Molecular Oncology

Cancer-associated fibroblasts (CAFs) are the dominant cell type in the stroma of solid organ cancers, including non-small cell lung cancer (NSCLC). Fibroblast heterogeneity is widely recognised in many cancers, with subpopulations of CAFs being identified and potentially being indicative of prognosis and treatment efficacy. Here, the subtypes displayed by CAFs isolated from human NSCLC resections are initially identified by flow cytometry, using the markers FAP, CD29, SMA, PDPN, CD90, FSP-1 and PDGFR{beta}, showing five distinct subpopulations, CAF-S1-S5. Our findings show that when comparing fibroblasts from tumour tissue with that from adjacent lung tissue, CAF-S2 and CAF-S3 are found in the normal tissue and marker expression suggests a less activated phenotype whereas CAF-S1, CAF-S4 and CAF-S5 are predominantly found in the tumour tissue and are positive for a combination of markers of fibroblast activation. We focus on these subtypes most associated with fibroblast activation, primarily focussing on a previously unreported CAF-S5 subtype, and comparing to the previously identified CAF-S1. Both these subsets express FAP and PDPN as markers of fibroblast activation, but CAF-S5 lacks expression of the common activation marker SMA. The spatial relevance of these subtypes in a cohort of 163 NSCLC patients was then investigated by multiplex immunofluorescence on a tumour micro-array of patient samples, revealing CAF-S5 are found further from tumour regions than CAF-S1. To understand the functional role of CAF-S5, scRNA sequencing data was used to compare the subset to the previously identified CAF-S1, finding that CAF-S5 displays an inflammatory phenotype, whereas CAF-S1 displays a contractile phenotype. We demonstrate that presence of either the CAF-S1 or CAF-S5 subtype is correlated to worse survival outcome in NSCLC, highlighting the importance of the identification of CAF subtypes in NSCLC.

MALAT1 is a long non-coding RNA with oncogenic roles in cancer but poorly studied in indolent B-cell neoplasms. Here, MALAT1 expression was analyzed using RNA-seq, microarrays or qRT-PCR in primary samples from various clinico-biological subtypes of chronic lymphocytic leukemia (CLL, n=266) and follicular lymphoma (FL, n=61). In peripheral blood (PB) CLL samples, high MALAT1 expression was associated with a significantly shorter time to treatment, independently from other known prognostic factors, such as IGHV mutational status. Coding genes whose expression levels were associated with MALAT1 in CLL were predominantly related to oncogenic pathways stimulated in the lymph node (LN) microenvironment. Further analysis of MALAT1 expression by microarrays in paired CLL samples from PB/LN showed that its levels were maintained between both anatomical compartments, supporting that the clinical value of MALAT1 expression found in PB is mirroring expression differences already present in LN. Similarly, high MALAT1 expression in FL predicted for a shorter progression-free survival, and its correlated expressed genes were associated with pathways promoting FL pathogenesis. In summary, MALAT1 expression is related to pathophysiology and clinical behavior of indolent B-cell neoplasms. Particularly in CLL its levels could be a surrogate marker of the microenvironment stimulation and may contribute to refine the clinical management of these patients.

