Molecular Cancer Research

Long noncoding RNAs (lncRNAs) are important regulators of gene expression and are frequently dysregulated in cancer. The mitotically associated lncRNA MANCR is highly expressed in aggressive cancers and contributes to genomic instability in triple-negative breast cancer (TNBC), but the molecular mechanisms underlying its activity remain poorly defined. Here we integrate computational and experimental approaches to examine the structure and regulatory interactions of MANCR isoforms. Analysis of transcriptomic datasets revealed tumor-type-specific expression patterns for seven MANCR isoforms in breast cancer cell lines. Computational prediction of RNA secondary structures identified conserved structural features across isoforms, suggesting potential functional specialization. We identify p53 as a MANCR-interacting protein through computational docking and RNA immunoprecipitation sequencing (RIP-seq) and demonstrate that MANCR depletion reduces p53-dependent transcriptional activity. Chromatin isolation by RNA purification sequencing (ChIRP-seq) revealed 1, 250 genomic regions associated with MANCR, including enrichment of p53 consensus motifs and GC-rich sequence elements. Motif analysis further identified candidate sequence features associated with MANCR-occupied chromatin regions. Computational prediction of RNA-miRNA interactions identified multiple potential miRNA binding sites across MANCR isoforms, including miR-6756-5p, which targets the androgen receptor (AR). Consistent with this prediction, AR expression decreased following MANCR knockdown in TNBC cells. Together, these results suggest that MANCR isoforms may contribute to transcriptional regulation in TNBC through interactions with chromatin, p53 signaling pathways, and potential miRNA regulatory networks. One Sentence SummaryMitotically-associated lncRNA (MANCR) is prevalent in aggressive cancers interacting with DNA, P53, and miRNAs, to mediate multiple levels of epigenetic transcriptional control in triple negative breast cancer.

The formation of the premetastatic niche prepares distant tissues for tumor cell engraftment. Endothelial cells are critical mediators of premetastatic niche formation, orchestrating extravasation of circulating tumor cells and critical pro-tumor immune cells, such as neutrophils. In mouse models of breast cancer, we show that primary tumors upregulate the non-signaling chemokine receptor ACKR1 in the endothelium of the lung premetastatic niche. ACKR1-expressing venules were found to be preferential sites of neutrophil and tumor cell localization within lung tissue. A newly generated conditional ACKR1 allele was used to show that endothelial-specific removal of ACKR1 expression significantly reduces metastatic engraftment in the lung. When ACKR1 is activated by tumor-secreted factors, endothelial ACKR1 functions to promote neutrophil recruitment within the lung parenchyma. We conclude that ACKR1 is a critical component of the endothelial response to tumors at the metastatic site of the lung, leading to neutrophil recruitment and promotion of tumor cell metastasis. SUMMARYEndothelial cells play critical roles in breast cancer metastasis. ACKR1 is upregulated in the endothelium of the lung metastatic niche in response to primary mammary tumors. Endothelial ACKR1 expression was found to promote neutrophil infiltration into the metastatic niche and support breast tumor cell metastasis to the lung.

Inactivation of VHL is a truncal alteration in clear cell renal cell carcinoma, but additional events are required for oncogenesis, most commonly PBRM1 inactivation. To better understand this co-operation, we used an oncogenic cell-tagging strategy to analyze the earliest transcriptional and cellular consequences of Vhl and/or Pbrm1 inactivation in the renal tubular epithelium, in vivo, at single-cell resolution. Pbrm1 inactivation did not globally alter HIF-dependent transcription or increase early tubular proliferation induced by Vhl inactivation. Instead, it had independent effects on epithelial organization. Combined genetic and morphological analyses suggested that Pbrm1 inactivation allows cells to sustain Vhl/HIF-dependent proliferation by disrupting tubular architectures that ordinarily restrain this proliferation, resulting in extra-tubular cell accumulation, multilayered epithelia, and tumor formation. Our findings frame a new model for the VHL-PBRM1 interaction that explains loss of epithelial homeostasis through an interaction between discrete effects that drive proliferation and remove structural tissue restraints on that proliferation. Statement of SignificanceVHL and PBRM1 are frequently co-inactivated in ccRCC. Combining transcriptomic and histological analyses of Vhl and/or Pbrm1-inactivated renal cells in vivo, this study highlights independent effects on transcription and epithelial organization that converge to promote sustained proliferation and dysplasia. The work illuminates how tissue homeostasis is disrupted by oncogenic co-operation.

