bims-tucedo Biomed News
on Tumor cell dormancy
Issue of 2020‒07‒19
twenty-two papers selected by
Isabel Puig Borreil
Vall d’Hebron Institute of Oncology

  1. Nat Cancer. 2020 Jan;1(1): 28-45
    Ganesh K, Basnet H, Kaygusuz Y, Laughney AM, He L, Sharma R, O'Rourke KP, Reuter VP, Huang YH, Turkekul M, Emrah E, Masilionis I, Manova-Todorova K, Weiser MR, Saltz LB, Garcia-Aguilar J, Koche R, Lowe SW, Pe'er D, Shia J, Massagué J.
      Metastasis-initiating cells with stem-like properties drive cancer lethality, yet their origins and relationship to primary-tumor-initiating stem cells are not known. We show that L1CAM+ cells in human colorectal cancer (CRC) have metastasis-initiating capacity, and we define their relationship to tissue regeneration. L1CAM is not expressed in the homeostatic intestinal epithelium, but is induced and required for epithelial regeneration following colitis and in CRC organoid growth. By using human tissues and mouse models, we show that L1CAM is dispensable for adenoma initiation but required for orthotopic carcinoma propagation, liver metastatic colonization and chemoresistance. L1CAMhigh cells partially overlap with LGR5high stem-like cells in human CRC organoids. Disruption of intercellular epithelial contacts causes E-cadherin-REST transcriptional derepression of L1CAM, switching chemoresistant CRC progenitors from an L1CAMlow to an L1CAMhigh state. Thus, L1CAM dependency emerges in regenerative intestinal cells when epithelial integrity is lost, a phenotype of wound healing deployed in metastasis-initiating cells.
  2. Semin Cancer Biol. 2020 Jul 11. pii: S1044-579X(20)30159-0. [Epub ahead of print]
    Ma B, Wells A, Wei L, Zheng J.
      Liver metastasis causes nearly half of death from solid cancers. Metastatic lesions, to the liver in particular, can become detectable years or decades after primary tumor removal, leaving an uncertain long-term prognosis in patients. Prostate cancer (PCa), a prominent metastatic dormant cancer, has the worst prognosis when found in the liver compared to other metastatic sites. These metastatic nodules in the liver pro-metastatic microenvironment display a therapy resistance; the resistance appears to be conferred both by dormancy and independent of dormancy when the nodules emerge. Within the review, the molecular underpinnings of how the liver aids and protects PCa cells seeding, colonization and resistance will be discussed.
    Keywords:  Dormancy; Liver metastasis; Metastatic microenvironment; Prostate cancer; Resistance
  3. Cancer Res. 2020 Jul 13. pii: canres.2486.2019. [Epub ahead of print]
    Ghergurovich JM, Esposito M, Chen Z, Wang JZ, Bhatt V, Lan T, White E, Kang Y, Guo JY, Rabinowitz JD.
      The enzyme glucose-6-phosphate dehydrogenase (G6PD) is a major contributor to NADPH production and redox homeostasis and its expression is upregulated and correlated with negative patient outcomes in multiple human cancer types. Despite these associations, whether G6PD is essential for tumor initiation, growth, or metastasis remains unclear. Here we employ modern genetic tools to evaluate the role of G6PD in lung, breast, and colon cancer driven by oncogenic K-Ras. Human HCT116 colorectal cancer cells lacking G6PD exhibited metabolic indicators of oxidative stress but developed into subcutaneous xenografts with growth comparable to that of wild-type controls. In a genetically engineered mouse model of non-small-cell lung cancer driven by K-Ras G12D and p53-deficiency, G6PD knockout did not block formation or proliferation of primary lung tumors. In MDA-MB 231-derived human triple-negative breast cancer cells implanted as orthotopic xenografts, loss of G6PD modestly decreased primary site growth without ablating spontaneous metastasis to the lung and moderately impaired the ability of breast cancer cells to colonize the lung when delivered via tail vein injection. Thus, in the studied K-Ras tumor models, G6PD is not strictly essential for tumorigenesis and at most modestly promotes disease progression.
