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Palmitoylation is critically required for cancer intrinsic PD-1 expression and functions

Programmed cell death protein 1 (PD-1) is a crucial anticancer target, but the relatively low response rate and acquired resistance to existing antibody drugs highlight an urgent need to develop alternative targeting strategies. Here we report the palmitoylation of PD-1, discovered the main DHHC enzyme for this modification, revealed the mechanism for its effect on PD-1 expression, and rationally developed a peptide for targeting PD-1 expression. Palmitoylation promoted the trafficking of PD-1 to recycling endosome, thus preventing its lysosome-dependent degradation. Palmitoylation was required for the activation of PD-1 downstream signaling, and targeting palmitoylation by pharmacological inhibitor or depleting the modification enzyme caused significant anti-tumor effects. A peptide was designed to competitively inhibit PD-1 palmitoylation and expression, opening a new route for developing PD-1 inhibitors as a strategy for cancer immunotherapy.\n\nSignificanceWe show for the first time that PD-1 is palmitoylated, identify DHHC9 as the predominant enzyme for its palmitoylation, and reveal the molecular mechanisms underlying its effects on PD-1 stability and functions. Importantly, we also designed a competitive inhibitor targeting PD-1 palmitoylation, and this first-in-class molecule may inspire the development of new checkpoint inhibitors.

cancer biology

CAIX forms a transport metabolon with monocarboxylate transporters in human breast cancer cells

Tumor cells rely on glycolysis to meet their elevated demand for energy. Thereby they produce significant amounts of lactate and protons, which are exported via monocarboxylate transporters (MCTs), supporting the formation of an acidic microenvironment. The present study demonstrates that carbonic anhydrase IX (CAIX), one of the major acid/base regulators in cancer cells, forms a protein complex with MCT1 and MCT4 in tissue samples from human breast cancer patients, but not healthy breast tissue. Formation of this transport metabolon requires binding of CAIX to the Ig1 domain of the MCT1/4 chaperon CD147 and is required for CAIX-mediated facilitation of MCT1/4 activity. Application of an antibody, directed against the CD147-Ig1 domain, displaces CAIX from the transporter and suppresses CAIX-mediated facilitation of proton-coupled lactate transport. In cancer cells, this \"metabolon disruption\" results in a decrease in lactate transport, reduced glycolysis and ultimately reduced cell proliferation. Taken together, the study shows that carbonic anhydrases form transport metabolons with acid/base transporters in human tumor tissue and that these interactions can be exploited to interfere with tumor metabolism and proliferation.

cancer biology

RNA binding kinase UHMK1 regulates therapy induced metabolic adaptation in BRAFV600 melanoma

Despite the success of therapies targeting oncogenes in cancer, clinical outcomes are limited by a residual disease that results in relapse. This residual disease is characterized by drug-induced adaptation, that in melanoma includes altered metabolism. Here, we examined how targeted therapy reprograms metabolism in BRAF-mutant melanoma cells using a genome-wide RNAi screen and global gene expression profiling. This systematic approach revealed post-transcriptional regulation of metabolism following BRAF inhibition, involving selective mRNA transport and translation. As proof of concept we demonstrate the RNA binding kinase UHMK1 interacts with mRNAs that encode metabolic proteins and selectively controls their transport and translation during adaptation to BRAF targeted therapy. Inactivation of UHMK1 improves metabolic response to BRAF targeted therapy and delays resistance to BRAF and MEK combination therapy in vivo. Our data support a model wherein post-transcriptional gene expression pathways regulate metabolic adaptation underpinning targeted therapy response and suggest inactivation of these pathways may delay disease relapse.

cancer biology

Dietary methionine restriction targets one carbon metabolism in humans and produces broad therapeutic responses in cancer

Nutrition exerts profound effects on health and dietary interventions are commonly used to treat diseases of metabolic etiology. Although cancer has a substantial metabolic component, the principles that define whether nutrition may be used to influence tumour outcome are unclear. Nevertheless, it is established that targeting metabolic pathways with pharmacological agents or radiation can sometimes lead to controlled therapeutic outcomes. In contrast, whether specific dietary interventions could influence the metabolic pathways that are targeted in standard cancer therapies is not known. We now show that dietary restriction of methionine (MR), an essential amino acid, and the reduction of which has aging and obesogenic properties, influences cancer outcome through controlled and reproducible changes to one carbon metabolism. This pathway metabolizes methionine and further is the target of a host of cancer interventions involving chemotherapy and radiation. MR produced therapeutic responses in chemoresistant RAS-driven colorectal cancer patient derived xenografts and autochthonous KRASG12D+/-;TP53-/- -driven soft tissue sarcomas resistant to radiation. Metabolomics revealed the therapeutic mechanisms to occur through tumor cell autonomous effects on the flux through one carbon metabolism that impacted redox and nucleotide metabolism, thus interacting with the antimetabolite or radiation intervention. Finally, in a controlled and tolerated feeding study in humans, MR resulted in similar effects on systemic metabolism as obtained in responsive mice. These findings provide evidence that a targeted dietary manipulation can affect specific tumor cell metabolism to mediate broad aspects of cancer outcome.