BackgroundCellular plasticity, involving loss of lineage determination and emergence of hybrid cell states, plays a pivotal role in non-small cell lung cancer (NSCLC) disease progression and therapy resistance. However, the full spectrum of atypical states generated in human NSCLC and the pathways that regulate them are yet to be fully elucidated. Here we examine the role of developmental programmes, alveogenesis and branching morphogenesis (BM), in regulating phenotypic diversity in NSCLC. MethodsTranscriptomic analysis of epithelial cells isolated from murine lungs at different stages of organogenesis were used to derive gene signatures for developmental programmes. Bulk tissue transcriptomic datasets from human NSCLC and non-neoplastic control samples were used to identify whether developmental programmes were associated with molecular, morphological, and clinical parameters. Single-cell RNA-sequencing was used to identify malignant cell states in human NSCLC (n = 16,621 epithelial cells from 72 samples) and protein level validation of these states was carried out using multiplexed immunohistochemistry (n = 40). ResultsMutually antagonistic regulation of alveogenesis and BM was found to account for a significant proportion of transcriptomic variance in human NSCLC bulk tissue datasets. BM activation was associated with poor overall survival rates in five independent lung adenocarcinoma (LUAD) cohorts (p=2.04e-13); and was significantly prognostic for resistance to tyrosine kinase inhibitors (TKIs; p=0.003) and immune checkpoint blockade (ICBs; p=0.014), in pre-treatment biopsies. Single-cell RNA-sequencing analysis revealed that malignant LUAD cells with loss of alveolar lineage fidelity predominantly acquired inflamed or basal-like cellular states, which were variably persistent in samples from TKI and ICB recurrence. ConclusionsOur results show LUAD tumours undergo reversion from an alveogenic to branching morphogenic phenotype during disease progression, generating inflamed or basal-like cell states that are variably persistent following TKI or ICB treatments. These findings identify prognostic biomarkers for therapy response and underscore the role of different cell states in resistance to multiple treatment modalities.

CK2 is considered a constitutively active protein kinase promoting/supporting several neoplastic properties and inducing a so-called non-oncogene addiction in tumor cells. Compared to the extensive body of pre-clinical research, the translational and clinical information on CK2 is still limited. The holoenzyme, composed by a tetrameric array of two catalytic (CSNK2A1 and/or CSNK2A1) and two regulatory (CSNK2B) subunits, remains to be clinically validated. Herein, we interrogated available cancer multiomics databases to unravel CK2 deregulated expression in NSCLC. We focused our analysis on individual CK2 subunits assuming subunit-specific tumor supportive roles across cancers and particularly, within two major NSCLC subtypes. Moreover, we performed meta-analysis to uncover associations between CK2 expression and patient survival, as well as further correlations analysis with components of the tumor-microenvironment. The genomic and transcriptomic data analysis was complemented by IHC evaluation of CSNK2A1, CSNK2A2 and CSNK2B subunit expression, and CK2 enzymatic activity thereof. Overall, our data suggests that epigenetic, transcriptional and post-transcriptional regulatory mechanisms rather than mutational/gene amplification events may account for differential CK2 subunits expression/activity in NSCLC. Of note, CSNK2A1 and CSNK2B mRNA up-regulation consistently determine a worse patient prognosis in LUAD and correlated with increased infiltration of MDSCs/CAFs. Importantly, we corroborated that CK2 protein subunits levels and enzymatic activity are significantly exacerbated in LUAD and LUSC, but only CSNK2A1 positively correlated with tumor size and disease stage in the analyzed patient cohort, thus supporting our transcriptomic-based correlation analysis. Finally, we concluded that CSNK2A1 alone and/or the homo-tetramer thereof may be more instrumental to support NSCLC than CSNK2A2; thus, tailored drugs against these molecular CK2 entities may achieve better therapeutic windows at least for advanced lung cancer treatment.

ABSTRACTNon-small cell lung cancer (NSCLC), the most frequent subtype of lung cancer, remains a highly lethal malignancy and one of the leading causes of cancer deaths worldwide. Mutant KRAS is the prevailing oncogenic driver of lung adenocarcinoma, the most common histological form of NSCLC. In this study, we examined the role of PKCε, an oncogenic kinase highly expressed in NSCLC and other cancers, in KRAS-driven tumorigenesis. Notably, database analysis revealed an association between PKCε expression and poor outcome in lung adenocarcinoma patients specifically having KRAS mutation. By generating a PKCε-deficient, conditionally activatable allele of oncogenic Kras (LSL-KrasG12D;PKCε−/− mice) we were able to demonstrate the requirement of PKCε for Kras-driven lung tumorigenesis in vivo, which is consistent with the impaired transformed growth observed in PKCε-deficient KRAS-dependent NSCLC cells. Moreover, PKCε-knockout mice were found to be less susceptible to lung tumorigenesis induced by benzo[a]pyrene, a carcinogen that induces mutations in Kras. Mechanistic analysis using RNA-Seq revealed little overlapping for PKCε and KRAS in the control of genes/biological pathways relevant in NSCLC, suggesting that a permissive role of PKCε in KRAS-driven lung tumorigenesis may involve non-redundant mechanisms. Our results thus highlight the relevance and potential of targeting PKCε for lung cancer therapeutics.Competing Interest StatementThe authors have declared no competing interest.View Full Text