  4. Cancer Cell. 2020 Jun 23. pii: S1535-6108(20)30309-3. [Epub ahead of print]
    Zhang Z, Karthaus WR, Lee YS, Gao VR, Wu C, Russo JW, Liu M, Mota JM, Abida W, Linton E, Lee E, Barnes SD, Chen HA, Mao N, Wongvipat J, Choi D, Chen X, Zhao H, Manova-Todorova K, de Stanchina E, Taplin ME, Balk SP, Rathkopf DE, Gopalan A, Carver BS, Mu P, Jiang X, Watson PA, Sawyers CL.
      Despite the development of second-generation antiandrogens, acquired resistance to hormone therapy remains a major challenge in treating advanced prostate cancer. We find that cancer-associated fibroblasts (CAFs) can promote antiandrogen resistance in mouse models and in prostate organoid cultures. We identify neuregulin 1 (NRG1) in CAF supernatant, which promotes resistance in tumor cells through activation of HER3. Pharmacological blockade of the NRG1/HER3 axis using clinical-grade blocking antibodies re-sensitizes tumors to hormone deprivation in vitro and in vivo. Furthermore, patients with castration-resistant prostate cancer with increased tumor NRG1 activity have an inferior response to second-generation antiandrogen therapy. This work reveals a paracrine mechanism of antiandrogen resistance in prostate cancer amenable to clinical testing using available targeted therapies.
    Keywords:  NRG1/neuregulin 1; cancer-associated fibroblast; drug resistance; hormone therapy; tumor microenvironment
  5. EMBO Mol Med. 2020 Jul 15. e11908
    Koch C, Kuske A, Joosse SA, Yigit G, Sflomos G, Thaler S, Smit DJ, Werner S, Borgmann K, Gärtner S, Mossahebi Mohammadi P, Battista L, Cayrefourcq L, Altmüller J, Salinas-Riester G, Raithatha K, Zibat A, Goy Y, Ott L, Bartkowiak K, Tan TZ, Zhou Q, Speicher MR, Müller V, Gorges TM, Jücker M, Thiery JP, Brisken C, Riethdorf S, Alix-Panabières C, Pantel K.
      Functional studies giving insight into the biology of circulating tumor cells (CTCs) remain scarce due to the low frequency of CTCs and lack of appropriate models. Here, we describe the characterization of a novel CTC-derived breast cancer cell line, designated CTC-ITB-01, established from a patient with metastatic estrogen receptor-positive (ER+ ) breast cancer, resistant to endocrine therapy. CTC-ITB-01 remained ER+ in culture, and copy number alteration (CNA) profiling showed high concordance between CTC-ITB-01 and CTCs originally present in the patient with cancer at the time point of blood draw. RNA-sequencing data indicate that CTC-ITB-01 has a predominantly epithelial expression signature. Primary tumor and metastasis formation in an intraductal PDX mouse model mirrored the clinical progression of ER+ breast cancer. Downstream ER signaling was constitutively active in CTC-ITB-01 independent of ligand availability, and the CDK4/6 inhibitor Palbociclib strongly inhibited CTC-ITB-01 growth. Thus, we established a functional model that opens a new avenue to study CTC biology.
    Keywords:  breast cancer; circulating tumor cells; functional studies; liquid biopsy; metastasis
  6. Mol Cancer Res. 2020 Jul 13. pii: molcanres.0311.2019. [Epub ahead of print]
    Ma Y, Shepherd J, Zhao D, Bollu LR, Tahaney WM, Hill J, Zhang Y, Mazumdar A, Brown PH.