cancer biology

RUNX1/RUNX1T1 controls alternative splicing in the t(8;21)-positive acute myeloid leukemia cells

The fusion oncogene RUNX1/RUNX1T1 encodes an aberrant transcription factor, which plays a key role in the initiation and maintenance of the t(8;21)-positive acute myeloid leukemia. Here we show that this oncogene is a regulator of the alternative RNA splicing for a sub-set of genes in the leukemia cells. We found two primary mechanisms underlying changes in the production of RNA isoforms: (i) RUNX1/RUNX1T1-mediated regulation of alternative transcription start sites selection in target genes, and (ii) direct or indirect control of the expression of the genes encoding splicing factors. The first mechanism leads to the expression of RNA isoforms with alternative structure of the 5-UTR regions. The second mechanism generates alternative transcripts with new junctions between internal cassettes and constitutive exons. We also show that RUNX1/RUNX1T1-mediated differential splicing affects several functional groups of genes and produces proteins with unique conserved domain structures. In summary, this study reveals a novel layer of RUNX1/RUNX1T1-dependent transcriptome organization in t(8;21)-positive acute myeloid leukemia.

cancer biology

Heterogeneous disease-propagating stem cells in juvenile myelomonocytic leukemia

Juvenile Myelomonocytic Leukemia (JMML) is a poor prognosis childhood leukemia usually caused by germline or somatic RAS-activating mutations. The cellular hierarchy in JMML is poorly characterized, including the identity of leukemia stem cells (LSCs). FACS and single-cell RNA-sequencing reveal marked heterogeneity of JMML hematopoietic stem/progenitor cells (HSPCs), including an aberrant Lin-CD34+CD38-CD90+CD45RA+ population. Single-cell HSPC index-sorting and clonogenic assays show that (1) all somatic mutations can be backtracked to the phenotypic HSC compartment with RAS-activating mutations as a \"first hit\", (2) mutations are acquired with both linear and branching patterns of clonal evolution and (3) mutant HSPCs are present after allogeneic HSC transplant before molecular/clinical evidence of relapse. Stem cell assays reveal inter-patient heterogeneity of JMML-LSCs which are present in, but not confined to, the phenotypic HSC compartment. RNA-sequencing of JMML-LSCs reveals upregulation of stem cell and fetal genes (HLF, MEIS1, CNN3, VNN2, HMGA2) and candidate therapeutic targets/biomarkers (MTOR, SLC2A1, CD96) paving the way for LSC-directed disease monitoring and therapy in this disease.

cancer biology

Protein Expression Patterns in ovarian cancer cells Associated with Monofunctional Platinums Treatment

Platinum drugs cisplatin and carboplatin, given in combination with paclitaxel, constitute the standard chemotherapy against ovarian cancer (OC). Oc chemoresistance is a major obstacle to effective treatment, but knowledge of the mechanisms that underlie it remains incomplete. We thus sought to discover key proteins associated with platinum resistance by comparing A2780 OC cells with A2780cisR cells (resistant cells derived from the A2780 line) to identify proteins with markedly altered expression levels in the resistant cells. We also determined which proteins in these cells had altered expression in response to treatment with either designed monofunctional platinum alone or a combination with cisplatin with selected phytochemical therapeutic agents.\n\nWe thus performed proteomic analysis using 2D-gel electrophoresis A2780 and A2780cisR to identify proteins with differential expression; these were eluted and analysed by mass spectrometry to identify them. A total of 122 proteins were found to be differentially expressed between A2780 and A2780cisR cell lines in the absence of any drug treatment. Among them, levels of 27 proteins in A2780cisR cell line were further altered (up-or down-regulated) in response to one or more of the drug treatments. We then investigated primary OC tissue RNA expression levels (compared to l ovarian tissue) of genes coding for these candidate 27 proteins using publically available datasets (The Cancer Genome Atlas). We assessed how expression of these genes in OC tissue associates with patient survival using Cox Proportional Hazard (PH) regression models to determine relative risk of death associated with each factor. Our Cox PH regression-based machine learning method confirmed a significant relationship of mortality with altered expression of ARHGDIA, CCT6A and HISTIH4F genes. This indicated that these genes affect OC patient survival, i.e., provided mechanistic evidence, in addition to that of the clinical traits, that these genes may be critical mediators of the processes that underlie OC progression and mortality.\n\nThus, we identified differentially expressed proteins that are implicated in platinum-based chemotherapy resistance mechanisms which may serve as resistance biomarkers. These drug resistance associated proteins may also serve as potential OC therapeutic targets whose blockade may enhance the effectiveness of platinum based drugs.