The epiCMIT (epigenetically-determined Cumulative MIToses) mitotic clock traces B-cell mitotic history via DNA methylation changes in heterochromatin and H3K27me3-containing chromatin. While high scores correlated with poor outcomes in CLL and MCL, its prognostic significance in SMZL remains unknown. Derived from 142 SMZL cases using DNA methylation microarrays, epiCMIT values were correlated with genomic, transcriptomic, and clinical data. EpiCMIT as a continuous variable was significantly higher in females (p=0.02), patients with IGHV1-2*04 allele usage (p<0001), intermediate IGHV somatic hypermutation load (97-99.9% identity, p=0.04), elevated mutational burden (25 vs. 17 mut/Mb, p=0.001), driver gene mutations [KLF2 (p<0.001), NOTCH2 (p<0.01), TP53 (p=0.01), KMT2D (p<0.001)], and del(7q) (p=0.01). Negative correlation between epiCMIT and telomere length (r=-0.29 p<0.001) supported the association between cumulated proliferation and telomere attrition. While univariate analysis highlighted epiCMIT as robust predictor of shorter treatment-free survival (TFS), multivariate analysis confirmed epiCMIT as an independent marker for shorter TFS. In summary, our matched multi-omic datasets facilitate the clinico-biological characterization of SMZL and introduces epiCMIT as a strong prognostic marker, identifying high-risk patients and predicting reduced treatment-free survival, hence providing a new tool for risk-adapted patient management.

The tumour suppressor gene BAP1 is mutated in more than half of the malignant mesothelioma patients. This catalytic subunit of Polycomb repressive deubiquitinating (PR-DUB) complex, plays an important role in maintaining gene expression levels by deubiquitinating the PRC1-mediated histone H2A lysine 119 mono-ubiquitination (H2AK119ub1). Published studies report varying degrees of importance of H2AK119ub1 in Polycomb-regulated gene expression in different cell types. Recently published data by our own lab suggests a global redistribution of the H2AK119ub1 mark from promoter to intergenic regions upon loss of BAP1. PRC1-mediated mono-ubiquitination is dependent on the E3 ubiquitin ligase function of RNF2 (RING1B). Here, by knocking-out Rnf2, we show that loss of H2AK119ub1 levels leads to a decrease in clonogenic potential of Bap1-deficient mesothelioma cells in vitro and a delay in tumour onset in vivo.

BackgroundBarretts Oesophagus (BO) presents a particular pathological dilemma, in that patients who have no dysplasia within their BO experience a small but significant risk of malignant progression each year. Screening programmes have attempted to reduce the mortality from BO associated oesophageal adenocarcinoma but cannot predict which BO patients will progress to invasive malignancy. We have previously identified the long non coding RNA, OR3A4, is differentially hypomethylated in progressive BO. We aimed to understand its role in BO pathogenicity MethodsThe stable BO cell line CP-A, as well as the oesophageal adenocarcinoma cells line OE-33 was transfected with a lentiviral OR3A4 over-expression vector, and underwent high resolution microscopy, immunofluorescence, RT-qPCR, RNA sequencing, and targeted drug screening with the p38-MAPK inhibitor domipramod to understand the effects of OR3A4 expression on progression. We then compared progressive vs. non-progressive BO samples using quantitative multi-fluorophore (Vectra) immunohistochemistry. ResultsOver-expression of OR3A4 in CP-A lines resulted in a hyperproliferative, dysplastic cellular phenotype, with strong over-expression of MAPK and anti-apoptotic pathways at the RNA and protein level, which was sensitive to the p38-MAPK inhibitor domipramod. Vectra immunohistochemistry demonstrated that progressive BO had reduced visibility associated with a reduction in CD8+ T-cells and CD68+ macrophages and reduced CD4+ T-cells in the stomal compartment. ConclusionThe overexpression of OR3A4, which we have previously shown is associated with progressive BO leads to a proliferative dysplastic cellular phenotype associated with increased, reversible MAPK signalling and loss of immune visibility.