      Triple-negative breast cancer (TNBC) has the worst prognosis of all breast cancers, and lacks effective targeted treatment strategies. Previously, we identified 33 transcription factors highly expressed in TNBC. Here, we focused on six SOX transcription factors (SOX4, 6, 8, 9, 10 and 11) highly expressed in TNBCs. Our siRNA screening assay demonstrated that SOX9 knock-down suppressed TNBC cell growth and invasion in vitro. Thus, we hypothesized that SOX9 is an important regulator of breast cancer survival and metastasis, and demonstrated that knockout of SOX9 reduced breast tumor growth and lung metastasis in vivo. In addition, we found that loss of SOX9 induced profound apoptosis, with only a slight impairment of G1 to S progression within the cell cycle, and that SOX9 directly regulates genes controlling apoptosis. Based on published CHIP-seq data, we demonstrated that SOX9 binds to the promoter of apoptosis-regulating genes (tnfrsf1b, fadd, tnfrsf10a, tnfrsf10b, and ripk1), and represses their expression. SOX9 knock-down upregulates these genes, consistent with the induction of apoptosis. Analysis of available CHIP-seq data showed that SOX9 binds to the promoters of several EMT- and metastasis-regulating genes. Using CHIP assays, we demonstrated that SOX9 directly binds the promoters of genes involved in EMT (vim, cldn1, ctnnb1, and zeb1) and that SOX9 knock-down suppresses the expression of these genes. Implications: Our studies identified the SOX9 protein as a "master regulator" of breast cancer cell survival and metastasis, and provide preclinical rationale to develop SOX9 inhibitors for the treatment of women with metastatic triple-negative breast cancer.
  7. J Clin Invest. 2020 Jul 13. pii: 129941. [Epub ahead of print]
    Paul MR, Pan TC, Pant DK, Shih NN, Chen Y, Harvey KL, Solomon A, Lieberman D, Morrissette JJ, Soucier-Ernst D, Goodman NG, Stavropoulos SW, Maxwell KN, Clark C, Belka GK, Feldman M, DeMichele A, Chodosh LA.
      Nearly all breast cancer deaths result from metastatic disease. Despite this, the genomic events that drive metastatic recurrence are poorly understood. We performed whole-exome and shallow whole-genome sequencing to identify genes and pathways preferentially mutated or copy-number altered in metastases compared with the paired primary tumors from which they arose. Seven genes were preferentially mutated in metastases - MYLK, PEAK1, SLC2A4RG, EVC2, XIRP2, PALB2, and ESR1 - 5 of which are not significantly mutated in any type of human primary cancer. Four regions were preferentially copy-number altered: loss of STK11 and CDKN2A/B, as well as gain of PTK6 and the membrane-bound progesterone receptor, PAQR8. PAQR8 gain was mutually exclusive with mutations in the nuclear estrogen and progesterone receptors, suggesting a role in treatment resistance. Several pathways were preferentially mutated or altered in metastases, including mTOR, CDK/RB, cAMP/PKA, WNT, HKMT, and focal adhesion. Immunohistochemical analyses revealed that metastases preferentially inactivate pRB, upregulate the mTORC1 and WNT signaling pathways, and exhibit nuclear localization of activated PKA. Our findings identify multiple therapeutic targets in metastatic recurrence that are not significantly mutated in primary cancers, implicate membrane progesterone signaling and nuclear PKA in metastatic recurrence, and provide genomic bases for the efficacy of mTORC1, CDK4/6, and PARP inhibitors in metastatic breast cancer.
    Keywords:  Bioinformatics; Breast cancer; Genetics; Oncology
  8. Nat Genet. 2020 Jul 13.
    Zhao SG, Chen WS, Li H, Foye A, Zhang M, Sjöström M, Aggarwal R, Playdle D, Liao A, Alumkal JJ, Das R, Chou J, Hua JT, Barnard TJ, Bailey AM, Chow ED, Perry MD, Dang HX, Yang R, Moussavi-Baygi R, Zhang L, Alshalalfa M, Laura Chang S, Houlahan KE, Shiah YJ, Beer TM, Thomas G, Chi KN, Gleave M, Zoubeidi A, Reiter RE, Rettig MB, Witte O, Yvonne Kim M, Fong L, Spratt DE, Morgan TM, Bose R, Huang FW, Li H, Chesner L, Shenoy T, Goodarzi H, Asangani IA, Sandhu S, Lang JM, Mahajan NP, Lara PN, Evans CP, Febbo P, Batzoglou S, Knudsen KE, He HH, Huang J, Zwart W, Costello JF, Luo J, Tomlins SA, Wyatt AW, Dehm SM, Ashworth A, Gilbert LA, Boutros PC, Farh K, Chinnaiyan AM, Maher CA, Small EJ, Quigley DA, Feng FY.