Renal cell carcinoma (RCC) is characterized by dysregulation of the kynurenine pathway (KP), which converts tryptophan to NAD+ while generating immunomodulatory metabolites. Therapeutic efforts have focused on inhibiting IDO1 at the pathway entry point, but the functional consequences of targeting downstream KP enzymes remain poorly characterized. We used CRISPR/Cas9 to generate knockouts of three KP enzymes in the RENCA murine RCC model--kynurenine 3-monooxygenase (KMO), quinolinic acid phosphoribosyltransferase (QPRT), and 3-hydroxyanthranilic acid dioxygenase (HAAO)--and evaluated effects on cell migration, colony formation, tumor burden, metastasis, and survival. KMO and QPRT knockouts consistently reduced migratory capacity and colony size in vitro. However, in vivo effects were distinct: while QPRT knockout reduced tumor burden, KMO knockout did not. Notably, we did not detect metastasis in female mice receiving KMO knockout RENCA cells. HAAO knockout produced divergent effects, increasing migration and colony size in vitro, but reducing tumor burden and metastasis in vivo. Mice challenged orthotopically with all three knockout cell lines had significantly extended survival compared to mice receiving wild type cells. These results indicate that individual KP enzymes exert distinct, context-dependent effects on RCC progression. The enhanced in vitro aggressiveness coupled with reduced in vivo tumorigenicity observed in HAAO knockout RENCA cells illustrates that cell culture phenotypes do not reliably predict tumor behavior, particularly when perturbing metabolic pathways with pleiotropic effects. Our findings suggest that targeting specific KP enzymes warrants further investigation as a therapeutic strategy in RCC.

The non-canonical translation of specific mRNAs has been implicated in oncogenesis and cancer progression. We previously identified eukaryotic Initiation Factor 5B (eIF5B) as a key factor in Internal Ribosome Entry Site (IRES)-mediated translation of a subset of mRNAs encoding anti-apoptotic proteins. Here, we demonstrate that EIF5B is predominantly expressed in cancer cells compared to other cell types in the Oral Squamous Cell Carcinoma (OSCC) microenvironment. Higher EIF5B mRNA and protein expression are associated with poor patient outcomes. We show that eIF5B depletion in OSCC cells blunted pro-growth, pro-inflammatory, and pro-angiogenic signaling pathways and significantly increased TNF-related apoptosis-inducing ligand (TRAIL)-induced cell death. This is achieved through decreased translation of mRNAs encoding critical factors associated with OSCC pathophysiology. Importantly, the level of interaction of eIF5B with tRNAiMet was significantly higher in OSCC cells compared to non-cancerous fibroblasts. This suggests that OSCC cells (but not non-cancerous fibroblasts) rely heavily on eIF5B for translation initiation. In an in vivo flank xenograft model using nude mice, eIF5B knockdown in UMSCC-29 cells led to a significant reduction in tumor volume compared to control tumors. Also, the immunohistochemical analysis of the xenografted tumor sections demonstrated decreased staining intensity of critical factors associated with OSCC pathophysiology in eIF5B-depleted tumors relative to controls. Collectively, our data demonstrate that OSCC cells are uniquely dependent on eIF5B-tRNA interactions to sustain translation of pro-survival mRNAs. Targeting eIF5B disrupts these oncogenic programs, sensitizing OSCC cells to apoptosis and suppressing pro-angiogenic and pro-growth signaling.