BackgroundWe report extended follow-up of TROG99.03, a randomised phase III trial in early-stage follicular lymphoma (ESFL) including new information on the role of adjuvant rituximab and translational studies. MethodsPatients with ESFL were randomised to involved-field radiotherapy (IFRT) or IFRT plus 6-cycles cyclophosphamide/vincristine/prednisolone (IFRT+CVP). From 2006 rituximab was added to IFRT+CVP (IFRT+R-CVP). Clinical and multi-omic parameters were evaluated. Findings were validated in two independent ESFL cohorts (99 and 60 patients respectively). FindingsBetween 2000-2012, 150 (75 per arm) patients were recruited. 48% were positron emission tomography (PET)-staged. Per protocol, at median follow-up 11.3-years, progression-free survival (PFS) remained superior for IFRT+(R)CVP vs. IFRT (hazard ratio [HR]=0.60, 95%CI=0.37-0.98, p=0.043; 10-year PFS 62% vs. 43%) respectively. Although no significant difference in overall survival was observed (HR=0.44, 95%CI=0.16-1.18, p=0.11, 10-year OS 95% vs 84%), patients receiving IFRT+(R)CVP experienced fewer composite (histological transformation and death) events (p=0.045). PFS of IFRT+R-CVP-treated patients compared with all other treatments lacking rituximab (IFRT alone plus IFRT+CVP) was superior (HR=0.36, 95%CI=0.13-0.82, p=0.013). Amongst PET-staged patients, PFS differences between IFRT+R-CVP vs. IFRT were maintained (HR=0.38, 95%CI=0.16-0.89, p=0.027) indicating benefit distinct from stage migration. FL-related mutations and BCL2-translocations were not associated with PFS. However, by multivariate analysis elevated CD8A gene expression in diagnostic biopsy tissue was independently associated with improved PFS (HR=0.45, 95%CI=0.26-0.79, p=0.037), a finding confirmed in both ESFL validation cohorts. CD8A gene expression was raised (p=0.02) and CD8+ T-cell density higher within follicles in ESFL vs. advanced-stage FL (p=0.047). Human leucocyte antigen class I specific neoantigens were detected in 43% of patients, suggesting neoantigen-specific CD8+ T-cells have a role in confining the spread of the disease. InterpretationAdjuvant R-CVP and elevated intratumoural CD8 expression were independently associated with sustained disease control after radiotherapy in ESFL. FundingCancer Council Victora; National Health and Medical Research Council; Leukaemia Foundation; Mater Foundation.