      Although DNA methylation is a key regulator of gene expression, the comprehensive methylation landscape of metastatic cancer has never been defined. Through whole-genome bisulfite sequencing paired with deep whole-genome and transcriptome sequencing of 100 castration-resistant prostate metastases, we discovered alterations affecting driver genes that were detectable only with integrated whole-genome approaches. Notably, we observed that 22% of tumors exhibited a novel epigenomic subtype associated with hypermethylation and somatic mutations in TET2, DNMT3B, IDH1 and BRAF. We also identified intergenic regions where methylation is associated with RNA expression of the oncogenic driver genes AR, MYC and ERG. Finally, we showed that differential methylation during progression preferentially occurs at somatic mutational hotspots and putative regulatory regions. This study is a large integrated study of whole-genome, whole-methylome and whole-transcriptome sequencing in metastatic cancer that provides a comprehensive overview of the important regulatory role of methylation in metastatic castration-resistant prostate cancer.
  9. Dev Cell. 2020 Jul 02. pii: S1534-5807(20)30500-1. [Epub ahead of print]
    Li Y, Lv Z, Zhang S, Wang Z, He L, Tang M, Pu W, Zhao H, Zhang Z, Shi Q, Cai D, Wu M, Hu G, Lui KO, Feng J, Nieto MA, Zhou B.
      Genetic lineage tracing unravels cell fate and plasticity in development, tissue homeostasis, and diseases. However, it remains technically challenging to trace temporary or transient cell fate, such as epithelial-to-mesenchymal transition (EMT) in tumor metastasis. Here, we generated a genetic fate-mapping system for temporally seamless tracing of transient cell fate. Highlighting its immediate application, we used it to study EMT gene activity from the local primary tumor to a distant metastatic site in vivo. In a spontaneous breast-to-lung metastasis model, we found that primary tumor cells activated vimentin and N-cadherin in situ, but only N-cadherin was activated and functionally required during metastasis. Tumor cells that have ever expressed N-cadherin constituted the majority of metastases in lungs, and functional deletion of N-cad significantly reduced metastasis. The seamless genetic recording system described here provides an alternative way for understanding transient cell fate and plasticity in biological processes.
    Keywords:  EMT; N-cadherin; genetic fate mapping; lineage tracing; metastasis; tumor; vimentin
  10. Nat Commun. 2020 Jul 14. 11(1): 3521
    Luthria G, Li R, Wang S, Prytyskach M, Kohler RH, Lauffenburger DA, Mitchison TJ, Weissleder R, Miller MA.
      Microtubules (MTs) mediate mitosis, directional signaling, and are therapeutic targets in cancer. Yet in vivo analysis of cancer cell MT behavior within the tumor microenvironment remains challenging. Here we developed an imaging pipeline using plus-end tip tracking and intravital microscopy to quantify MT dynamics in live xenograft tumor models. Among analyzed features, cancer cells in vivo displayed higher coherent orientation of MT dynamics along their cell major axes compared with 2D in vitro cultures, and distinct from 3D collagen gel cultures. This in vivo MT phenotype was reproduced in vitro when cells were co-cultured with IL4-polarized MΦ. MΦ depletion, MT disruption, targeted kinase inhibition, and altered MΦ polarization via IL10R blockade all reduced MT coherence and/or tumor cell elongation. We show that MT coherence is a defining feature for in vivo tumor cell dynamics and migration, modulated by local signaling from pro-tumor macrophages.
  11. Oncogene. 2020 Jul 16.
    Buschhaus JM, Humphries BA, Eckley SS, Robison TH, Cutter AC, Rajendran S, Haley HR, Bevoor AS, Luker KE, Luker GD.
