MYC proteins are classically viewed as oncoproteins because they act as DNA-bound transcription factors that drive characteristic gene expression programs. Building on this view, recent work has shown that MYC proteins engage in multiple protein complexes that resolve transcription-associated stress and that they function as both DNA- and RNA-binding proteins. These findings suggest that, through these activities, MYC proteins enhance the stress resilience of proliferating cells and enable tumor cells to sustain nonphysiological, oncogenic gene expression programs.
Metabolic plasticity and flexibility are key characteristics that allow cancer cells to adapt and thrive in different environments. Specifically, cancer cells can dynamically change the routing of metabolic pathways in response to environmental changes and adapt their metabolic activity depending on local nutrient availability. The tumor microenvironment (TME) plays crucial roles in cancer development and progression. It is now widely accepted that different stromal cells, as well as soluble factors, including metabolites, derived from the TME support cancer cell proliferation and survival and drive migration, invasion, and the formation of metastases. Some cancer types grow in the proximity of adipose tissue (AT), which is mostly composed of mature adipocytes, a specialized cell type responsible for the storage and controlled release of lipids. In response to specific stimuli released by cancer cells, adipocytes can transform into cancer-associated adipocytes (CAAs). CAAs release signaling molecules, and provide fatty acids to cancer cells and other cell types in the TME, which can then utilize these fatty acids as fuel. The interaction between cancer cells and adipocytes creates a dynamic cross-talk that promotes disease progression through multiple mechanisms. In this review, we aim to provide an overview of the main factors in the CAA-cancer cell cross-talk, with a focus on the metabolic consequences of this interaction.
Developmental pattern formation requires patterning cues to be converted into discrete, gene- and cell-specific regulatory outputs, but how this conversion is achieved remains unclear. We address this problem in Caenorhabditis elegans anterior-posterior patterning, where quantitatively asymmetric Wnt/β-catenin cues, namely anterior-enriched POP-1/TCF and posterior-enriched SYS-1/β-catenin, are decoded into binary, switch-like fate decisions. We show that these cues are resolved into embryo-wide binary regulatory outputs through ZIP-7/DBP, a transcription factor with stage-specific, lineage-wide posterior-exclusive expression that is essential for multiple posterior fate decisions. We define a model for this cue-to-decision decoding. At the zip-7 promoter, the transcription factor ZIP-8/NFIL3, which begins to be expressed during mid-embryogenesis prior to ZIP-7 onset, provides an activating input while recruiting POP-1 and SYS-1. POP-1 restrains this activity anteriorly, whereas the POP-1-SYS-1 complex promotes it posteriorly, thereby generating a binary pattern of zip-7 transcription. This recruitment-mediated promoter control couples Wnt/β-catenin cues to gene-specific transcriptional regulation and enables flexible spatiotemporal control of cue-dependent transcription. Genome-wide analyses further suggest that recruitment-mediated cotargeting may extend beyond zip-7 and point to additional candidate factors with similar recruitment functions, supporting a scalable framework for decoding patterning cues into context-specific regulatory decisions.
MYC-driven (MYC+) cancers are highly aggressive and often fatal. MYC dysregulation is a key event in these cancers, yet MYC overexpression alone is often insufficient to initiate or sustain tumorigenesis. Plasmocytoma variant translocation 1 (PVT1), a long noncoding RNA (lncRNA) adjacent to MYC on chromosome 8q24, is frequently co-amplified with MYC in many of these cancers. Our prior work showed that PVT1 potentiates MYC function, although the underlying mechanism has remained unclear. Here we show that, in addition to amplification with MYC, genomic rearrangements at PVT1 frequently involve unbalanced translocations that asymmetrically enrich 5'-PVT1 while depleting 3'-PVT1 The retained 5'-PVT1 region generates a circular RNA, CircPVT1, that encodes a novel protein we have named Firefox (FFX). We show that FFX is essential for MYC-mediated oncogenic signaling, as its depletion markedly reduces MYC protein abundance and transcriptional output. Mechanistically, FFX stimulates AKT-mTORC1 signaling and enhances cap-dependent translational and biosynthetic capacity, thereby establishing a self-reinforcing oncogenic circuit that amplifies MYC activity. Inducible depletion of FFX in vivo significantly impairs tumor growth in MYC+ xenograft models. These findings define FFX as a critical effector within the MYC-PVT1 locus and reveal a therapeutically actionable vulnerability in MYC+ cancers.