Long-term responders (LTRs) to immune checkpoint inhibitor (ICI) therapy in advanced non-small cell lung cancer (NSCLC) are rare. As no robust biomarkers for LTRs have been defined so far, oncologists are unable to define the optimal treatment duration for this cohort. Hence, standard practice of ICI administration for at least 2 years, regardless of response, does not rely on a solid biological rationale. In this multi-center retrospective study, we analyzed baseline clinical, genetic, and transcriptomic profiles of 14 non-responders (NRs) and 21 LTRs, defined by disease progression shortly after treatment initiation and no evident progression for at least one year after ICI cessation, resp. Comparative analysis of clinical and serological parameters identified an adenocarcinoma histology, low neutrophil-to-lymphocyte ratio (NLR) and low platelet-to-lymphocyte ratio (PLR) to be significantly associated with LTRs. Genetic profiling demonstrated that LTRs were twice as frequently associated with mutations in KRAS (56.3% in LTRs, 25% in NRs) while the opposite held true for mutations in STK11 (25% in NRs, 12.5% in LTRs). Transcriptomic analysis of tumor biopsies from 5 LTRs and 5 NRs treated with pembrolizumab monotherapy at the Universitair Ziekenhuis Brussel (UZB, Belgium) revealed that LTRs show a significantly raised adaptive immune profile, predominantly characterized by T cell- and B cell-related immunity. In addition, we found LTRs to have a significantly lower expression of a drug metabolizing enzyme (DME) gene signature, mainly defined by isotypes of the uridine diphosphate glucuronosyltransferase 1A (UGT1A) gene family. The latter was validated in additional biopsies from UZB, Jessa Ziekenhuis (Hasselt, Belgium), and Amsterdam Universitair Medisch Centrum (The Netherlands), as well as in a publicly available dataset. Functional validation using an in vitro human tumor cell specific T cell killing assay demonstrated that diclofenac and atazanavir, inhibitors of the DMEs UGT1A enzyme family, enhance ICI efficacy. These findings suggest that baseline expression of the DME signature may inform personalized ICI treatment strategies and support further investigation into the co-administration of ICIs with clinically approved DME inhibitors to improve long-term response rates in advanced NSCLC. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=145 SRC="FIGDIR/small/25339842v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@19e462forg.highwire.dtl.DTLVardef@11e07forg.highwire.dtl.DTLVardef@1a9c24borg.highwire.dtl.DTLVardef@130646_HPS_FORMAT_FIGEXP M_FIG C_FIG

In the last years, several efforts have been made to classify colorectal cancer (CRC) into well-defined molecular subgroups, representing the intrinsic inter-patient heterogeneity, known as Consensus Molecular Subtypes (CMSs). In this work, we performed a meta-analysis of 1700 CRC patients stratified into four CMSs. We identified a negative correlation between a high level of anaplastic lymphoma kinase (ALK) expression and relapse-free survival, exclusively in CMS1 subtype. Stemming from this observation, we tested several CMSs in vitro models with crizotinib (CZB) or alectinib (ALC), potent ALK inhibitors, already approved for clinical use. ALK interception strongly inhibits cell proliferation already at nanomolar doses, specifically in CMS1 cell lines, while no effect was found in CMS2/3/4 groups. Furthermore, in vivo imaging identified a role for ALK in the dynamic formation of 3D spheroids, which was impaired by the pharmacological inhibition of ALK. Consistently, CZB was responsible for the dampened activation of ALK along with the downstream AKT cascade. Mechanistically, we found a specific pro-apoptotic effect of ALK inhibition in CMS1 cell lines, both in 2D and 3D. Confocal analysis suggests that inhibition in CMS1 cells enhances cell-cell adhesion when growing in 3D. In agreement with our findings, an ALK signature encompassing 65 genes statistically associated with worse relapse-free survival in CMS1 subtype. Finally, the efficacy of ALK inhibition treatment was demonstrated in patient-derived organoids. Collectively, our findings suggest that ALK inhibition may represent an attractive therapy for CRC, and CMS classification may provide a useful tool to identify patients who could benefit from this treatment. These findings offer rationale and pharmacological strategies for the treatment of CMS1 CRC.