Well- and dedifferentiated liposarcomas (WDLPS and DDLPS) are characterized by extensive copy- number alterations rather than recurrent gene-inactivating mutations, obscuring the molecular mechanisms that drive disease progression and, critically, the transition from well-differentiated to the more aggressive dedifferentiated tumor states. Despite marked differences in clinical behavior and prognosis, the regulatory events underlying adipocytic lineage destabilization in DDLPS remain poorly understood. Here, we establish an in vivo model of retroperitoneal liposarcoma in Xenopus tropicalis through early embryonic mosaic perturbation of p53 and Rb pathway components. Combined disruption reproducibly induced retroperitoneal WDLPS development, demonstrating that pathway-level deregulation of the MDM2-p53 and CDK4-Rb axes is sufficient to initiate liposarcoma development in vivo. Strikingly, additional perturbation of transcriptional co-activator ep300 in this context resulted in increased tumor dedifferentiation, yielding lesions composed of spatially coexisting well- and dedifferentiated adipocytic states. In contrast, direct targeted disruption of downstream adipogenic regulators recurrently lost in human DDLPS, including cebpa, g0s2, and dgat2, failed to induce dedifferentiation in the same genetic context in vivo. These findings indicate that dedifferentiation cannot be explained by loss of downstream adipocytic effectors alone but instead reflects destabilization of higher-order regulatory programs governing adipocytic identity. Together, these results establish an in vivo model that closely reflects the clinical situation on a pathway level and provides initial mechanistic insight into how adipocytic differentiation may become destabilized during disease progression. This framework offers a foundation for future studies leveraging higher-order and multi-omic approaches to dissect the molecular processes underlying the WDLPS-to-DDLPS transition.

In synovial sarcoma, the BAF subunit SS18 is fused to SSX, a transcriptional repressor, generating the oncogenic SS18::SSX fusion protein. Incorporation of SS18::SSX into BAF complexes leads to their aberrant retargeting to Polycomb-repressed genes via SSX, while simultaneously altering their composition and activity. The presence of BAF at Polycomb target sites is widely assumed to be essential for gene activation. Here, we directly tested the requirement for BAF activity in synovial sarcoma cell survival and SS18::SSX-driven transcription. Using targeted degradation of BAF ATPase subunits and deletion of core components, we show that BAF loss has modest effects on sarcoma cell viability and does not impede SS18::SSX target gene expression. Consistently, deletion of the BAF ATPase subunit Smarca4 does not impair SS18::SSX-driven tumor formation in vivo. Using domain-specific SS18::SSX mutants, we further demonstrate that the fusion can activate oncogenic transcription independently of BAF interaction, and that this activity depends on the C-terminal QPGY-rich domain of SS18. Mechanistically, SS18::SSX promotes transcription by engaging the histone acetyltransferase EP300, independently of BAF. Accordingly, pharmacologic degradation of EP300/CREBBP suppresses SS18::SSX-driven transcriptional programs and impairs synovial sarcoma cell survival. Together, these findings challenge the view that BAF activity is required for SS18::SSX-mediated transcriptional activation and demonstrate that aberrant Polycomb target gene expression is sustained through recruitment of transcriptional coactivators in the absence of BAF. Our work reveals new therapeutic vulnerabilities in synovial sarcoma and suggests broader relevance for targeting coactivator-dependent transcription in fusion-driven cancers. HighlightsO_LIBAF degradation does not alter SS18::SSX-activated transcriptional programs C_LIO_LIDirect SS18::SSX transcriptional activation is independent of BAF interaction C_LIO_LIThe SS18 C-terminus engages the co-activator EP300 to promote gene expression C_LIO_LISmall molecule degraders of EP300/CREBBP abolish SS18::SSX-mediated transcription C_LI

MET exon 14 skipping is a pathogenic event that results in decreased ubiquitin-mediated degradation of the MET receptor, sustained oncogenic signaling, and conferred sensitivity to MET tyrosine kinase inhibitors. While exon 14 skipping is most commonly caused by somatically acquired base substitutions and small indels near the exon 14 splice sites, here we report nine cases in which long interspersed element-1 (LINE-1, L1)-mediated insertions within or adjacent to MET exon 14, including one case of a LINE-1-mediated pseudogene insertion, appear to cause exon 14 skipping. These describe the first recurrent and clinically actionable mutations caused by LINE-1 retrotransposition in cancer.

Ionizing radiation can be an effective therapy for prostate cancer. Unfortunately, however, more aggressive prostate cancers such as neuroendocrine prostate cancer (NEPC) are often radiation resistant, which contributes to their high degree of morbidity and mortality. In this study, we used an unbiased approach to identify novel mechanisms that contribute to resistance to radiation and that are associated with neuroendocrine differentiation. Specifically, we compared the expression of cell surface proteins by mass spectrometry in prostate cancer cell lines that had been either untreated or treated with radiation to induce resistance, a process that also promotes neuroendocrine differentiation. Among the proteins identified by this screen, we focused on folate receptor (FR) because of its known biological functions and the fact that it is a validated therapeutic target. Our data reveal that FR has a causal role in enabling prostate cancer cells to resist radiation. Importantly, we also demonstrate that the expression of FR is regulated by HIF-1, which also has a causal role in radiation resistance and neuroendocrine differentiation. Given that the ability of cells to resist damage and death in response to ionizing radiation depends largely on their ability to buffer the substantial increase in reactive oxygen species (ROS) that is generated by radiation, we also demonstrate that the folate-FR axis promotes radiation resistance by sustaining intracellular glutathione levels that buffer this increase in ROS. In summary, the data reported here highlight a novel role for FR in resistance to ionizing radiation that is intimately associated with the hypoxic microenvironment of NEPC and the ability of the folate-FRa axis to maintain redox homeostasis.