Genomic rearrangements can drive cancer through mechanisms that extend beyond classical oncogenic fusions such as BCR-ABL A substantial fraction of these events involve long noncoding RNAs (lncRNAs), yet their functional impact on tumorigenesis has remained largely opaque. The lncRNA plasmacytoma variant translocation 1 (PVT1), positioned adjacent to MYC at chromosome 8q24, is among the most frequently altered loci in MYC-driven (MYC+) cancers. We recently showed that PVT1 translocations produce a characteristic asymmetric architecture that preserves the 5'-PVT1 region, generating a circular RNA (CircPVT1) that encodes Firefox (FFX), a novel oncoprotein that activates AKT-mTORC1 signaling and cooperates with MYC. Here, we uncover a complementary and opposing function for the deleted 3'-PVT1 segment, which encodes a tumor-suppressive micropeptide we term Honeybadger (HNB). HNB binds KRAS and dampens RAS-MAPK signaling, and its loss derepresses this pathway and stabilizes MYC via Ser62 phosphorylation. Thus, a single class of structural alterations at PVT1 simultaneously installs FFX-mediated AKT-mTORC1 activation and removes HNB-mediated RAS-MAPK regulation, creating a dual mechanism that synergistically amplifies MYC output. This oncoprotein gain coupled with tumor-suppressor loss provides a mechanistic explanation for the particularly poor prognosis of PVT1-rearranged cancers and establishes PVT1 as a central regulatory hub in MYC+ malignancies.
The eukaryotic nucleolus is a highly organized, multilayered structure essential for ribosomal RNA (rRNA) processing and ribosome assembly. While rRNA transcription is known to drive nucleolar assembly, the contribution of downstream processing steps to nucleolar organization remains less well defined. Here, we show that disruption of endonucleolytic cleavage of the 5' external transcribed spacer (5'ETS), a key early step mediated by the SSU processome, leads to pronounced changes in nucleolar structure and organization. These altered nucleoli display reduced dynamic exchange behavior consistent with altered material properties and exhibit changes in the NPM1-associated nucleolar interactome. In parallel, we observe redistribution of heterochromatin markers, indicating broader effects on nuclear organization. Together, our findings support a model in which progression of pre-rRNA processing contributes to maintaining nucleolar compartmentalization and links early steps of ribosome biogenesis to nuclear organization. The nucleolus is a defining feature of eukaryotic cells, yet the principles that maintain its multilayered organization remain incompletely understood. While rRNA transcription is known to initiate nucleolar assembly, we show that a specific downstream processing step, the cleavage of the 5' external transcribed spacer (5'ETS), plays a key role in maintaining nucleolar organization. By functionally uncoupling rRNA transcription from processing, we demonstrate that defects in 5'ETS maturation are associated with alteration of the NPM1-associated interactome and changes in nucleolar dynamics. These findings support a model in which the progression of rRNA processing contributes to the material organization of the nucleolus, linking enzymatic steps in ribosome biogenesis to nuclear architecture.
PIF1 family helicases promote genome stability during DNA replication and repair, yet the biochemical activity of human PIF1 (hPIF1) remains poorly understood. Here, we directly compare full-length hPIF1 and budding yeast Pif1 (yPif1) and show that the two enzymes operate differently. In bulk assays, hPIF1 displays weak net DNA unwinding because its robust intrinsic single-stranded DNA (ssDNA) annealing activity rapidly reforms duplex DNA behind the helicase motor. Single-molecule magnetic tweezers experiments reveal that hPIF1 is only modestly slower than yPif1 and similarly processive, indicating that poor apparent unwinding primarily reflects rapid reannealing rather than impaired motor activity. Mutagenesis and structural modeling indicate that this functional divergence depends on a yeast-specific insertion within the catalytic domain. Unlike yPif1, hPIF1 fails to stimulate Polδ-dependent displacement-loop (D-loop) extension, arguing that it does not promote DNA unwinding ahead of the migrating bubble. However, similarly to yPif1, hPIF1 likely unwinds newly synthesized DNA coupled with DNA reannealing behind the migrating D-loop. hPIF1 efficiently remodels intramolecular G-quadruplex DNA into fully base-paired dsDNA, whereas yPif1 generates ssDNA products. Together, our data support a model in which hPIF1 acts primarily as a DNA translocase that couples local unwinding with rapid rewinding to clear secondary DNA structures without generating extensive ssDNA.