      Estrogen receptor-positive (ER+) breast cancer can recur up to 20 years after initial diagnosis. Delayed recurrences arise from disseminated tumors cells (DTCs) in sites such as bone marrow that remain quiescent during endocrine therapy and subsequently proliferate to produce clinically detectable metastases. Identifying therapies that eliminate DTCs and/or effectively target cells transitioning to proliferation promises to reduce risk of recurrence. To tackle this problem, we utilized a 3D co-culture model incorporating ER+ breast cancer cells and bone marrow mesenchymal stem cells to represent DTCs in a bone marrow niche. 3D co-cultures maintained cancer cells in a quiescent, viable state as measured by both single-cell and population-scale imaging. Single-cell imaging methods for metabolism by fluorescence lifetime (FLIM) of NADH and signaling by kinases Akt and ERK revealed that breast cancer cells utilized oxidative phosphorylation and signaling by Akt to a greater extent both in 3D co-cultures and a mouse model of ER+ breast cancer cells in bone marrow. Using our 3D co-culture model, we discovered that combination therapies targeting oxidative phosphorylation via the thioredoxin reductase (TrxR) inhibitor, D9, and the Akt inhibitor, MK-2206, preferentially eliminated breast cancer cells without altering viability of bone marrow stromal cells. Treatment of mice with disseminated ER+ human breast cancer showed that D9 plus MK-2206 blocked formation of new metastases more effectively than tamoxifen. These data establish an integrated experimental system to investigate DTCs in bone marrow and identify combination therapy against metabolic and kinase targets as a promising approach to effectively target these cells and reduce risk of recurrence in breast cancer.
  12. Cancer Res. 2020 Jul 13. pii: canres.0014.2020. [Epub ahead of print]
    Westcott JM, Camacho S, Nasir A, Huysman ME, Rahhal R, Dang TT, Riegel AT, Brekken RA, Pearson GW.
      Defining how interactions between tumor subpopulations contribute to invasion is essential for understanding how tumors metastasize. Here, we find that the heterogeneous expression of the transcription factor ΔNp63 confers distinct proliferative and invasive EMT states in subpopulations that establish a leader-follower relationship to collectively invade. A ΔNp63-high EMT program coupled the ability to proliferate with an interleukin 1α (IL-1α) and miR-205-dependent suppression of cellular protrusions that are required to initiate collective invasion. An alternative ΔNp63-low EMT program conferred cells with the ability to initiate and lead collective invasion. However, this ΔNp63-low EMT state triggered a collateral loss of fitness. Importantly, rare growth-suppressed ΔNp63-low EMT cells influenced tumor progression by leading the invasion of proliferative ΔNp63-high EMT cells in heterogeneous primary tumors. Thus, heterogeneous activation of distinct EMT programs promotes a mode of collective invasion that overcomes cell intrinsic phenotypic deficiencies to induce the dissemination of proliferative tumor cells.
  13. Science. 2020 Jul 17. pii: eaay1813. [Epub ahead of print]369(6501):
    Taniguchi S, Elhance A, Van Duzer A, Kumar S, Leitenberger JJ, Oshimori N.
      Targeting the cross-talk between tumor-initiating cells (TICs) and the niche microenvironment is an attractive avenue for cancer therapy. We show here, using a mouse model of squamous cell carcinoma, that TICs play a crucial role in creating a niche microenvironment that is required for tumor progression and drug resistance. Antioxidant activity in TICs, mediated by the transcription factor NRF2, facilitates the release of a nuclear cytokine, interleukin-33 (IL-33). This cytokine promotes differentiation of macrophages that express the high-affinity immunoglobulin E receptor FcεRIα and are in close proximity to TICs. In turn, these IL-33-responding FcεRIα+ macrophages send paracrine transforming growth factor β (TGF-β) signals to TICs, inducing invasive and drug-resistant properties and further upregulating IL-33 expression. This TIC-driven, IL-33-TGF-β feedforward loop could potentially be exploited for cancer treatment.
  14. Cancer Res. 2020 Jul 14. pii: canres.3713.2019. [Epub ahead of print]
    Bridges AE, Ramachandran S, Pathania R, Parwal U, Lester A, Rajpurohit P, Morera DS, Patel N, Singh N, Korkaya H, Manicassamy S, Prasad PD, Lokeshwar VB, Lokeshwar BL, Ganapathy V, Thangaraju M.
