PaperPlayer biorxiv cancer biology

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.13.249029v1?rss=1

Authors: Pozo, K., Kollipara, R. K., Kelenis, D. P., Rodarte, K. E., Zhang, X., Minna, J. D., Johnson, J. E.

Abstract:

Lineage-defining transcription factors (LTFs) play key roles in tumor cell growth, making them highly attractive, but currently undruggable, small cell lung cancer (SCLC) vulnerabilities. Delineating LTF genomic binding sites and associated chromatin features would provide important insights into SCLC dependencies. Here we map super-enhancers (SEs) across multiple patient-derived SCLC preclinical models, and find SE patterns are sufficient to classify the models into the recently defined, LTFbased, SCLC subtypes. 3D-chromatin conformation analysis identified genes associated with SEs that define subtype-specific tumor signatures with genes functioning in diverse processes. Focusing on ASCL1-high SCLC (SCLC-A), we found ASCL1 physically interacts with NKX2-1 and PROX1. These factors bind overlapping genomic regions, and co-regulate a set of genes, including genes encoding cell surface proteins, SCN3A and KCNB2 enriched in SCLC-A. Genetic depletion of NKX2-1 or PROX1 alone, or in combinations with ASCL1, did not inhibit SCLC growth more than that achieved by depleting ASCL1 alone. We demonstrate the SE signature supports the LTF classification of SCLC, identify NKX2-1 and PROX1 as ASCL1 co-factors, and substantiate the central importance of ASCL1 as a key dependency factor in the majority of SCLC. The LTF and SE gene sets provide a molecular roadmap for future ASCL1 therapeutic targeting studies.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.12.246660v1?rss=1

Authors: Huang, L., Zhang, X.-O., Verdejo-Torres, O., Wigglesworth, K., Sun, X., Sallis, B., Moon, D., Huang, T., Rozen, E., Zhang, L., Wang, G., Shohet, J. M., Lee, M. M., Wu, J. Q.

Abstract:

Protein arginine methyltransferase 5 (PRMT5) generates most of the symmetric di-methyl-arginine marks on histones and non-histone proteins by which it regulates a wide range of physiological processes including cancer cell proliferation and metastasis. Here, we report that PRMT5 directly regulates epidermal growth factor receptor (EGFR) transcription and thus controls EGF stimulated EGFR signaling. PRMT5 modulates protein kinase B (AKT) activation by methylation of AKT1 Arg 15, which is required for its subsequent phosphorylation at AKT1 Thr 308 and Ser 473. The PRMT5/EGFR/AKT axis converges to regulate transcription factors ZEB1, SNAIL, and TWIST1 to promote the epithelial-mesenchymal transition (EMT), which supports tumor cell invasion and metastasis. Inhibiting PRMT5 methyltransferase activity with a small molecule inhibitor attenuated primary tumor growth and prevented hepatic metastasis in aggressive tumor models in vivo. Collectively, our results support the use of PRMT5 based therapies for metastatic cancer.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.12.247817v1?rss=1

Authors: Talwelkar, S. S., Mäyranpää, M. I., Soraas, L., Potdar, S., Bao, J., Hemmes, A., Linnavirta, N., Lomo, J., Räsänen, J., Knuuttila, A., Wennerberg, K., Verschuren, E. W.

Abstract:

Functional profiling of a cancer patient's tumor cells holds potential to tailor personalized cancer treatment. Here we report the utility of Fresh Uncultured Tumor-derived EpCAM+ epithelial Cells (FUTC) for ex vivo drug response interrogation. Analysis of murine Kras mutant FUTCs demonstrated pharmacological and adaptive signaling profiles comparable to subtype-matched cultured cells. Applying FUTC profiling on non-small cell lung cancer patient samples, we generated robust drug response data in 18 of 19 cases, where the cells exhibited targeted drug sensitivities corresponding to their oncogenic drivers. In one of these cases, an EGFR mutant lung adenocarcinoma patient refractory to osimertinib, FUTC profiling was used to guide compassionate treatment. FUTC profiling identified selective sensitivity to disulfiram and the combination of carboplatin plus etoposide and the patient received substantial clinical benefit from the treatment with these agents. We conclude that FUTC profiling provides a robust, rapid, and actionable assessment of personalized cancer treatment options.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.11.246785v1?rss=1