cancer biology

An in vivo inflammatory loop potentiates KRAS blockade

KRAS inhibitors perform inferior to other targeted drugs. To investigate a possible reason for this, we treated cancer cells with KRAS inhibitors deltarasin (targeting phosphodiesterase-{delta}), cysmethynil (targeting isoprenylcysteine carboxylmethyltransferase), and AA12 (targeting KRASG12C), and silenced/overexpressed mutant KRAS using custom vectors. We show that KRAS-mutant tumor cells exclusively respond to KRAS blockade in vivo, because the oncogene co-opts host myeloid cells via a C-C-motif chemokine ligand 2/interleukin-1{beta} signaling loop for sustained tumorigenicity. Indeed, KRAS-mutant tumors did not respond to deltarasin in Ccr2 and Il1b gene-deficient mice, but were deltarasin-sensitive in wild-type and Ccr2-deficient mice adoptively transplanted with wild-type murine bone marrow. A KRAS-dependent pro-inflammatory transcriptome was prominent in human cancers with high KRAS mutation prevalence and predicted poor survival. Hence the findings support that in vitro systems are suboptimal for anti-KRAS drug screens, and suggest that interleukin-1{beta} blockade might be specific for KRAS-mutant cancers.

cancer biology

MEK1/2 in Rhabdomyosarcoma

Alveolar and embryonal rhabdomyosarcoma (RMS) are soft-tissue cancers that affect children, adolescents, and young adults. Sometimes referred to as muscle cancer, RMS is a cancer of muscle and non-muscle origin that phenocopies incompletely differentiated myoblasts or activated satellite (muscle stem) cells. Interestingly, embryonal RMS (ERMS) has been observed to undergo terminal myogenic differentiation in response to stress induced by chemotherapy and radiation therapy4, 9, 24. Given the propensity of rhabdomyosarcoma to differentiation, in this report we explore the use of differentiation therapy combining MEK inhibitor (MEKi) cobimetinib and chemotherapy as a strategy to halt RMS growth. We evaluated a representative panel of RMS cell lines with cobimetinib and chemotherapy in two dosing schedules that mimic clinical use followed by cell growth evaluation and high content analysis (differentiation) assays. We uncovered that cobimetinib does not have significant additive or synergistic effects on cell differentiation or cell growth with chemotherapy in RMS and can have unanticipated antagonistic effects; specifically, pre-exposure of cobimetinib to cells can decrease the effectiveness of chemotherapy-mediated cell growth inhibition in vitro. Although differentiation-therapy is still a potential viable strategy in RMS, our data do not support MEKi/chemotherapy co-treatment in this context.

cancer biology

Modeling glioblastoma invasion using human brain organoids and single-cell transcriptomics

Glioblastoma multiforme (GBM) are devastating neoplasms with high invasive capacity. GBM has been difficult to study in vitro. Therapeutic progress is also limited by cellular heterogeneity within and between tumors. To address these challenges, we present an experimental model using human cerebral organoids as a scaffold for patient-derived glioblastoma cell invasion. By tissue clearing and confocal microscopy, we show that tumor cells within organoids extend a network of long microtubes, recapitulating the in vivo behavior of GBM. Single-cell RNA-seq of GBM cells before and after co-culture with organoid cells reveals transcriptional changes implicated in the invasion process that are coherent across patient samples, indicating that GBM cells reactively upregulate genes required for their dispersion. Functional therapeutic targets are identified by an in silico receptor-ligand pairing screen detecting potential interactions between GBM and organoid cells. Taken together, our model has proven useful for studying GBM invasion and transcriptional heterogeneity in vitro, with applications for both pharmacological screens and patient-specific treatment selection at a time scale amenable to clinical practice.

cancer biology

Amplification of genomic regions harbouring genes with dose-limiting effects provides selection pressure for acquiring aberrant epigenetic silencing in ovarian cancer