      RAD51AP1 (RAD51-associated protein 1) plays an integral role in homologous recombination (HR) by activating RAD51 recombinase. HR is essential for preserving genome integrity and RAD51AP1 is critical for D-loop formation, a key step in HR. Although RAD51AP1 is involved in maintaining genomic stability, recent studies have shown that RAD51AP1 expression is significantly upregulated in human cancers. However, the functional role of RAD51AP1 in tumor growth and the underlying molecular mechanism(s) by which RAD51AP1 regulates tumorigenesis have not been fully understood. Here we use Rad51ap1 knockout mice in genetically engineered mouse (GEM) models of breast cancer to unravel the role of RAD51AP1 in tumor growth and metastasis. RAD51AP1 gene transcript was increased in both luminal estrogen receptor-positive breast cancer (ER+BC) and basal triple-negative breast cancer (TNBC), which is associated with a poor prognosis. Conversely, knockdown of RAD51AP1 (RADP51AP1 KD) in breast cancer cell lines reduced tumor growth. Rad51ap1-deficient mice were protected from oncogene-driven spontaneous mouse mammary tumor growth and associated lung metastasis. In vivo, limiting dilution studies provided evidence that Rad51ap1 plays a critical role in breast cancer stem cell (BCSC) self-renewal. RAD51AP1 KD improved chemotherapy and radiation therapy response by inhibiting BCSC self-renewal and associated pluripotency. Overall, our study provides genetic and biochemical evidences that RAD51AP1 is critical for tumor growth and metastasis by increasing BCSC stem cell self-renewal and may serve as a novel target for chemotherapy- and radiation therapy-resistant breast cancer.
  15. Trends Cancer. 2020 Jul 09. pii: S2405-8033(20)30188-6. [Epub ahead of print]
    Ben-Eliyahu S.
      Uncertainty regarding the development of postoperative metastatic disease is highly prevalent. Here we assert that numerous processes that occur during the immediate perioperative period (IPP) markedly affect the probability of postoperative metastatic disease and that these processes can be manipulated to improve cancer survival. Specifically, tumor excision facilitates both prometastatic and antimetastatic processes, which, within each domain, are often synergistic and self-propagating. Consequently, minor perioperative dominance of either prometastatic or antimetastatic processes can trigger a 'snowball-like effect' leading to either accelerated progression of minimal residual disease (MRD) or its dormancy/elimination, establishing the 'surgical metastatic roulette'. Thus, the IPP should become a significant antimetastatic therapeutic arena, exploiting feasible approaches including immunotherapies and manipulations/modifications of inflammatory-stress responses, surgical procedures, and hormonal status.
    Keywords:  COX2 inhibitor; cancer; metastases; perioperative; surgery; β-adrenergic blocker
  16. Genome Biol. 2020 Jul 15. 21(1): 174
    Eyler CE, Matsunaga H, Hovestadt V, Vantine SJ, van Galen P, Bernstein BE.
      BACKGROUND: Tumors can evolve and adapt to therapeutic pressure by acquiring genetic and epigenetic alterations that may be transient or stable. A precise understanding of how such events contribute to intratumoral heterogeneity, dynamic subpopulations, and overall tumor fitness will require experimental approaches to prospectively label, track, and characterize resistant or otherwise adaptive populations at the single-cell level. In glioblastoma, poor efficacy of receptor tyrosine kinase (RTK) therapies has been alternatively ascribed to genetic heterogeneity or to epigenetic transitions that circumvent signaling blockade.RESULTS: We combine cell lineage barcoding and single-cell transcriptomics to trace the emergence of drug resistance in stem-like glioblastoma cells treated with RTK inhibitors. Whereas a broad variety of barcoded lineages adopt a Notch-dependent persister phenotype that sustains them through early drug exposure, rare subclones acquire genetic changes that enable their rapid outgrowth over time. Single-cell analyses reveal that these genetic subclones gain copy number amplifications of the insulin receptor substrate-1 and substrate-2 (IRS1 or IRS2) loci, which activate insulin and AKT signaling programs. Persister-like cells and genomic amplifications of IRS2 and other loci are evident in primary glioblastomas and may underlie the inefficacy of targeted therapies in this disease.