Ribosome biogenesis is a resource-consuming process that facilitates rapid growth and feeds uncontrolled, cancerous traits. Constraining ribosome biogenesis and protein translation has become a tenable therapeutic strategy for cancer. Yet, we do not know how cells that rely on high metabolic activity adapt and sustain their growth when deprived of their translational capacity. Conversely, stem cells and treatment-resistant cells persist under low metabolic states challenging their eradication. These are critical questions in cancer therapies. To delineate survival mechanisms that allow cancer cells to adapt to ribosome biogenesis defects, we conducted functional genomics screens during inhibition of RNA polymerase I. We identified that inactivation of mTOR enabled cell survival despite severe translational suppression. This was paradoxical as activation of mTOR is considered oncogenic by boosting ribosome biogenesis and cellular translational programs. We show that mTORC1 inhibition does neither restore rRNA synthesis nor ribosome biogenesis, but redistributes limited ribosomes from highly translated 5'TOP mRNAs to survival-essential transcripts. This mTOR inactivation-mediated prioritization of translational resources represents a minimal requirement for cell survival when translational capacity is compromised, which we term "translational fitness." Our findings redefine the role of mTOR in cell survival and highlight the need for strategic targeting of translation regulation in cancer therapy.
ELAV/Hu RNA-binding proteins (RBPs) are key regulators of neuronal alternative splicing and polyadenylation programs across animals. How ELAV/Hu RBPs achieve gene-specific regulation by recognizing spaced U-rich motifs through multimerization, remains uncertain. We determined X-ray crystal structures of ELAV RNA recognition motif 3 (RRM3) to reveal that multimerization is mediated by two evolutionarily conserved interfaces in non-RNA-binding parts of the RRM to form a tetramer and RNA binding is not required for multimerization. Mutational probing of these two interfaces in Drosophila photoreceptor neurons shows that both interfaces contribute to ELAV function in development. Notably, multimerization defective Drosophila elav mutants are embryonic lethal. Genomic profiling demonstrates that multimerization is required to direct neuronal alternative splicing and polyadenylation programs of some, but not all ELAV target genes. Our study provides a structural basis for a mechanistic understanding how ELAV/Hu proteins can extract gene-specific regulation from a landscape of redundant sequence motifs.
Pediatric sarcomas are a heterogeneous group of rare mesodermal malignancies. These cancers, which affect children from infancy through adolescence and young adulthood, are in general challenging to treat with currently available therapies. Biologically, many are characterized by quiet genomes, fusion oncoproteins, immune “cold” microenvironments, and vast epigenetic deregulation that contributes to diverse and complex mechanistic drivers. Multifaceted advancements in research strategies, including high-throughput screening, new model systems, surfaceome profiling, and study of oncogenic fusion condensates have led to new opportunities for understanding the biology of pediatric sarcomas. To continue to make progress for these difficult to treat cancers, it will be critical to continue to improve access to bioinformatic data, approach patient care using innovative clinical trial frameworks, and foster interdisciplinary partnerships among medicinal chemists, scientists, clinicians, advocates, and industry partners.
The unfolded protein response (UPR) preserves endoplasmic reticulum proteostasis through coordinated signaling pathways, including the IRE1α-XBP1 axis, which promotes adaptive transcriptional programs via noncanonical XBP1 mRNA splicing. However, upstream mechanisms regulating this pathway remain incompletely defined. Here, we apply CRASP-seq, a scalable RNA-coupled CRISPR screening platform, to systematically identify regulators of XBP1 splicing. We uncovered the U2 snRNP auxiliary factor RBM39 as a critical positive regulator of this process. Perturbation of RBM39 or U2 snRNP components induces alternative splicing of ERN1, leading to exon-18 skipping and the production of an unstable transcript subject to nonsense-mediated decay, as well as a truncated IRE1α isoform that acts in a dominant-negative manner to suppress XBP1 splicing. Mechanistically, we show that heat shock reduces RBM39 functional activity and promotes ERN1 exon-18 skipping, thereby attenuating IRE1α-XBP1 signaling. Functionally, hyperactivation of this pathway is detrimental under proteotoxic stress, suggesting that exon-18 skipping serves as a stress-adaptive mechanism to limit UPR output. Together, our findings reveal a previously unrecognized regulatory axis linking the canonical splicing machinery to UPR signaling and establish alternative splicing of ERN1 as a key modulator of cellular stress responses.