Non-Small Cell Lung Cancer (NSCLC) patients are diagnosed late when the disease has metastasized. Kras is a prevalent mutation in NSCLC besides EGFR and TP53 and targeted therapies against this have been challenging. We have explored deregulation of an endocytic adapter protein, Huntingtin Interacting Protein-1(HIP1) and its relevance in a Kras mutant lung adenocarcinoma cell line as a model system. HIP1 RNA expression is observed to be significantly reduced in high-grade and metastatic lung cancer patients as compared to low-grade tumours and this correlates with poor survival. HIP1 depletion followed by global proteome profiling in A549 cells identified metabolic pathways to be majorly upregulated, followed by RNA transport and surveillance, amongst others. HIP1 depletion also significantly increased anchorage independent growth and invasion of these cells. However, the EMT markers did not follow the canonical regulation. We observed E-Cadherin and Vimentin induction, which is suggestive of collective migration. Additionally, we observed a hypoxic microenvironment to induce HIP1 expression, mediated by Hypoxia Inducible Factor 2 (HIF2), suggesting that a HIF2-HIP1 axis can cause tumour suppression and needs further exploration.

Myeloproliferative neoplasms (MPNs) are caused by somatic driver mutations, such as JAK2V617F, which might also affect cellular aging and senescence. Here, we analyzed the heterogeneity of aging in MPN patients and if this can be used to specifically target malignant cells. The mean epigenetic age was significantly accelerated in 129 MPN patients across all disease-entities, whereas premature telomere attrition was particularly observed in primary myelofibrosis. Overall, accelerated cellular aging correlated with JAK2V617F allele frequency and was more pronounced in colony forming cells with JAK2V617F as compared to JAK2 wild- type colonies. JAK2V617F mutation did not evoke clear acceleration of aging in syngeneic iPSC models upon short-term hematopoietic differentiation. On the other hand, a murine Jak2V617F model revealed epigenetic age-acceleration that therefore appears as sequel of disease progression. To investigate if the malignant clone might be targeted, we tested eight senolytic compounds, of which JQ1 and piperlongumine showed a reduction in allele burden and an increase in telomere length. Notably, treatment with the telomerase inhibitor BIBR-1532 reduced mutated colonies, particularly in patients with preexisting short telomeres. Our results indicate that cellular aging is accelerated in malignant MPN clones and this can provide a target for treatment with senolytic drugs or telomerase inhibitors.

Polo-like kinase 4 (Plk4), the major regulator of centriole biogenesis, has emerged as a putative therapeutic target in cancer due to its abnormal expression in human carcinomas, leading to centrosome number deregulation, mitotic defects and chromosomal instability. Moreover, Plk4 deregulation promotes tumor growth and metastasis in mouse models and is significantly associated with poor patient prognosis. Here, we further investigate the role of Plk4 in carcinogenesis and show that its overexpression significantly potentiates resistance to cell death by anoikis of non-tumorigenic p53 knock-out (p53KO) mammary epithelial cells. Importantly, this effect is independent of Plk4s role in centrosome biogenesis, suggesting that this kinase has additional cellular functions. Interestingly, the Plk4-induced anoikis resistance is associated with the induction of a stable hybrid epithelial-mesenchymal phenotype and is partially dependent on P-cadherin upregulation. Furthermore, we found that the conditioned media of Plk4-induced p53KO mammary epithelial cells also induces anoikis resistance of breast cancer cells in a paracrine way, being also partially dependent on soluble P-cadherin secretion. Our work shows, for the first time, that high expression levels of Plk4 induce anoikis resistance of both mammary epithelial cells with p53KO background, as well as of breast cancer cells exposed to their secretome, which is partially mediated through P-cadherin upregulation. These results reinforce the idea that Plk4, independently of its role in centrosome biogenesis, functions as an oncogene, by impacting the tumor microenvironment to promote malignancy.