Authors: Franco Nitta, C., Green, E. W., Jhamba, E. D., Keth, J. M., Ortiz-Caraveo, I., Grattan, R. M., Schodt, D. J., Gibson, A. C., Rajput, A., Lidke, K. A., Steinkamp, M. P., Wilson, B. S., Lidke, D. S.

Abstract:

Crosstalk between disparate membrane receptors is thought to drive oncogenic signaling and allow for therapeutic resistance. EGFR and RON are members of two unique receptor tyrosine kinase (RTK) subfamilies that engage in crosstalk through unknown mechanisms. We combined high resolution imaging with biochemical studies and structural mutants to understand how EGFR and RON communicate. We found that EGF stimulation results in EGFR-dependent RON phosphorylation. Crosstalk is unidirectional, since MSP stimulation of RON does not trigger EGFR phosphorylation. Two-color single particle tracking captured the formation of complexes between RON and EGFR, supporting a role for direct interactions in propagating crosstalk. We further show that RON is a substrate for EGFR kinase, and transactivation of RON requires the formation of a signaling competent EGFR dimer. These results identify critical structural features of EGFR/RON crosstalk and provide new mechanistic insights into therapeutic resistance.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.12.247460v1?rss=1

Authors: Lang, J.-Y., Wang, X., Xie, Q., Ji, Y., Shen, J., Wang, C., Jiang, X., Chen, Z., Zhang, Y., Kong, X., Ding, J.

Abstract:

KRAS is widely mutated in human cancers, resulting in nearly unchecked tumour proliferation and metastasis. No therapies have been developed for targeting KRAS-mutant tumours. Herein, we observed that KRAS-mutant stomach/colorectal tumour cells were hypersensitive to the MEK1/2 kinase inhibitor trametinib, which elicits strong apoptotic responses. Genome-wide screening revealed that TP53 is critical for executing trametinib-induced apoptosis of KRAS-mutant tumours, as validated by TP53 knockout and rescue experiments. Mechanistically, p53 physically associates with phosphorylated ERK2 in the presence of mutant KRAS, which inactivates p53 by preventing the recruitment of p300/CBP. Trametinib disrupts the p53-ERK2 complex by inhibiting ERK2 phosphorylation, allowing the recruitment of p300/CBP to acetylate p53 protein; acetylated p53 activates PUMA transcription and thereby promotes the apoptosis of KRAS-mutant tumours. Our study unveils an important role of the ERK2-p53 axis and provides a potential therapeutic strategy for treating KRAS- mutant cancer via ERK2 inhibition.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.12.248443v1?rss=1

Authors: Otvos, B., Alban, T. J., Grabowski, M. M., Bayik, D., Mulkearns-Hubert, E. E., Radivoyevitch, T., Rabljenovic, a., Johnson, S., Androjna, C., Mohammadi, A. M., Barnett, G., Ahluwalia, M. S., Vogelbaum, M. A., Fecci, P. E., Lathia, J. D.

Abstract:

Recent advances in cancer immunotherapy have created a greater appreciation of potential anti-tumoral impacts by the immune system; however, individual patient responses have been variable. While immunotherapy is often given after standard-of-care treatment, the effects of initial interventions on the ability of the immune system to mount a response are not well understood and this may contribute to the variable response. For glioblastoma (GBM), initial disease management includes surgical resection, perioperative high-dose steroid therapy, chemotherapy, and radiation treatment. While new discoveries regarding the impact of chemotherapy and radiation on immune response have been made and translated to clinical trial design, the impact of surgical resection and steroids on the anti-tumor immune response has yet to be determined. Further, it is now accepted that steroid usage needs to be closely evaluated in the context of GBM and immunotherapy trials. To better model the clinical scenario in GBM, we developed a mouse model that integrates tumor resection and steroid treatment to understand how these therapies affect local and systemic immune responses. Using this model, we observed a systemic reduction in lymphocytes associated with surgical resection and identified a correlation between increased tumor volume and decreased circulating lymphocytes, a relationship that was obviated by dexamethasone treatment. Furthermore, we investigated the possibility of there being similar relationships in a cohort of patients with GBM and found that prior to steroid treatment, circulating lymphocytes inversely correlated with tumor volume. Lastly, correlating GBM patient data and outcomes demonstrated that peripherally circulating lymphocyte content varies with progression-free and overall survival, independent of tumor volume, steroid use, or tumor molecular profiles. These results highlight the systemic immunosuppressive effects that initial therapies can have on patients. Such effects should be considered when designing current and future immunotherapy clinical trials and underscore the importance of circulating lymphocytes as a possible correlate of GBM disease progression.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.12.248559v1?rss=1

Authors: Constantin, D., Widmann, C.

Abstract:

It is of clinical importance to identify biomarkers predicting the efficacy of DNA damaging drugs (genotoxins) so that non-responders are not unduly exposed to the deleterious effects of otherwise inefficient drugs. Using a whole genome CRISPR/Cas9 gene knockout approach we have identified that low levels of ASH2L cause resistance to genotoxins. ASH2L is a core component of the H3K4 methyl transferase complex. We show that ASH2L absence decreases cell proliferation and favors DNA repair upon genotoxin exposure. The cell models we have used are derived from cancers currently treated either partially (Hodgkins lymphoma), or entirely (testicular cancer) with genotoxins. For such cancers, ASH2L levels could be used as a biomarker to predict the response to genotoxins. Our data also indicate that patients with low ASH2L expressing tumors do not develop resistance to ATR inhibitors. In these patients, such inhibitors may represent an alternative treatment to DNA damaging drugs.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.11.245787v1?rss=1

Authors: Simeonov, K. P., Byrns, C. N., Clark, M. L., Norgard, R. J., Martin, B., Stanger, B. Z., McKenna, A., Shendure, J., Lengner, C. J.

Abstract:

Metastatic cancer remains largely incurable due to an incomplete understanding of how cancer cells disseminate throughout the body. However, tools for probing metastatic dissemination and associated molecular changes at high resolution are lacking. Here we present multiplexed, activatable, clonal, and subclonal GESTALT (macsGESTALT), an inducible lineage recorder with concurrent single cell readout of transcriptional and phylogenetic information. By integrating multiple copies of combined static barcodes and evolving CRISPR/Cas9 barcodes, macsGESTALT enables clonal tracing and subclonal phylogenetic reconstruction, respectively. High barcode editing and recovery rates produce deep lineage reconstructions, densely annotated with transcriptomic information. Applying macsGESTALT to a mouse model of metastatic pancreatic cancer, we reconstruct dissemination of tens-of-thousands of single cancer cells representing 95 clones and over 6,000 unique subclones across multiple distant sites, e.g. liver and lung metastases. Transcriptionally, cells exist along a continuum of epithelial-to-mesenchymal transition (EMT) in vivo with graded changes in associated signaling, metabolic, and regulatory processes. Lineage analysis reveals that from a majority of non-metastatic, highly epithelial clones, a single dominant clone that has progressed along EMT drives the majority of metastasis. Within this dominant clone a parallel process occurs, where a small number of aggressive subclones drive clonal outgrowth. By precisely mapping subclones along the EMT continuum, we find that size and dissemination gradually increase, peaking at late-hybrid EMT states but precipitously falling once subclones are highly mesenchymal. Late-hybrid EMT states are selected from a predominately epithelial ancestral pool, enabling rapid metastasis but also forcing extensive and continuous population bottlenecking. Notably, late-hybrid gene signatures are associated with decreased survival in human pancreatic cancer, while epithelial, early-hybrid, and highly mesenchymal states are not. Our findings illuminate features of metastasis and EMT with the potential for therapeutic exploitation. Ultimately, macsGESTALT provides a powerful, accessible tool for probing cancer and stem cell biology in vivo.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.11.246777v1?rss=1

