tractable target than a transcription factor. By identifying the regulators upstream of TFEB, the study converts an aspirational goal, pharmacological control of the cell’s recycling master switch, into a concrete set of engineering problems that pharmaceutical researchers know how to approach.

“The identification of the TBK1/ULK1 pathway expands the therapeutic opportunities for modulating TFEB,” says Napolitano, the study’s lead investigator. “Because this mechanism acts upstream of TFEB, it could offer new opportunities not only in TFEB-dependent cancers but also in a broader spectrum of diseases where improving lysosomal function may be beneficial.” That broader spectrum is large. Lysosomal dysfunction lies at the heart of dozens of rare genetic diseases, collectively affecting a substantial number of patients worldwide, and has been implicated in common neurodegenerative disorders, metabolic conditions and aging itself. A single druggable pathway that modulates lysosomal clearance could therefore have applications that span from ultra-rare pediatric storage diseases to some of the most prevalent illnesses of old age.

The study, published under the title describing a TBK1-ULK1 signaling axis that couples lysosomal stress to TFEB activation, marks a turning point in a research story that began in 2009. For fifteen years, the field has known what TFEB does; now it knows how cells control it, and the control points are druggable. Translating that knowledge into medicines will take years of further work, from developing selective modulators of the pathway to testing them in disease models and, eventually, patients. But the direction is clear. By uncovering the molecular sensors and kinases that stand between lysosomal stress and the master regulator of cellular recycling, the TIGEM-led team has brought researchers a decisive step closer to turning one of lysosomal biology’s most celebrated discoveries into real therapies for rare genetic diseases, cancer and beyond.

Subject of Research: The TBK1-ULK1 signaling pathway that regulates TFEB activation in response to lysosomal stress

Article Title: Newly discovered pathway unlocks the therapeutic potential of TFEB

Article References: Newly discovered pathway unlocks the therapeutic potential of TFEB. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: TFEB, lysosomes, TBK1, ULK1, FNIP1, autophagy, lysosomal storage diseases, follicular lymphoma, v-ATPase, TAX1BP1, drug targets, TIGEM

Autophagy is the evolutionarily conserved process by which eukaryotic cells engulf their own cytoplasmic contents and deliver them to lysosomes for degradation. Long caricatured as a blunt recycling program switched on during starvation, it is now understood to be a highly selective operation that targets protein aggregates, damaged mitochondria, and invading microbes with remarkable precision. In the intestine, this matters enormously. The gut lining exists in a state of permanent negotiation with trillions of microbes, and the epithelial cells, Paneth cells, goblet cells, and immune populations that maintain the barrier all depend on autophagy to clear cellular debris, secrete antimicrobial peptides, and keep inflammatory signaling in check. When the machinery falters, the result is precisely the pathology seen in inflammatory bowel disease: bacterial persistence, epithelial death, and runaway cytokine production.

The review dissects the canonical pathway in three sequential phases. Initiation begins with the ULK1 kinase complex, composed of ULK1, ATG13, FIP200, and ATG101, which senses cellular energy status through its upstream regulators AMPK and mTOR. In intestinal epithelial cells, this regulatory node behaves in strikingly context-dependent ways. Under glucose deprivation, AMPK activation can suppress ULK1 and dampen autophagy, yet during energy crisis it also protects ULK1 from caspase-mediated degradation, preserving the cell’s capacity to recover. mTOR, frequently activated in inflammatory bowel disease by cytokines such as TNF-alpha and IL-6, does the opposite: it inhibits ULK1, crippling the clearance of intracellular pathogens and damaged organelles. ULK1 is further fine-tuned by ATG8-family proteins, with GABARAP and GABARAPL1 acting as positive regulators while LC3B and LC3C exert negative control, and its activity is modulated by post-translational modifications including ZDHHC13-mediated palmitoylation, which promotes its translocation to autophagosome formation sites.

The clinical consequences of ULK1 dysfunction are vividly illustrated by its relationship with ATG16L1, a Crohn’s disease susceptibility gene. Under nutrient deprivation or infectious stress, ULK1-mediated phosphorylation of ATG16L1 at serine 278 is essential for efficient xenophagy, the selective destruction of intracellular bacteria. But in patients carrying the ATG16L1 T300A variant, that same phosphorylation event triggers caspase-3-mediated cleavage of ATG16L1, destroying the protein and precipitating more severe inflammation. This single molecular interaction explains why T300A carriers are disproportionately susceptible to disease flares during infection. ULK1 signaling also protects the epithelial barrier by promoting the degradation of claudin-2, a pore-forming tight junction protein that is upregulated in active disease and linked to diarrhea, meaning that defective ULK1 activity can directly worsen barrier leakiness in genetically vulnerable individuals.