Keratin-positive giant cell-rich tumor (KPGCT) is a newly described bone and soft tissue tumor. The tumor is characterized by scattered keratin-positive cells and the presence of HMGA2::NCOR2 fusions. It is not known if the HMGA2::NCOR2 fusion is located in the keratin-positive cells, and little is known about how KPGCT develops. KPGCT shares some histologic features with tenosynovial giant cell tumor (TGCT), a soft tissue tumor with CSF1 rearrangements. Single-nuclei RNA sequencing (snRNA-seq) and Xenium spatial transcriptomics were used to elucidate the mechanisms driving KPGCT and compare KPGCT to TGCT. We show that the neoplastic cells in KPGCT constitute only a minority of cells in the tumor, and that they co-express keratin, HMGA2 and CSF1. The neoplastic cells in KPGCT express no synovial markers, confirming KPGCT as a distinct entity, separate from TGCT. The bulk of the tumor consists of CSF1R-expressing macrophages and osteoclast-like giant cells, suggesting an important role for CSF1-CSF1R signaling. In addition, we find that the cells with the HMGA2 translocation show activation of the hippo signaling pathway, which is known to regulate CSF1 expression. We show that the CSF1-CSF1R axis, possibly regulated through the hippo signaling pathway, plays an important role in KPGCT. This axis likely stimulates the migration and proliferation of macrophages, which form the majority of cells in the tumor, as well as their differentiation into osteoclasts-like giant cells. These results provide a rationale for the use of CSF1R inhibitors, which have already shown efficacy in TGCT, as a therapy for KPGCT. SignificanceKeratin-positive giant cell-rich tumor (KPGCT) is a rare, newly described soft tissue and bone tumor. By examining this tumour on a single-cell level, we confirm the identity of the neoplastic cells on a molecular level, showing these form a minority of cells in the tumor. We show that activation of the hippo pathway in the neoplastic cells is a likely driver of tumorigenesis. Additionally, we show the neoplastic cells produce large amounts of CSF1, attracting the macrophages that form the majority of cells in the tumor. This finding gives supporting evidence for anecdotal reports of response to CSF1 inhibitor therapy. Finally, we identify key differences between KPGCT and tenosynovial giant cell tumor, a tumor that shares histological features with KPGCT.

Macrophages/osteoclasts are highly fusogenic cells that interact closely with bone-metastatic breast cancer cells. These cancer cells adapt to bone microenvironments by undergoing osteomimicry, acquiring bone-like phenotypes. Exploration using human breast cancer-bone metastases dataset revealed that a small population of epithelial breast cancer cells express osteoclast-like and osteomimicry genes at the single-cell level. Cell fusion and cell-in-cell (CIC) processes are two uncommon yet prognostically significant mechanisms in cancer. We showed that co-culture between murine breast cancer cells and osteoclasts yielded a unique osteoclast phenotype through dynamic cell-in-cell (CIC) interactions and fusion-like behaviours between pre-osteoclasts/mature osteoclasts and breast tumor cells, resulting in osteoclast-tumor hybrid-like cells. These tumor cell interactions characterized by membrane retention and nuclear adjacency to host nuclei were consistently observed throughout osteoclast differentiation. Single-cell sequencing analysis and interpretative assays on hybrid-like cells revealed altered extracellular matrix (ECM) modification processes, immunoregulatory, and cancer-associated pathways compared to unfused osteoclasts. Tumor cells co-cultured with osteoclasts expressed hematopoietic and osteoclast-lineage factors more strongly than tumor cells cultured alone with their effects amplified under direct cell-cell contact. The presence of these hybrid-like cells was validated in human breast cancer-bone metastases. We propose that disseminated bone-tropic breast cancer cells were stimulated by osteoclasts to undergo a non-canonical, dynamic osteoclast differentiation and CIC formation to form hybrid-like cells that may facilitate bone metastatic lesions.