Faithful genome reactivation after mitosis is essential for cell identity, yet the mechanisms driving global postmitotic transcription remain unclear. Here, we show that the MYC oncogene and its obligate partner MAX drive a postmitotic hypertranscriptional state in mouse embryonic stem cells. Cell cycle-resolved single-cell RNA-seq in inducible Max -/- cells reveals that early G1 hypertranscription is strongly impaired without MAX. Mechanistically, MAX remains bound to thousands of promoters during mitosis, while MYC is largely excluded. Using high-temporal-resolution profiling, pharmacological inhibition of MYC/MAX, and acute MAX degradation at mitotic exit, we demonstrate that MAX mitotic binding triggers rapid MYC recruitment and transcriptional amplification of TBP-bound promoters by enhancing RNA polymerase II occupancy and efficient initiation and elongation. These findings redefine MYC/MAX as master regulators of gene regulatory inheritance across mitosis.
Longevity and stress resilience require precise coordination of gene expression programs across tissues. Here, we demonstrate that overexpression of the chromatin reader bet-1 specifically in neurons of Caenorhabditis elegans promotes organismal longevity and stress resistance via cell-nonautonomous signaling. Neuronal bet-1 elicits a neurotransmitter-dependent signal that activates the conserved stress-responsive transcription factor HSF-1 in the intestine, enhancing proteostasis, oxidative stress resistance, metabolic remodeling, and immune defense. Life span extension by neuronal bet-1 requires both hsf-1 and daf-16 in neurons but only requires hsf-1 in peripheral tissues. Using bulk RNA sequencing, we reveal distinct prolongevity pathways that include enhanced heat-shock response, proteostasis, increased actin stability, and resistance to pathogens, which likely together coordinate the prolongevity effects of neuronal bet-1 . Our findings establish BET-1 as a potent nonautonomous regulator of aging and stress response, highlighting chromatin readers as upstream modulators of intertissue signaling and systemic resilience.
A nucleus is a remarkably arranged organelle partitioned from the cytosol by a nuclear envelope to encapsulate a highly structured space including a well-organized genome and nucleolus. Despite the conservation, our understanding of the molecular mechanisms driving and maintaining nuclear structure are limited. Here, we investigated the influence of myosin motors in the nucleus. Classically, motor proteins are known for mediating the active transport of cargo facilitating cytoplasmic organization yet how the spacing of nucleoplasmic biomolecules is coordinated was not well defined. We found that nuclear type I myosins were essential for cell division whereas nuclear type II and V myosins were not. Depletion of type I myosin from the nucleus triggered 3D genome disorganization, gene expression changes, nucleolar disruption, and nuclear envelope morphology disfigurement. Declined nucleolar function, including rRNA synthesis and processing, occurred first followed by disorganization of the genome. Notably, nuclear depletion of type I myosin correlated with altered dynamic mobilities of the nucleolar Nop1 (fibrillarin) protein and RNA polymerase I. Overall, nuclear type I myosin is critical for the shape and activities of the nucleolus and nucleus.
Pancreatic ductal adenocarcinoma (PDAC) grows within a highly fibrotic, pressurized microenvironment that collapses vasculature and restricts delivery of oxygen and circulating nutrients. To survive this metabolic stress, PDAC cells activate lysosome-centered nutrient acquisition and recycling programs, including macroautophagy, RAS-driven macropinocytosis, and receptor-mediated endocytosis, that traffic intracellular and extracellular cargo to lysosomes for degradation and metabolite export. These pathways are reinforced by oncogenic signaling and MiT/TFE-dependent lysosomal biogenesis, and they support core outputs of tumor metabolism such as iron bioavailability, amino acid and nucleotide pools, lipid homeostasis, and immune evasion. Lysosomal programs in nonmalignant compartments (fibroblasts, stellate cells, and immune cells) further shape nutrient exchange, matrix production, and whole-body metabolism, positioning the lysosome as a key node at the tumor-host interface. Although genetic and pharmacologic blockade of autophagy/lysosome function can produce potent antitumor effects in preclinical models, clinical trials with lysosomotropic agents have shown limited benefit, highlighting challenges in target engagement, biomarkers, and rational combination strategies. Here we review current tools and concepts for interrogating lysosomal flux in PDAC, integrate emerging insights from systemic metabolism and dietary interventions, and outline therapeutic opportunities for more effectively exploiting lysosome dependence in pancreatic cancer.