    CONCLUSIONS: A method for combined lineage tracing and scRNA-seq reveals the interplay between complementary genetic and epigenetic mechanisms of resistance in a heterogeneous glioblastoma tumor model.
    Keywords:  Epigenetic; Genetic; Glioma stem cells; Insulin receptor substrate/IRS; Lineage tracing; Single-cell RNA-seq; Therapy resistance; Tumor heterogeneity
  17. Nat Commun. 2020 Jul 14. 11(1): 3515
    Uttam S, Stern AM, Sevinsky CJ, Furman S, Pullara F, Spagnolo D, Nguyen L, Gough A, Ginty F, Lansing Taylor D, Chakra Chennubhotla S.
      An unmet clinical need in solid tumor cancers is the ability to harness the intrinsic spatial information in primary tumors that can be exploited to optimize prognostics, diagnostics and therapeutic strategies for precision medicine. Here, we develop a transformational spatial analytics computational and systems biology platform (SpAn) that predicts clinical outcomes and captures emergent spatial biology that can potentially inform therapeutic strategies. We apply SpAn to primary tumor tissue samples from a cohort of 432 chemo-naïve colorectal cancer (CRC) patients iteratively labeled with a highly multiplexed (hyperplexed) panel of 55 fluorescently tagged antibodies. We show that SpAn predicts the 5-year risk of CRC recurrence with a mean AUROC of 88.5% (SE of 0.1%), significantly better than current state-of-the-art methods. Additionally, SpAn infers the emergent network biology of tumor microenvironment spatial domains revealing a spatially-mediated role of CRC consensus molecular subtype features with the potential to inform precision medicine.
  18. J Biol Chem. 2020 Jul 15. pii: jbc.RA120.013519. [Epub ahead of print]
    Ray P, Raghunathan K, Ahsan A, Allam US, Shukla S, Basrur V, Veatch S, Lawrence TS, Nyati MK, Ray D.
      The discovery of activating epidermal growth factor receptor (EGFR) mutations spurred the use of EGFR tyrosine kinase inhibitors (TKIs), such as erlotinib, as the first-line treatment of lung cancers. We previously reported that differential degradation of TKI-sensitive (e.g. L858R) and resistant (T790M) EGFR mutants upon erlotinib treatment correlates with drug sensitivity. We also reported that SMAD ubiquitination regulatory factor 2 (SMURF2) ligase activity is important in stabilizing EGFR. However, the molecular mechanisms involved remain unclear. Here, using in vitro and in vivo ubiquitination assays, mass spectrometry, and super-resolution microscopy, we show SMURF2-EGFR functional interaction is important for EGFR stability and response to TKI. We demonstrate that L858R/T790M EGFR is preferentially stabilized by SMURF2-UBCH5 (an E3-E2) mediated polyubiquitination. We identified four lysine residues as the sites of ubiquitination, and showed that replacement of one of them with acetylation-mimicking glutamine increases the sensitivity of mutant EGFR to erlotinib-induced degradation. We show that SMURF2 extends membrane retention of EGF bound EGFR, whereas SMURF2 knockdown increases receptor sorting to lysosomes. In lung cancer cell lines, SMURF2 overexpression increased EGFR levels, improving TKI tolerance, while SMURF2 knockdown decreased EGFR steady state levels and sensitized lung cancer cells. Overall, we propose that SMURF2-mediated polyubiquitination of L858R/T790M EGFR may be competing with acetylation-mediated receptor internalization that correlates with enhanced receptor stability, therefore, disruption of the E3-E2 complex may be an attractive target to overcome TKI resistance.
    Keywords:  E3 ubiquitin ligase; Epidermal growth factor receptor (EGFR); Smad ubiquitination regulatory factor 2 (SMURF2); Ubiquitin conjugating enzyme H5 (UBCH5); epidermal growth factor receptor (EGFR); protective ubiquitination; receptor regulation; tyrosine kinase inhibitor (TKI) resistance; tyrosine-protein kinase (tyrosine kinase); ubiquitylation (ubiquitination)
  19. EMBO Mol Med. 2020 Jul 16. e11987
    Zecchin D, Moore C, Michailidis F, Horswell S, Rana S, Howell M, Downward J.