The nuclear oncoprotein SET (patient "SE" translocation) has been implicated in the etiology of MLL/KMT2A-fusion induced leukemia. Here we examine the details of this dependency in murine, primary hematopoietic cells. Experiments demonstrated Set as downstream target of HoxA9 and a direct interactor of Mll/Kmt2A. Mll/Kmt2A and Set globally co-bound promoter regions. Impairing Set expression induced a metabolic shift towards oxidative phosphorylation phenocopying a knockdown of Mll/Kmt2A fusion targets. Set acted predominantly as transcriptional activator driving a pro-proliferative gene expression program with features indicative for Mll/Kmt2A involvement. Molecularly, Set depletion caused dissociation of Mll/Kmt2A from chromatin accompanied by a selective loss of elongating RNA PolymeraseII Ser2-P. Concomitant with a function of Set as inhibitor of protein phosphatase 2A (PP2A), specific recruitment of PP2A to the Meis1 promoter, a known Mll/Kmt2A target, inhibited transcription in reporter assays and in a natural chromatin environment. We identified Mitogen and stress induced kinase 1 (Msk1) as potential substrate protected by Set from dephosphorylation. Active and phosphorylated Msk1-P colocalized with Mll and disappeared from chromatin upon Set depletion. Biochemically, Msk-1 bound directly to Mll/Kmt2A as well as to menin, a known Mll/Kmt2a tethering factor. Loss of Set/Mll/Msk1 selectively affected H3K14 acetylation at promoters and this could be partially attributed to the reduced presence of the histone acetyltransferase Moz/Kat6a. Finally, we show that kinase and menin inhibitors cooperate in leukemia cells indicating that the relay function of Mll/Kmt2A, allowing control of hematopoiesis by cellular signaling, is retained in MLL-fusion proteins.

BackgroundOvarian cancer (OC) progression and chemoresistance are closely linked to dysregulated oncogenic signaling, including Wnt/{beta}-catenin pathways that contribute to cancer stem-like traits. However, the upstream mechanisms connecting cytoskeletal regulation to Wn/{beta}-catenin signaling in OC remain incompletely understood. Keratin 17 (KRT17), a type I intermediate filament protein, has been implicated in tumor progression, but its mechanistic role in OC requires clarification. MethodsGene Expression Omnibus (GEO) datasets and clinical specimens were analyzed to assess KRT17 and EPN1 expression and prognostic significance. Functional assays, xenograft models, co-immunoprecipitation, ubiquitination analyses, and rescue experiments with wild-type and ubiquitination-resistant EPN1 mutants were performed to investigate molecular mechanisms. ResultsKRT17 expression was elevated in OC tissues and correlated with poor patient survival. KRT17 depletion suppressed proliferation, migration, stem-like properties, tumor growth, and cisplatin resistance. Mechanistically, KRT17 interacted with EPN1 and weakened its association with the E3 ligase SMURF1, reducing SMURF1-mediated ubiquitination at lysine 107 and preventing proteasomal degradation. Stabilized EPN1 was associated with increased {beta}-catenin abundance and stemness-associated markers, and enhanced self-renewal capacity. ConclusionsThese findings identify a KRT17-EPN1 axis that links intermediate filament dynamics to ubiquitin-dependent regulation of EPN1 stability and Wnt/{beta}-catenin signaling outputs in ovarian cancer.

Y-box binding protein 1 (YB-1; YBX1) is a multifunctional DNA- and RNA-binding protein involved in cell cycle regulation, DNA repair, stress adaptation, and therapy resistance. Elevated YBX1 mRNA expression is associated with aggressive disease across multiple cancers, yet its pan-cancer genomic and clinical correlates remain unclear. Here, we performed a comprehensive pan-cancer analysis across 53 datasets spanning 33 tumour types, integrating RNA expression, somatic mutations, copy number, hypoxia, and clinical outcomes. YBX1 was rarely mutated or amplified, indicating that oncogenic relevance is primarily driven by its expression. Tumours with high YBX1 mRNA exhibited a conserved transcriptional program enriched for cell cycle, DNA repair, and chromatin regulation pathways, and were preferentially mutated in genes involved in maintaining genomic stability, including TP53. These tumours were associated with increased mutation burden, fraction of genome altered, homologous recombination deficiency, and elevated hypoxia. Clinically, high YBX1 mRNA associated with advanced stage, higher grade, shorter progression-free survival, and reduced overall survival. Collectively, high YBX1 mRNA expression defines a conserved, genomically unstable, and clinically aggressive tumour state across multiple cancer types.