best4 + cells are a recently described vertebrate intestinal epithelial cell type. best4 + cells are altered in inflammatory bowel disease and colorectal cancer, suggesting that stimulation of their homeostatic replenishment may have therapeutic potential. However, the development and function of best4 + cells remain unclear. Since mice lack best4 + cells, we established zebrafish as a tractable in vivo model to observe, manipulate, and remove best4 + cells in an organismal context. We dissected best4 + cell developmental regulation in vivo from birth to differentiation and specialization, focusing on factors conserved in best4 + cells across vertebrates. Lineage tracing demonstrated that best4 + cells arise from secretory progenitors, where Notch/Dll4 signaling mediates a decision between best4 + and enterochromaffin cells by triggering meis1b expression. Following specification by meis1b , pbx3a spatially diversifies best4 + cells, which develop regional heterogeneity in gene expression, intracellular pH, and function. In vivo live imaging and removal of best4 + cells showed that best4 + cells sense luminal pH changes and extend dynamic luminal and stromal projections, but are not required to restore global luminal pH after challenge. Altogether, this study experimentally delineates best4 + cell developmental regulation and develops a genetic toolkit to examine their function in vivo, both of which will aid investigating how best4 + cells are altered or can be restored during disease.
Deregulated inflammatory signaling via STAT family transcription factors, particularly STAT1, underlies a variety of immune-related diseases, including inflammatory bowel disease. Whereas activation of STATs by JAKs via canonical receptor-driven JAK-STAT signaling is well understood, little is known about JAK-independent mechanisms of STAT activation. Here, we identify the understudied nonreceptor tyrosine kinase TNK1 as a therapeutically targetable, JAK-independent activator of STAT signaling. Using a multiomics approach, we mapped a network of TNK1 substrates associated with protein condensates and proinflammatory signaling, including STAT1. We found that TNK1, but not its sister kinase ACK1, directly phosphorylates STATs at well described STAT-activating JAK sites. In cells, TNK1-mediated STAT1 phosphorylation and activation occurs independently of JAKs. Imaging and interactomics data suggest that TNK1 interacts with STAT1 in cytosolic condensates, which likely compartmentalize TNK1-substrate interactions. We show that an intrinsically disordered proline-rich region in TNK1, which includes a 14-3-3 docking phosphorylation site, is required for the formation of kinase-active TNK1 condensates and STAT1 phosphorylation. Mutations within the proline-rich region that eliminate 14-3-3 binding increase formation of TNK1 condensates, suggesting a model in which 14-3-3 acts as a clamp that constrains the flexible PRR to inhibit condensate formation and STAT1 activation. Finally, we show that TNK1 is a targetable driver of STAT1-mediated inflammation in the gut as inhibition of TNK1 reduces active STAT1 in the colon and ameliorates colitis symptoms in mice.
Splicing factors are frequently mutated in myeloid cancers, causing splicing aberrations that derail the expression of tumor suppressor genes. In SRSF2 mutated cancers, a key oncogenic splicing event is the inclusion of a “poison” exon that introduces an early stop codon in EZH2 mRNA, causing its destabilization. In this issue of Genes & Development , Islam et al. (doi:10.1101/gad.353628.126) define how mutant SRSF2 binding to the poison exon mediates its inclusion and identify an antisense oligonucleotide that represses the exon to restore EZH2 function and rescues hematopoietic defects. Thus, targeting of poison exons, many of which show protumorigenic and antitumorigenic properties, is a promising new avenue to treat cancer.
A long-standing observation in studies of neurological disorders is that broadly expressed disease genes can cause dysfunctions that are limited to certain brain regions or cell types. In this issue of Genes & Development, Lee et al. (doi:10.1101/gad.353596.125) address the mystery of this selective vulnerability by studying ATXN1-CIC interactions implicated in spinocerebellar ataxia type 1. They provide compelling evidence that specific ATXN1 paralogs preferentially interact with specific CIC isoforms tissue-dependently. Whereas ATXN1-CIC-L complexes regulate hippocampal gene expression and learning, ATXN1L-CIC-S complexes regulate lung alveolarization, postnatal survival, and hydrocephalus risk. This work thus demonstrates the potential contribution of isoform-paralog specificity to tissue-specific vulnerabilities in neurological disorders.
This memorial reflects on the extraordinary ability of Gregory J. Hannon (1964-2026) to develop transformative technologies, ask bold biological questions, and repeatedly redefine entire fields. Equally, it celebrates his profound influence as a mentor who fostered originality, intellectual rigor, authenticity, and generosity. Greg's greatest legacy extends beyond his discoveries to the generations of scientists whose approach to science, and to life, continues to be shaped by his example.