Lung cancer is the leading cause of mortality by cancer worldwide. Non-small cell lung cancer is the most common type of lung cancer and mutations in the KRAS gene are frequently found in this pathology. While immune checkpoint inhibitors are providing new hope for lung cancer care, only a subset of patients show durable benefit from these new therapies designed to drive an efficient anti-tumor immune response. Hence, it is crucial to better understand the mechanisms through which the tumor immune microenvironment is established in lung tumors. Using bioinformatics, we observed that high expression of the STimulator of INterferon Gene (STING) associates with a longer overall survival specifically in KRAS mutant cancer patients. In lung cancer cell lines, STING expression is linked to interferon response and epithelial-to-mesenchymal transition. Because STING activation in immune cells of the tumor microenvironment using specific agonists is an emerging strategy to trigger an anti-tumor immune response, we took advantage of two transplantable models of Kras driven lung cancer, expressing high or low levels of STING, to investigate the function of STING directly in cancer cells in vivo. We observed that high-STING expression and constitutive STING signaling were critical for transplanted tumor formation rather than playing a major role in tumor immunogenicity. Besides, low-STING expression in cancer cells is associated with an immunosuppressive tumor microenvironment characterized by the accumulation of tumor promoting SiglecF+ neutrophils and CD103+ regulatory T cells. In that model, knocking out STING increased the early response to anti-PD1 treatment. We conclude that low-STING expression in cancer cells might confer them an independence from pro-inflammatory signals and a greater immunosuppressive capability and aggressiveness.

BackgroundGenome-wide association studies (GWAS) have identified genetic susceptibility variants for both leukocyte telomere length (LTL) and lung cancer susceptibility. Recently, 108 novel genetic loci within genes involved in telomere biology and DNA repair have been linked to LTL in UK Biobank. In the current work, we investigated the relationship between genetically predicted LTL and lung cancer. MethodsTo explore the shared genetic basis between LTL and lung cancer, we performed genetic correlation, Mendelian Randomization (MR), and colocalisation analyses using the largest available GWASs of LTL (N=464,716) and lung cancer (29,239 cases; 56,450 controls). To further characterize the molecular mechanisms underlying this relationship, principal component analysis (PCA) was used to summarize gene expression profiles in lung adenocarcinoma tumours from The Cancer Genome Atlas. ResultsAlthough there was no genome-wide genetic correlation between LTL and lung cancer risk (rg=-0.01, p=0.88), MR analyses using 144 instruments identified a putatively causal association. Longer LTL conferred an increased risk of lung cancer (OR=1.62, 95%CI=1.44-1.83, p=9.9x10-15), lung cancer in never smokers (OR=2.02, 95%CI=1.45-2.83, p=3.78x10-05), and lung adenocarcinoma (OR=2.43, 95%CI=2.02-2.92, p=3.8x10-21). Of these 144 LTL genetic instruments, 12 showed evidence of colocalisation with lung adenocarcinoma risk and revealed novel susceptibility loci, including MPHOSPH6 (rs2303262), PRPF6 (rs80150989), and POLI (rs2276182). A polygenic risk score for LTL was associated with the second principal component (PC2) of gene expression (Beta=0.17, p=1.0x10-3). The aspect of PC2 associated with longer LTL was also associated with being female (p=0.005), never smokers (p=0.04), and earlier tumour stage (p=0.002). PC2 was strongly associated with cell proliferation score (p=3.6x10-30) and genomic features related to genome stability, including copy number changes (p=1.6x10-5) and telomerase activity (p=1.3x10-5) in the multivariate regression analyses. ConclusionsThis study identified an association between longer genetically predicted LTL and lung cancer and sheds light on the potential molecular mechanisms related to LTL in lung adenocarcinomas.

PTEN is the most frequently lost tumor suppressor in primary prostate cancer (PCa) and its loss is associated with aggressive disease. However, the transcriptional changes associated with PTEN loss in PCa have not been described in detail. Here, we applied a meta-analysis approach, leveraging two large PCa cohorts with experimentally validated PTEN and ERG status, to derive a transcriptomic signature of PTEN loss, while also accounting for potential confounders due to ERG rearrangements. Strikingly, the signature indicates a strong activation of both innate and adaptive immune systems upon PTEN loss, as well as an expected activation of cell-cycle genes. Moreover, we made use of our recently developed FC-R2 expression atlas to expand this signature to include many non-coding RNAs recently annotated by the FANTOM consortium. With this resource, we analyzed the TCGA-PRAD cohort, creating a comprehensive transcriptomic landscape of PTEN loss in PCa that comprises both the coding and an extensive non-coding counterpart.