High-grade serous carcinoma (HGSC) is the most common and aggressive form of ovarian cancer. Advanced HGSCs exhibit pronounced cellular heterogeneity, including a subset of cancer-propagating cells (CPCs, also known as cancer stem cells) that are highly tumorigenic and display stem cell-associated properties such as self-renewal and chemoresistance. In contrast, a substantial fraction of HGSC cells is non-tumorigenic. The role of these non-cancer-propagating cells (non-CPCs) and their relationship to CPCs remain poorly understood. Here, we demonstrate that neoplastic cells expressing the intermediate filament protein keratin 5 (KRT5) represent bona fide CPCs. KRT5 cells form cancer organoids over successive passages, are tumorigenic in serial dilution xenograft assays, and are resistant to the antineoplastic agents, doxorubicin and cisplatin. Single-cell lineage-tracing experiments show that KRT5 CPCs give rise to KRT5- cells. KRT5 and KRT5- populations exhibit distinct gene expression profiles, with KRT5- cells characterized by expression of SPP1, which encodes the secreted factor osteopontin (OPN). Treatment with OPN enhances HGSC organoid growth and chemoresistance, whereas SPP1 knockdown reverses these effects. Together, these findings support a model in which HGSC contains two hierarchically related cell populations: KRT5, OPN-responsive CPCs and KRT5-, non-tumorigenic cells that form a niche producing OPN. Targeting pathways that sustain both stem-like tumor cells and their supportive niche may enable reduced dosing of highly toxic chemotherapeutic agents while enhancing therapeutic efficacy in HGSC.

Ewing sarcoma (EwS) is a rare, aggressive pediatric malignancy driven by FET::ETS family fusions (EWSR1::FLI1 in >85% of cases) with no established environmental risk factors. To investigate germline predisposition, we analyzed 2,014 EwS cases and 10,525 cancer-free controls in a two-stage analysis that combined an international genome-wide association study and a case{square}parent trio study. The combined meta-analysis identified 18 variants at 14 susceptibility loci (9 novel, 5 replicated) with moderate effect sizes (odds ratios[≥]1.25). Integrative analyses of the EwS loci revealed enrichment of expanded GGAA microsatellites, with evidence for binding of the EWSR1::FLI1 chimeric oncogenic activator. EWSR1::ETS knockdown in EwS cell lines resulted in dysregulated genes at susceptibility loci related to skeletal/muscle development, RNA binding/processing, and chromatin regulation. Our findings provide insights into the inherited component of EwS, highlighting a genetic architecture in which common germline variations with moderate effects interact with somatic EWSR1::FLI1 fusions to promote sarcomagenesis by dysregulating local genes.

Invasive Lobular Carcinoma (ILC) is a subtype of breast cancer characterized by distinct biological features, and limited glucose uptake coupled with increased reliance on amino acid and lipid metabolism. Our prior studies highlight the importance of glutamate as a key regulator of ILC tumor growth and therapeutic response. Here we examine the expression of four key proteins involved in glutamate transport and metabolism - SLC3A2, SLC7A11, GPX4, and GLUD1/2 - in a racially diverse cohort of 72 estrogen receptor-positive (ER+) ILC and 50 ER+ invasive ductal carcinoma, no special type (IDC/NST) patients with primary disease. All four proteins associate with increased tumor size in ILC, with three showing stronger associations in Black women, but not in IDC/NST. Among these three proteins in ILC, GLUD1/2 uniquely associates with ER expression in all women, while GLUD1/2 and SLC3A2 are enriched in hypertensive women. GLUD1/2 and GPX4 are upregulated in endocrine therapy-resistant ILC cell lines, and pharmacological inhibition of GLUD1 reduces ER protein levels and cell viability. Together, these findings support a potentially important role for glutamate metabolism in ILC and suggest GLUD1 and other glutamate-handling proteins as candidate targets for therapeutic intervention in ILC.