      Triple-negative breast cancer (TNBC) has poorer prognosis compared to other types of breast cancers due to the lack of effective therapies and markers for patient stratification. Loss of PTEN tumor suppressor gene expression is a frequent event in TNBC, resulting in over-activation of the PI 3-kinase (PI3K) pathway and sensitivity to its inhibition. However, PI3K pathway inhibitors show limited efficacy as monotherapies on these tumors. We report a whole-genome screen to identify targets whose inhibition enhanced the effects of different PI3K pathway inhibitors on PTEN-null TNBC. This identified a signaling network that relies on both the G protein-coupled receptor for thrombin (PAR1/F2R) and downstream G protein βγ subunits and also epidermal growth factor receptor (EGFR) for the activation of the PI3K isoform p110β and AKT. Compensation mechanisms involving these two branches of the pathway could bypass PI3K blockade, but combination targeting of both EGFR and PI3Kβ suppressed ribosomal protein S6 phosphorylation and exerted anti-tumor activity both in vitro and in vivo, suggesting a new potential therapeutic strategy for PTEN-null TNBC.
    Keywords:   PTEN ; G protein; p110β; resistance; triple-negative breast cancer
  20. Cancer Cell. 2020 Jul 06. pii: S1535-6108(20)30311-1. [Epub ahead of print]
    Siersbæk R, Scabia V, Nagarajan S, Chernukhin I, Papachristou EK, Broome R, Johnston SJ, Joosten SEP, Green AR, Kumar S, Jones J, Omarjee S, Alvarez-Fernandez R, Glont S, Aitken SJ, Kishore K, Cheeseman D, Rakha EA, D'Santos C, Zwart W, Russell A, Brisken C, Carroll JS.
      The cytokine interleukin-6 (IL6) and its downstream effector STAT3 constitute a key oncogenic pathway, which has been thought to be functionally connected to estrogen receptor α (ER) in breast cancer. We demonstrate that IL6/STAT3 signaling drives metastasis in ER+ breast cancer independent of ER. STAT3 hijacks a subset of ER enhancers to drive a distinct transcriptional program. Although these enhancers are shared by both STAT3 and ER, IL6/STAT3 activity is refractory to standard ER-targeted therapies. Instead, inhibition of STAT3 activity using the JAK inhibitor ruxolitinib decreases breast cancer invasion in vivo. Therefore, IL6/STAT3 and ER oncogenic pathways are functionally decoupled, highlighting the potential of IL6/STAT3-targeted therapies in ER+ breast cancer.
    Keywords:  FOXA1; IL6; STAT3; breast cancer; estrogen receptor; metastasis; mouse intraductal xenograft model; pioneer factor
  21. Nat Commun. 2020 Jul 17. 11(1): 3586
    Abu-Thuraia A, Goyette MA, Boulais J, Delliaux C, Apcher C, Schott C, Chidiac R, Bagci H, Thibault MP, Davidson D, Ferron M, Veillette A, Daly RJ, Gingras AC, Gratton JP, Côté JF.
      Aberrant expression of receptor tyrosine kinase AXL is linked to metastasis. AXL can be activated by its ligand GAS6 or by other kinases, but the signaling pathways conferring its metastatic activity are unknown. Here, we define the AXL-regulated phosphoproteome in breast cancer cells. We reveal that AXL stimulates the phosphorylation of a network of focal adhesion (FA) proteins, culminating in faster FA disassembly. Mechanistically, AXL phosphorylates NEDD9, leading to its binding to CRKII which in turn associates with and orchestrates the phosphorylation of the pseudo-kinase PEAK1. We find that PEAK1 is in complex with the tyrosine kinase CSK to mediate the phosphorylation of PAXILLIN. Uncoupling of PEAK1 from AXL signaling decreases metastasis in vivo, but not tumor growth. Our results uncover a contribution of AXL signaling to FA dynamics, reveal a long sought-after mechanism underlying AXL metastatic activity, and identify PEAK1 as a therapeutic target in AXL positive tumors.