High-grade serous ovarian cancer (HGSOC) feature widespread genomic rearrangements that alter the copy number of genes. Genes for which elevated expression is detrimental to growth may be passengers in rearrangements that increase the copy number of strongly selective driver genes. There would then be selection pressure for compensatory epigenetic silencing of such passenger genes, such as through promoter DNA methylation.\n\nWe have used two independent cohorts of primary HGSOC tumour samples to provide evidence of consistent dosage-compensating promoter methylation (DCPM) genome-wide. Mapping CpG methylation to genomic copy number, we show that bias due to variable tumour cellularity of tissue samples results in false positive associations between methylation and copy number. Adjusting for this bias, we found that approximately 5-10% of all measured promoter CpGs with copy number gain showed a statistically significant increase in methylation. DCPM nullifies the association between increased copy number and increased gene expression. We confirmed a functional basis for selective pressure against over-expressing two candidate passenger genes in the 3q12 locus, as overexpressing either gene reduced spheroid formation efficiency in two HGSOC cell lines. DCPM represents a novel class of specific functional interactions between genetic and epigenetic landscapes of cancers.

cancer biology

Co-regulation and functional cooperativity of FOXM1 and RHNO1 bidirectional genes in ovarian cancer

We report that the oncogenic transcription factor FOXM1 is arranged in a head-to-head configuration with RHNO1, a gene involved in the ATR/CHK1-dependent DNA replication stress (DRS) response. FOXM1 and RHNO1 are both amplified and upregulated in high-grade serous ovarian cancer (HGSC). FOXM1 and RHNO1 expression are closely associated in normal and cancer tissues, including single cells, and a bidirectional promoter (F/R-BDP) mediates balanced expression. Targeting of FOXM1 and RHNO1 in HGSC cells using shRNA, CRISPR mutagenesis, or CRISPR interference directed to the F/R-BDP reduced DNA homologous recombination repair (HR) capacity, increased DNA damage, reduced clonogenic survival, and sensitized HGSC cells to the poly-ADP ribosylase inhibitor (PARPi) olaparib. Thus, there is functional cooperativity between FOXM1 and RHNO1 in cancer cells, and combinatorial targeting of this bidirectional gene pair may be a novel cancer therapeutic strategy. More broadly, our data provide evidence that bidirectional gene units function in human cancer.

cancer biology

A reference model for the combination of an arbitrary number of drugs: A generalization of the Bliss independence model

It is commonplace to determine the effectiveness of the combination of drugs by comparing the observed effects to a reference model that describes the combined effect under the assumption that the drugs do not interact. Depending on what is to be understood by non-interacting behavior, several reference models have been developed in the literature. One of them is the celebrated Bliss independence model, which assimilates non-interaction with statistical independence. Intuitively, this requires the dose-response curves to have zero as minimal effect and one as maximal effect, a restriction that was indeed adopted by Bliss. However, we show how non-interaction can be interpreted in terms of statistical independence, while nevertheless allowing arbitrary values for the minimal and the maximal effect. Furthermore, our reference model allows the maximal effects of the dose-response curves to be different. In a first step, we construct a basic reference model for the case of two drugs and where the maximal effects of the two individual dose-response curves are assumed to be equal. By relying on the notion of non-interaction in terms of statistical independence, and by introducing two consistency principles, we show how a unique reference model can be derived. In a second step, a more general reference model, allowing the maximal effects to be different while still restricting to two drugs, is then easily constructed from the basic reference model. Finally, an induction step is applied to generalize the reference model to the case of an arbitrary number of drugs, allowing each dose-response curve to have a possibly different maximal effect. Although the minimal effect of the dose-response curves are restricted to be equal, which we show to be a necessary consequence of consistency rules, its value is arbitrary.\n\nAuthor summaryThe Bliss independence model is a very popular reference model for drug combinations, meaning that it predicts the combined effect of doses of given drugs under the assumption of non-interaction between these drugs. However, because Bliss described non-interaction as statistical independence, he thought that he had to assume that the minimal effect of all dose-response curves are zero, while the maximal effect of all dose-response curves are one. While it is acceptable that all dose-response curves have minimal effect zero, because this amounts to having a common reference state (i.e. the response when no drug at all is given), it is a severe restriction to force all dose-response curves to have maximal effect one. On the other hand, the Bliss independence model has the advantage that it relies on sound statistical theory, and the assimilation of non-interaction with statistical independence is rather intuitive. We have extended the Bliss independence model to allow the involved dose-response curves to have different maximal effects. This has been done in a rigorous way, where the statistical underlying theory that was used by Bliss remains essentially intact.

cancer biology

Predicting patient-specific radiotherapy responses in head and neck cancer to personalize radiation dose fractionation

