Telomeres, coated by the shelterin complex, prevent end-to-end fusions and aberrant DNA repair, yet how telomere-binding proteins coordinate chromatin remodeling during the DNA damage response remains unclear. Here we show that the telomeric protein TRF1 is phosphorylated at serine 11 (S11) in response to DNA double-strand breaks, a modification that enhances cellular resistance to DNA damage. We found that CDK2 directly mediates this phosphorylation, which triggers recruitment of the histone methyltransferase SETD5 to telomeric chromatin. SETD5-dependent deposition of H3 trimethylation at lysine 36 (H3K36me3) promotes local chromatin decompaction and enables subsequent recruitment of the phosphatase PPP4C to dephosphorylate γH2AX. Loss of TRF1 S11 phosphorylation results in persistent γH2AX foci, delayed DNA repair, and compromised telomere integrity. Our results define a CDK2-TRF1-SETD5-PPP4C signaling axis that orchestrates phosphorylation-dependent chromatin remodeling at telomeres to ensure genome maintenance during DNA damage stress.

Mitochondria are semi-autonomous organelles whose functions critically depend on nucleus-encoded proteins. TOM40 is the core β-barrel protein of the translocase of the outer mitochondrial membrane (TOM) complex that mediates the import of most nucleus-encoded mitochondrial proteins. Here, we show that the small GTPase RAB32 facilitates the mitochondrial localization of TOM40 and the mitochondrial protein homeostasis in non-small cell lung cancer (NSCLC) cells. Accordingly, knockout of RAB32 results in mitochondrial dysfunction and inhibits NSCLC progression in xenograft and autochthonous NSCLC mouse models. We further identify ubiquitin-specific peptidase 13 (USP13) that removes the K48-linked polyubiquitin chains from RAB32 to prevent its proteasomal degradation. Consistently, knockout of USP13 causes destabilization of RAB32, impairs TOM40 mitochondrial localization and mitochondrial function, and inhibits NSCLC progression, which are restored by reconstitution of wild-type USP13 or RAB32, but not the catalytically inactive USP13[C345A/M664/739E]. Our study has revealed a previously uncharacterized RAB32-USP13 axis for mitochondrial functions and NSCLC progression.

The ATP synthase-associated macromolecular complex plays a crucial role in cellular energy homeostasis. However, the regulation and potential function of this complex remain poorly understood in cancer. Here, we identify a 170-amino acid protein encoded by the lncRNA LINC00528, which we term ATP synthase-associated macromolecular complex enhancing microprotein (ATHENA). Mechanistically, ATHENA localizes to the mitochondrial inner membrane, in which ATHENA directly interacts with ATP synthase subunits (β and γ) and solute carrier proteins, including ANT and PiC, thereby promoting the assembly of these macromolecular complexes, enhancing ATP synthesis, and preserving mitochondrial and cristae architecture. Functionally, ATHENA promotes the proliferation, migration, and invasion of renal cell carcinoma (RCC) cells in vitro and drives RCC tumor growth and metastasis in vivo. Clinically, ATHENA is upregulated in RCC tissues and associated with poorer prognosis in RCC patients. Collectively, our findings identify ATHENA as a previously unrecognized mitochondrial microprotein that facilitates the assembly of ATP synthase-associated macromolecular complex and drives RCC progression.

Macrophage-driven inflammation plays a critical role in the progression of acute myocardial infarction (AMI). This study revealed that USP7 expression was elevated in peripheral blood mononuclear cells (PBMCs) from patients with coronary artery disease (CAD). Furthermore, in a mouse model of myocardial infarction (MI), after AMI cardiac inflammation was suppressed by macrophage-specific USP7 knockout. Mechanistically, USP7 directly interacted with STING and suppressed its K63-linked ubiquitination at residue K289, thereby preventing STING degradation via the endosomal sorting complex required for transport (ESCRT)-lysosomal pathway and enhancing STING-mediated inflammatory signaling. The cardioprotective effects of USP7 ablation were abrogated by STING overexpression. Moreover, pharmacological inhibition of USP7 or adenovirus-mediated knockdown of USP7 similarly attenuated AMI-induced cardiac injury and inflammation in mice. These findings identify USP7 as a novel deubiquitinating enzyme that regulates STING ubiquitination and degradation via the ESCRT pathway, thus establishing USP7 as a critical regulator of macrophage inflammatory responses in AMI.