The equilibrium between cell death and cell division is crucial for maintaining tissue homeostasis in a multicellular organism. Apoptosis plays an essential role in preserving homeostasis and hence occurs in a coordinated manner. However, inhibition of apoptosis is one of the hallmarks of cancer. Apoptosis Inhibitor 5 (Api5), an anti-apoptotic protein, is upregulated in various cancers, including ovarian, bladder, cervical, and lung cancers. Studies have demonstrated that altered expression of Api5 leads to the transformation of non-tumorigenic breast epithelial cells. However, the mechanism regulating this process is not well-elucidated. Our study demonstrates that overexpression of Api5 increased FGF2 (Fibroblast Growth Factor 2) levels both at protein and transcript levels. We studied the mechanistic details of changes in morphology, proliferation, and polarity observed upon FGF2/FGFR1 deregulation in Api5-overexpressing cells. Deciphering the signalling mechanism underlying Api5-FGF2-mediated breast tumorigenesis revealed that the PDK1/Akt and Ras/MAPK/ERK pathways regulated multiple transformation phenotypes. PDK1/Akt enhanced proliferation and altered morphology during initial stages, whereas Ras/MAPK/ERK regulated polarity disruption, proliferation, and reduced apoptosis during later stages of morphogenesis. In conclusion, this study provides insights into the signalling mechanism regulating the transformation phenotypes associated with Api5 overexpression in a non-tumorigenic breast epithelial cell line.

Constitutively active KRAS mutations are highly prevalent in lung cancers, but the direct role of its downstream phosphatidylinositol 3-kinase (PI3K) pathway in tumor progression remains unclear. A previous study established the requirement for PIK3CA, the alpha catalytic isoform, in lung tumor development in mouse models with an intact Trp53 tumor suppressor. In this study, we further investigated the requirement for PIK3CA for tumor growth both in vitro and in vivo. We first generated a "KPA" cell line by genetically deleting Pik3ca from a murine lung adenocarcinoma "KP" cell line harboring oncogenic KrasG12D and lacking Trp53. We found that Pik3ca is not required for cell survival and growth in vitro, even under anchorage-independent conditions but reduced the growth rate by 20%. We next orthotopically implanted KP and KPA cells into syngeneic mice and found that PIK3CA is absolutely required for tumor progression, even in the absence of Trp53. Implantation of KP cells, or a "KPS" cell line lacking the Stk11 gene, led to rapid tumor growth and death of all host animals. In contrast, mice implanted with KPA cells all survived with no detectable lung tumors. The gene expression profiles from cultured cell lines suggest KPA cells may be vulnerable to oxidative stress. Indeed, we found KPA cells were more sensitive to hydrogen peroxide and diethyl maleate-induced oxidative stress as compared to KP and KPS cells. Together, these results demonstrate that PIK3CA is not required for lung cancer cell growth induced by mutant KRAS in vitro but is critically needed for in vivo progression and growth.

The tumour suppressor kinase LKB1 is known to regulate the activity of the metabolic sensor AMPK, that when under energy stress shifts metabolism from anabolism to catabolism, thus linking LKB1 to AMPK-mediated gene expression. Coupled with its role as a tumour suppressor kinase, LKB1 is an important metabolic regulator implicated in multiple malignancies and is frequently mutated in lung cancer. Previously, we discovered that LKB1 binds to the SWI/SNF chromatin remodelling ATP-dependent helicase subunit SMARCA4, directly linking LKB1 to gene expression. How LKB1 and SMARCA4 collaborate to regulate gene expression in lung cancer has not been well characterized. We used an in-silico approach to explore how LKB1 and SMARCA4 may cooperate to regulate gene expression. We mined our previous scRNA-seq dataset from 4 lung cancer cell lines with differential LKB1 and SMARCA4 expression status to identify genes regulated by both LKB1 and SMARCA4. We correlated our results using bulk RNA-seq results from human lung tumours. We show that LKB1 and SMARCA4 likely function together to regulate gene expression in multiple biological processes in lung cancer cell lines. Gene expression profiles from LKB1 and SMARCA4 mutant cells are similar, suggesting LKB1 and SMARCA4 function in a linear pathway to regulate gene expression. Furthermore, we observed similar results in human lung tumours, particularly in late-stage disease. We propose a model where LKB1 acts as a nexus between metabolism and gene expression, acting via the SMARCA4-SWI/SNF complex to regulate gene expression in lung cancer.