Human papillomavirus (HPV) related oropharyngeal cancer (OPC) is one of the few types of cancers increasing in incidence. HPV+ OPC treatment with radiotherapy (RT) provides 75-95% five-year locoregional control (LRC). Why some but not all patients with similar clinical stage and molecular profile are controlled remains unknown. We propose the proliferation saturation index, PSI, as a mathematical modeling biomarker of tumor growth and RT response. The model predicts that patients with PSI<0.75 are likely to be cured by radiation, and that hyperfractionated radiation could improve response rates for patients with higher PSI that are predicted to fail standard of care RT. Prospective evaluation is currently ongoing.

cancer biology

HYPER-sol: flash-frozen results from archival FFPE tissue for clinical proteomics

Massive formalin-fixed, paraffin-embedded (FFPE) tissue archives exist worldwide, representing a potential gold mine for clinical proteomics research. However, current protocols for FFPE proteomics lack standardization, efficiency, reproducibility, and scalability. Here we present High-Yield Protein Extraction and Recovery by direct SOLubilization (HYPERsol), an optimized workflow using adaptive-focused acoustics (AFA) ultrasonication and S-Trap sample processing that enables proteome coverage and quantification from FFPE samples comparable to that achieved from flash-frozen tissue (average R = 0.936).

cancer biology

Well-Differentiated Papillary Mesothelioma of the Peritoneum is Genetically Distinct from Malignant Mesothelioma

Well-differentiated papillary mesothelioma (WDPM) is an uncommon mesothelial proliferation that is most commonly encountered as an incidental finding in the peritoneal cavity. There is controversy in the literature about whether WDPM is a neoplasm or a reactive process, and if neoplastic, whether it is a variant or precursor of epithelial malignant mesothelioma or is a different entity. Using whole exome sequencing of five WDPM of the peritoneum, we have identified distinct mutations in EHD1, ATM, FBXO10, SH2D2A, CDH5, MAGED1, and TP73 shared by WDPM cases but not reported in malignant mesotheliomas. Furthermore, we show that WDPM is strongly enriched with C>A transversion substitution mutations, a pattern that is also not found in malignant mesotheliomas. The WDPMs lacked alterations involving BAP1, SETD2, NF2, CDKN2A/B, LASTS1/2, PBRM1, and SMARCC1 that are frequently altered in malignant mesotheliomas. We conclude that WDPMs are neoplasms that are genetically distinct from malignant mesotheliomas, and based on observed mutations do not appear to be precursors of malignant mesotheliomas.

cancer biology

Liquid condensation drives telomere clustering during ALT

Telomerase-free cancer cells employ a recombination-based alternative lengthening of telomeres (ALT) pathway that depends on ALT-associated promyelocytic leukemia (PML) nuclear bodies (APBs), whose function is unclear. We find that APBs behave as liquid condensates, suggesting two potential mechanisms to promote telomere elongation: condensation to enrich DNA repair factors for telomere synthesis and coalescence to cluster telomeres to provide repair templates. Using chemically-induced dimerization, we show that telomere sumoylation nucleates APB condensation via SUMO-SIM (SUMO interaction motif) interactions and clusters telomeres. The induced APBs lack DNA repair factors, indicating that these factors are clients recruited to the APB scaffold rather than components that drive condensation. Telomere clustering, however, relies only on liquid properties of the condensate, as an alternative condensation chemistry also induces clustering. Our results demonstrate how the material properties and chemical composition of APBs independently contribute to ALT, suggesting a general framework for how liquid condensates promote cellular functions.

cancer biology

DYRK2 activates heat shock factor 1 promoting resistance to proteotoxic stress and tumour growth in triple-negative breast cancer

To survive aneuploidy-induced proteotoxic stress, cancer cells activate the proteotoxic-stress response pathway, which is controlled by heat shock factor 1 (HSF1). This pathway supports cancer initiation, cancer progression and chemoresistance and thus is an attractive target. As developing HSF1 inhibitors is challenging, the identification and targeting of upstream regulators of HSF1 presents a tractable alternative strategy. Here we demonstrate that in triple negative breast cancer (TNBC) cells, the dual-specificity tyrosine-regulated kinase 2 (DYRK2) phosphorylates HSF1, promoting its nuclear stability and transcriptional activity. Thus, DYRK2 depletion reduces HSF1 activity and sensitises TNBC cells to proteotoxic stress. Importantly, in tumours from TNBC patients, DYRK2 levels positively correlate with active HSF1 and associates with poor prognosis, suggesting that DYRK2 could be promoting TNBC. In agreement with this, DYRK2 depletion reduces tumour growth in a TNBC xenograft model. These findings identify DYRK2 as both, a key modulator of the HSF1 transcriptional program, and a potential therapeutic target.

cancer biology