Authors: Kim, J. H., Megquier, K. J., Thomas, R., Sarver, A. L., Song, J. M., Kim, Y. T., Schulte, A. J., Cheng, N., Linden, M. A., Murugan, P., Oseth, L., Foster, C. L., Elvers, I., Swofford, R., Turner-Maier, J., Karlsson, E. K., Breen, M., Lindblad-Toh, K., Modiano, J. F.

Abstract:

Sporadic angiosarcomas (ASs) are aggressive vascular sarcomas whose rarity and genomic complexity present significant obstacles in deciphering the pathogenic significance of individual genetic alterations. Numerous fusion genes have been identified across multiple types of cancers, but their existence and significance remain unclear in sporadic ASs. In this study, we leveraged RNA sequencing data from thirteen human ASs and 76 spontaneous canine hemangiosarcomas (HSAs) to identify fusion genes associated with spontaneous vascular malignancies. Ten novel protein-coding fusion genes, including TEX2-PECAM1 and ATP8A2-FLT1, were identified in seven of the thirteen human tumors, with two tumors showing mutations of TP53. HRAS and NRAS mutations were found in ASs without fusions or TP53 mutations. We found fifteen novel protein-coding fusion genes including MYO16-PTK2, GABRA3-FLT1, and AKT3-XPNPEP1 in eleven of the 76 canine HSAs; these fusion genes were seen exclusively in tumors of the angiogenic molecular subtype that contained recurrent mutations in TP53, PIK3CA, PIK3R1, and NRAS. In particular, fusion genes and mutations of TP53 co-occurred in tumors with higher frequency than expected by random chance, and they enriched gene signatures predicting activation of angiogenic pathways. Comparative transcriptomic analysis of human ASs and canine HSAs identified shared molecular signatures associated with activation of PI3K/AKT/mTOR pathways. Our data suggest that genomic instability induced by TP53 mutations might create a predisposition for fusion events that may contribute to tumor progression by promoting selection and/or enhancing fitness through activation of convergent angiogenic pathways in this vascular malignancy.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.11.245886v1?rss=1

Authors: Rieunier, G., Wu, X., Harris, L., Mills, J., Nandakumar, A., Colling, L., Seraia, E., Hatch, S. B., Ebner, D., Folkes, L., Weyer-czernilofsky, U., Bogenrieder, T., Ryan, A. J., Macaulay, V. M.

Abstract:

IGF receptor (IGF-1R) inhibition delays repair of radiation-induced DNA double-strand breaks (DSBs), prompting us to investigate whether IGF-1R influences endogenous DNA damage. We demonstrate that IGF-1R inhibition generates endogenous DNA lesions protected by 53BP1 bodies, indicating under-replicated DNA. We detect delayed replication fork progression in IGF-inhibited or IGF-1R depleted cancer cells, with activation of ATR-CHK1 signaling and the intra-S-phase checkpoint. This phenotype reflects unanticipated regulation of global replication by IGF-1, mediated via AKT, MEK/ERK and JUN to influence expression of ribonucleotide reductase (RNR) subunit RRM2. IGF-1R inhibition or depletion downregulate RRM2, compromising RNR function and dNTP supply. The resulting delay in fork progression and hallmarks of replication stress are rescued by RRM2 overexpression, confirming RRM2 as the critical factor through which IGF-1 regulates replication. Following targeted compound screens, we identify synergy between IGF inhibition and ATM loss, with evidence that IGF inhibition compromises growth of ATM null cells and xenografts. This synthetic lethal effect reflects conversion of single-stranded lesions in IGF-inhibited cells into toxic DSBs upon ATM inhibition. These data implicate IGF-1R in alleviating replication stress, and the identified reciprocal IGF:ATM co-dependence provides an approach to exploit this effect in ATM-deficient cancers.

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