Selecting appropriate experimental systems is crucial in cancer research, where factors such as model relevance, cost, and resource availability guide decisions. A detailed understanding of the strengths and limitations of each model helps ensure their optimal use. We recently developed a human lung squamous cell carcinoma (LUSC) model using genetically engineered human bronchial epithelial cells (hBECs). These were studied through organotypic air-liquid interface (ALI) cultures and standard in vitro assays, including proliferation, invasion, and anchorage-independent growth. However, we did not evaluate whether the same mutant hBECs behaved similarly in vivo, or if in vivo models offered distinct advantages. To address this, we conducted a comparative phenotypic analysis of mutant hBECs derived from the same donor in both ALI cultures and xenografts in immunocompromised mice. Both models followed a similar oncogenic trajectory, involving squamous differentiation and activation of Nrf2 and PI3K/Akt pathways, characteristic of the classical LUSC subtype. However, some transcriptomic differences related to an increase in microtubule formation and cell motility in xenografts emerged. Additionally, xenograft gene expression profiles more closely matched classical LUSC tumours than ALI cultures. Importantly, we observed spontaneous squamous differentiation in the absence of SOX2 overexpression and detected selection for NOTCH1 mutations in specific in vivo mutants. Truncation of NOTCH1 promoted squamous differentiation and suppressed mucociliary features in ALI cultures, underscoring its role as a potential LUSC driver. In summary, mutant hBECs in vitro and in vivo showed largely consistent phenotypes, validating both systems. However, in vivo models can enable the unbiased discovery of new genetic LUSC driver genes. This highlights the complementary value of integrating both model types in LUSC research.

By a classical approach, the invasive margins of colorectal carcinomas can be typed as expansive or infiltrative, the latter portending a poor prognosis. Colorectal carcinomas with infiltrative-type invasive margins have long been known for their peculiar stroma and the relative absence of a lymphohistiocytic host response, but they have not been studied with contemporary gene expression techniques. Therefore, we submitted 18 microsatellite-stable colorectal carcinomas that could be typed as having invasive margins of the infiltrative (N = 7) or expansive type (N = 11) with confidence to nanoString nCounter(R) analysis (Tumor Signaling 360 Panel). Tissue microarray punch samples were obtained from the tumors and prior to RNA extraction histological sections were prepared. The invasive margin types were mirrored surprisingly well in the two main clusters delineated by an unsupervised cluster analysis of the gene expression data, but tumor budding, the second type of colorectal carcinoma invasion phenotype, was not. Nanostring Annotation Scores were significant for signaling pathways (TGFb, PDGF, MET, FGFR), extracellular matrix remodeling, and anti-tumor immunity processes. However, any hopes that the tumour biology behind the two phenotypes of invasion could be pinpointed to differential expressions of a small set of genes were not fulfilled. Taken together, the data indeed give a molecular underpinning to the two invasion phenotypes, pointing out that matrix features and anti-tumor immunity are key. Nevertheless, we failed to gain a more detailed insight into the mechanics at work, and this may well be due to general limitations of the technology employed.

The risk of ALK-ve ALCL associated with textured breast implants (BIA-ALCL) is a notable example of lymphomas associated with medical devices. We describe 2 cases of ALK-ve ALCL associated with meshes, commonly used devices in surgical procedures such as herniorrhaphy. Our cases, each presenting some 10 years following mesh insertions, show anatomical and causal association to index tumours. In addition, we show that the genetic profile has significant overlaps with BIA-ALCL, invoking similar etiopathogenesis. Hence, we propose that mesh implant associated-ALCL (MIA-ALCL) is an unrecognised association and unreported disease entity that merits recognition, broader investigation, and surveillance.