This perspective brings together multiple observations concerning the regulatory architecture and functional interactions of the TP53 gene and its isoforms. The TP53 gene encompasses an internal enhancer-promoter region (P2) located between exons 2 and 5, which is transactivated by full-length TAp53α, to drive the expression of truncated TP53 isoforms ΔN133p53α, β or γ. ΔN133p53α homo-monomers or dimers very likely form hetero-tetramers with homo-dimers of full-length TAp53α. The TAp53α-ΔN133p53 tetramer then acts as a transcription factor augmenting mitochondrial efficiency, DNA repair, telomere restoration and reversing cellular senescence, thus opposing many outputs of tumor suppressive TAp53α homo-tetramers. Other transcription factors, such as estrogen receptor (ER), OCT1, and SOX9 also may bind the P2 promoter-enhancer to promote transcription of oncogenic TP53 isoforms. These transcription factors, together with full-length TAp53α, appear to cooperate to maintain an open chromatin state in the P2 region in a manner reminiscent of a neural "associative memory" network.

The development and functional maintenance of CD8[+] T cells are metabolically regulated processes in which mitochondria serve as the central hub. Here, we identify glucose-regulated protein 75 (GRP75) as a critical mitochondrial regulator controlling these processes. Using T cell-specific Hspa9 (encodes GRP75) knockout mice, we demonstrate that GRP75 deficiency disrupts CD8[+] T cell fate, leading to defective T cell homeostasis and impaired memory differentiation. Mechanistically, impaired mitochondrial function in GRP75-deficient CD8[+] T cells leads to perturbation of IL-7R signaling and aberrant expression of effector-associated molecules. Further studies reveal that GRP75 deficiency leads to upregulation of interferon regulatory factor 4 (IRF4), a critical transcription factor for effector versus memory fate, which in turn suppresses memory CD8[+] T cell differentiation. Our findings establish GRP75 as a pivotal mitochondrial checkpoint that coordinates metabolic state and functional fate in CD8[+] T cells.

Yes-associated protein (YAP), a key effector of the Hippo pathway, plays a well-established role in colorectal cancer (CRC). However, the functional relevance of site-specific post-translational modifications (PTMs) in YAP, particularly methylation, remains insufficiently explored. SET-domain-containing protein 8 (SETD8), the sole mono-methyltransferase for histone 4 lysine 20 (H4K20), is implicated in various cancers, yet its biological function and underlying mechanisms in CRC are elusive. While SETD8 is primarily known for its histone methylation activity, its capacity to modify non-histone proteins, such as YAP, remains largely unexplored. This study aimed to demonstrate that SETD8 exerted a tumor-suppressive effect on CRC by inhibiting YAP protein expression. Mechanistically, SETD8 physically interacts with YAP to catalyze mono-methylation at lysine 76 (K76me). This modification enhances the interaction between YAP and the E3 ubiquitin ligase RING finger protein 31 (RNF31), promoting YAP K48-linked polyubiquitination and subsequent proteasomal degradation. Clinically, patients with CRC and high SETD8 expression, including elevated YAP K76me levels, exhibited favorable pathological grading and improved prognosis. Collectively, our findings identify a novel SETD8-YAP K76me regulatory axis that restricts CRC progression, suggesting that targeting this axis may represent a promising therapeutic strategy.