The elongation phase, during which the phagophore membrane expands and seals into a double-membraned autophagosome, is governed by the Beclin 1-VPS34 complex and the ATG12-ATG5-ATG16L1 conjugation system, which drives lipidation of LC3 into its membrane-bound LC3-II form. Here the review issues an important methodological warning: the widely used LC3-II/I ratio is ambiguous, since an elevated value may reflect either enhanced autophagosome formation or blocked downstream degradation. Interpreting it requires flux assays with lysosomal inhibitors such as bafilomycin A1. With that caveat, the evidence points to a Goldilocks principle. In interleukin-10-deficient mice, a reduced LC3-II/I ratio was restored by xylo-oligosaccharide supplementation, coinciding with decreased bacterial penetration and restored goblet cell function. Conversely, in several colitis models where the ratio was pathologically elevated, traditional formulations such as Huangkui Lianchang Decoction lowered it along with pro-inflammatory cytokines, and excessive autophagic activity damaged the interstitial cells of Cajal that coordinate intestinal motility. Both too little and too much elongation, it seems, sabotage the gut.

Perhaps the most clinically revealing section concerns termination. Counterintuitively, several major IBD risk variants do not impair the final fusion of autophagosomes with lysosomes at all. Cells carrying the T300A variant display normal LC3-II flux and SQSTM1 degradation during starvation, indicating intact fusion machinery. IRGM deficiency instead impairs autolysosomal acidification and cargo degradation during infection with adherent-invasive E. coli, a defect rescued by wild-type IRGM, while the MTMR3 risk variant suppresses early autophagosome formation without affecting degradation of those that do form. The pathophysiology, the authors conclude, resides not in a universal failure of the disposal system but in defective selective autophagy, particularly within specialized secretory cells.

That selective layer comprises three specialist pathways. Mitophagy, mediated by the PINK1-Parkin axis or receptors such as Nix/BNIP3L, clears depolarized mitochondria before they spill reactive oxygen species and mitochondrial DNA that activate the NLRP3 inflammasome. Its importance is cell-type specific: CD8-positive T cells and memory lymphocytes depend critically on mitophagy to sustain mitochondrial quality and fatty acid oxidation, whereas CD4-positive T cells tolerate its loss far better. In ulcerative colitis patients, the transcription factor ATF7, which directly activates PINK1 expression, is reduced in colonic mucosa and correlates negatively with disease severity. Yet mitophagy is a double-edged sword: Parkin can paradoxically worsen colitis by degrading the vitamin D receptor, and abnormally activated Piezo1 channels can drive mitochondrial calcium overload and ferroptosis through excessive mitophagy. ER-phagy, the second pathway, manages endoplasmic reticulum stress in protein-secreting Paneth and goblet cells, where the IRE1-alpha-XBP1 arm of the unfolded protein response supports mucin production under moderate stress but collapses into apoptosis and mucus layer disruption when chronically engaged. Xenophagy, the third, directly destroys intracellular bacteria, and its genetic disruption, whether through ATG16L1 T300A or a 20-kilobase IRGM deletion that impairs phagosome maturation in a dose-dependent manner, allows persistent bacterial survival, prolonged antigen exposure, and heightened risk of colitis-associated cancer.

Adding a further layer of complexity, the review catalogues the non-autophagic functions of autophagy-related genes. ATG16L1 influences epithelial sensitivity to interferon-gamma-induced apoptosis, secretory granule architecture, and NOD1/2-driven cytokine release through mechanisms that may operate independently of autophagosome formation, though the extent of that independence remains debated. ATG5 modulates Toll-like receptor signaling in B cells and antigen presentation in the thymus, while TRIM31-mediated surrogate autophagy can clear Shigella even without ATG5, and TRIM31 is downregulated by 45 percent in Crohn’s disease epithelium despite unchanged ATG5 mRNA. IRGM, meanwhile, binds the NLRP3 inflammasome and scaffolds the NOD2-ATG16L1 complex at bacterial entry sites through ubiquitin-dependent mechanisms that do not require full autophagic flux. These findings complicate any simple equation of autophagy gene variants with autophagy defects alone.

The therapeutic implications are already tangible. Infliximab and other TNF-alpha inhibitors restore xenophagic clearance of adherent-invasive E. coli and enhance autophagic flux in macrophages, yet patients carrying NOD2 or ATG16L1 risk alleles show accelerated drug clearance and higher relapse rates within six months. Ustekinumab, by contrast, appears to work through the STAT3-p62 axis of selective autophagy and retains effectiveness in T300A carriers, while the JAK1 inhibitor upadacitinib activates AMPK-driven protective autophagy and alleviates ER stress. The overarching message of the review is that autophagy in inflammatory bowel disease is neither hero nor villain but a context-dependent force: protective during acute inflammation, potentially pathogenic when chronically hyperactivated or suppressed, and exquisitely sensitive to cell type, genetic background, and microbial environment. Mapping that context, the authors argue, is the prerequisite for the next generation of autophagy-targeted precision therapies.

Subject of Research: The role of canonical and selective autophagy pathways in the pathogenesis of inflammatory bowel disease

Article Title: Canonical pathways and selective mechanisms of autophagy in inflammatory bowel disease

Article References: Lin, R., Xu, Z., & Zhi, M. (2026). Canonical pathways and selective mechanisms of autophagy in inflammatory bowel disease. Advanced Biotechnology, 4(1), Article 4. https://doi.org/10.1007/s44307-026-00094-y

Image Credits: AI Generated

DOI: 10.1007/s44307-026-00094-y

Keywords: autophagy, inflammatory bowel disease, Crohn's disease, ulcerative colitis, ATG16L1, ULK1, mitophagy, xenophagy, ER-phagy, IRGM, intestinal barrier, biologics