Non-small cell lung cancer (NSCLC) is frequently refractory to mitochondrial apoptosis despite oncogenic and therapeutic stress. Although individual anti-apoptotic BCL-2 family members have been implicated in NSCLC survival, it has remained unclear whether this reflects dominant single-protein dependencies or a cooperative pro-survival network. This uncertainty is exacerbated by the high prevalence of p53 mutations, which compromise DNA damage-induced apoptotic signaling. Here, we systematically dissected intrinsic apoptotic dependencies across a panel of human NSCLC cell lines using selective BH3 mimetics targeting BCL-2, BCL-XL or MCL-1. Consistent with previous reports, BH3 mimetics alone provided only limited and heterogeneous sensitization to cisplatin across NSCLC models. Likewise, single-agent inhibition of BCL-2, BCL-XL or MCL-1 elicited weak and variable apoptotic responses. In striking contrast, combined targeting of BCL-XL and MCL-1 was sufficient to trigger rapid, synergistic and irreversible apoptosis in the majority of NSCLC cell lines, even in the absence of genotoxic stress. Commitment to cell death occurred within minutes and was characterized by early mitochondrial outer membrane permeabilization, cytochrome c release and robust effector caspase activation. This apoptotic response strictly required the intrinsic mitochondrial machinery and BAX/BAK function but was entirely independent of p53 status. Apparent resistance to first-generation (WEHI-539) BCL-XL inhibition in a subset of models reflected incomplete target engagement rather than compensatory survival rewiring. Accordingly, apoptosis was fully restored by next-generation BCL-XL inhibition (A-1331852) or by PROTAC-mediated BCL-XL degradation (DT2216). Importantly, platelet-sparing BCL-XL targeting strategies retained strong synergy with MCL-1 inhibition, addressing a key translational limitation of earlier BH3-mimetic approaches. Together, these data redefine apoptotic control in NSCLC as a cooperative restraint imposed by BCL-XL and MCL-1 rather than discrete, context-dependent dependencies, revealing a rapid, p53-independent mitochondrial apoptotic vulnerability with clear therapeutic implications.

Inducing ferroptosis in hepatocellular carcinoma (HCC) cells represents an important therapeutic strategy, but intrinsic resistance mechanisms often limit efficacy. Therefore, elucidating the mechanisms underlying ferroptosis resistance in HCC cells can facilitate the development of effective therapeutic strategies. Here, we performed genome-wide CRISPR/Cas9 library screens to identify TRIM27 as a key determinant of ferroptosis resistance. TRIM27 knockdown markedly potentiated erastin-induced ferroptosis in HCC cells, whereas TRIM27 overexpression suppressed the expression of fatty-acid metabolic enzymes including ACSL4 and reduced oxidized lipid accumulation. Mechanistically, TRIM27 directly binds with ACSL4 and promotes its K48-linked ubiquitination and degradation, thereby attenuating ferroptosis in HCC cells. Furthermore, we developed TRIM27-Cas9-loaded EVs with robust editing efficiency. These engineered EVs were readily internalized by HCC cells and preferentially accumulated in the liver. Functionally, TRIM27-Cas9-loaded EVs inhibited HCC cell proliferation by enhancing ACSL4-mediated ferroptosis and significantly improved the anti-tumor efficacy of anti-PD-1 therapy in HCC. Collectively, our findings suggest that TRIM27 confers ferroptosis resistance via facilitating K48-linked ubiquitination and subsequent proteasomal degradation of ACSL4. TRIM27-Cas9-loaded EVs restore cellular sensitivity to ferroptosis, inhibit HCC proliferation, and sensitize HCC lesions to anti-PD-1 immunotherapy.

Persistent neuroinflammation is a hallmark of central nervous system (CNS) injury, driving neuronal loss and functional deficits. While microglial lipid metabolic reprogramming, particularly lipid droplet accumulation, has been implicated in chronic inflammation, the underlying mechanisms remain poorly understood. Using single-cell transcriptomics, we identified a previously defined lipid droplet-accumulating microglia (LDAM) subpopulation in spinal cord injury (SCI), characterized by elevated PLIN2 expression. Genetic deletion of Plin2 markedly reduced lipid droplet burden, attenuated neuroinflammation, and promoted neuronal survival and functional recovery in vivo. Mechanistically, PLIN2 interacts with the mitochondrial outer membrane protein PGAM5 to regulate lipid droplet-mitochondria contacts. This interaction inverts canonical metabolic flux by redirecting fatty acids from mitochondria back to lipid droplets, thereby suppressing β-oxidation and inducing mitochondrial dysfunction, which subsequently triggers STING-dependent inflammation. Notably, the PLIN2 220-392 domain is essential for PGAM5 binding and contact formation; disrupting this interaction attenuates STING signaling and enhances neuroprotection and functional recovery in vivo. Our findings identify the PLIN2-PGAM5 as a critical metabolic-immune pathway and suggest that targeting organelle-contact-mediated metabolic reprogramming represents a potential therapeutic strategy for CNS injury.

Lung cancer remains the leading cause of cancer-related death worldwide, and long noncoding RNAs (lncRNAs) have been implicated in its tumourigenesis and progression. However, the roles lncRNAs play in lung cancer remain unclear. In this study, we discovered an important role for the lncRNA MNX1 Antisense RNA 1 (MNX1-AS1) as a critical regulator of one-carbon metabolism reprogramming. Glutamine depletion altered chromatin accessibility, leading to downregulation of MNX1-AS1, while elevated expression of MNX1-AS1 was correlated with poor prognosis in patients with non-small cell lung cancer. Functional studies showed that MNX1-AS1 promoted cell proliferation and sphere formation in vitro, and subcutaneous and orthotopic tumour growth in vivo. Mechanistically, MNX1-AS1 directly binds to calcyclin binding protein (CACYBP), protecting it from ubiquitin-mediated degradation; thus, the MNX1-AS1/CACYBP complex accelerates the transcription of key one-carbon metabolism-related genes through the Wnt/β-catenin pathway. MNX1-AS1/CACYBP/β-catenin axis upregulated key one-carbon metabolism-related genes, which were essential for generating related metabolites and maintaining cellular redox balance to support lung cancer cell proliferation. These findings established that the lncRNA MNX1-AS1 acts as a crucial driver of one-carbon metabolism reprogramming in non-small cell lung cancer and highlight that the newly identified MNX1-AS1/CACYBP/β-catenin axis may serve as a potential prognostic biomarker and therapeutic target for lung cancer intervention.

Somatic mutations rewire the ubiquitin-proteasome system (UPS) to support tumor growth, but the proteome-wide consequences of cancer-driver alterations on UPS composition remain incompletely understood. Using harmonized proteogenomic data from up to 11 CPTAC cohorts, we performed an integrated pan-cancer analysis of UPS protein dysregulation, prognostic associations, and mutation-driven remodeling. We show that mRNA poorly predicts UPS protein abundance, that a defined set of E3 ligases is recurrently dysregulated across cancers, and that somatic mutations (most strikingly TP53 loss) produce coherent UPS protein-quantitative trait locus (pQTL) signatures. Two case studies (UBR5 and TRIM28) illustrate orthogonal modes of UPS rewiring: a mutation-driven axis in which TP53-mutant tumors elevate UBR5 to support replication stress tolerance, and a lineage-driven axis in which TRIM28 engages tissue-restricted regulatory networks with opposing prognostic effects in glioblastoma versus head and neck cancer. Each axis exposes context-specific therapeutic vulnerabilities, including sensitivity to DNA damage response inhibitors (UBR5-high) and lineage-specific drug responses (TRIM28-high). Together, these analyses define a mechanistic framework for how cancer-driver mutations reshape proteostasis through the UPS and nominate mutation- and lineage-defined dependencies for precision degrader therapy. The harmonized pan-tissue atlas and the UbiDash interactive resource that underpin parts of this analysis are reported in our companion paper [1].

Schizophrenia (SCZ) and bipolar disorder (BD) share cognitive impairments and autophagy disruptions, with haploinsufficiency of AKAP11 (A-kinase anchoring protein 11) emerging as a major genetic risk factor for both disorders, though its functional role remains poorly understood. Here, we demonstrate that acute Akap11 depletion in the mouse hippocampus induces cognitive deficits, accompanied by synaptic dysfunction and autophagy dysregulation, implicating Akap11 deficiency in cognitive impairments via disrupted autophagic processes. Using in vitro models, we show that AKAP11 regulates autophagy initiation and lysosomal activity in various cell types, including neuronal cells. Mechanistically, AKAP11 deficiency results in increased phosphorylation of transcription factor EB (TFEB), impairing its nuclear translocation and downregulating its target genes critical for autophagy and lysosome biogenesis. Further, we identify an interaction between AKAP11 and PPP3CB, a phosphatase responsible for TFEB dephosphorylation, and demonstrate that inhibition of PPP3CB abrogates AKAP11-mediated TFEB dephosphorylation. Importantly, in vivo administration of a TFEB activator reduces the accumulation of autophagy substrates and mitigates cognitive impairments in Akap11-deficient mice, highlighting TFEB activation as a potential therapeutic strategy. Collectively, our findings establish AKAP11 as a key regulator of the autophagy-lysosome pathway and cognitive function, providing novel insights into the pathophysiology of SCZ and BD and suggesting therapeutic potential in targeting TFEB-mediated autophagy.