Mechanisms of Cancer Cell Dormancy--Another Hallmark of Cancer?

Disease relapse in cancer patients many years after clinical remission, often referred to as cancer dormancy, is well documented but remains an incompletely understood phenomenon on the biologic level. Recent reviews have summarized potential models that can explain this phenomenon, including angiogenic, immunologic, and cellular dormancy. We focus on mechanisms of cellular dormancy as newer biologic insights have enabled better understanding of this process. We provide a historical context, synthesize current advances in the field, and propose a mechanistic framework that treats cancer cell dormancy as a dynamic cell state conferring a fitness advantage to an evolving malignancy under stress. Cellular dormancy appears to be an active process that can be toggled through a variety of signaling mechanisms that ultimately downregulate the RAS/MAPK and PI(3)K/AKT pathways, an ability that is preserved even in cancers that constitutively depend on these pathways for their growth and survival. Just as unbridled proliferation is a key hallmark of cancer, the ability of cancer cells to become quiescent may be critical to evolving malignancies, with implications for understanding cancer initiation, progression, and treatment resistance.

Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties

BACKGROUND

Krishna Tulsi, a member of Lamiaceae family, is a herb well known for its spiritual, religious and medicinal importance in India. The common name of this plant is 'Tulsi' (or 'Tulasi' or 'Thulasi') and is considered sacred by Hindus. We present the draft genome of Ocimum tenuiflurum L (subtype Krishna Tulsi) in this report. The paired-end and mate-pair sequence libraries were generated for the whole genome sequenced with the Illumina Hiseq 1000, resulting in an assembled genome of 374 Mb, with a genome coverage of 61 % (612 Mb estimated genome size). We have also studied transcriptomes (RNA-Seq) of two subtypes of O. tenuiflorum, Krishna and Rama Tulsi and report the relative expression of genes in both the varieties.

RESULTS

The pathways leading to the production of medicinally-important specialized metabolites have been studied in detail, in relation to similar pathways in Arabidopsis thaliana and other plants. Expression levels of anthocyanin biosynthesis-related genes in leaf samples of Krishna Tulsi were observed to be relatively high, explaining the purple colouration of Krishna Tulsi leaves. The expression of six important genes identified from genome data were validated by performing q-RT-PCR in different tissues of five different species, which shows the high extent of urosolic acid-producing genes in young leaves of the Rama subtype. In addition, the presence of eugenol and ursolic acid, implied as potential drugs in the cure of many diseases including cancer was confirmed using mass spectrometry.

CONCLUSIONS

The availability of the whole genome of O.tenuiflorum and our sequence analysis suggests that small amino acid changes at the functional sites of genes involved in metabolite synthesis pathways confer special medicinal properties to this herb.

Abstract NG08: Transcriptional mechanisms for autophagy regulation and metabolic reprogramming in pancreatic cancer

How do cancer cells escape tightly controlled regulatory circuits that link their growth to extracellular signaling cues? An emerging theme in cancer biology is how, in addition to genetic alterations in signaling pathways (eg. MAPK and PI3K), cancer cells can hijack normal stress response pathways to overcome reliance on external nutrients for growth. Pancreatic adenocarcinoma (PDA) is the quintessence of an aggressive malignancy that relies on constitutive activation of stress response pathways for growth and survival, with the tumors progressing rapidly in the context of extreme hypoxia, poor vascularity, and limited nutrient availability. As such, PDA employ profoundly altered networks of biosynthetic and catabolic pathways, including constitutive activation of autophagy (cellular self-catabolism) and macropinocytosis (bulk uptake of extracellular proteins), which are necessary to maintain metabolic homeostasis and drive tumorigenesis. While, these pathways are essential for tumor growth, the precise mechanism of autophagy-lysosome activation and how this organellar system contributes to metabolic reprogramming in PDA were unknown.

MiT/TFE TRANSCRIPTION FACTORS ARE OVEREXPRESSED IN PDA AND REGULATED THE EXPRESSION OF AUTOPAHGY-LYSOSOME GENES.

We now show that autophagy induction in PDA occurs as part of a broader transcriptional program that coordinates activation of lysosome biogenesis and function, and nutrient scavenging, mediated by the MiT/TFE family transcription factors; MITF, TFE3 and TFEB. These factors show increased expression in primary human PDA tumor datasets compared to matched normal tissue and correlate with expression of a coherent network of autophagy-lysosome genes, incorporating essential autophagy genes, structural lysosomal proteins, hydrolases, solute transporters and luminal enzymes. Importantly, autophagy-lysosome components also show elevated expression in human PDA samples and cell lines, which is dependent on MiT/TFE activity.

CONSTITUTIVE ACTIVITY OF MiT/TFE PROTEINS IS MEDIATED THROUGH ENHANCED NUCLEAR IMPORT.

In non-transformed cells, MiT/TFE factors are phosphorylated by mTORC1 and retained in the cytoplasm in an inactive state under nutrient replete conditions. However, in addition to increased expression, these factors show constitutive nuclear localization and activation in PDA. Mechanistically, we show that this occurs through increased binding to nuclear import factors (IPO) that mediates their escape from mTORC1 inhibition and efficient nuclear translocation in PDA cells. Importantly, IPO expression is up-regulated in PDA cells compared to non-transformed pancreatic epithelial cells and other types of pancreatic tumors (pancreatic neuroendocrine tumor; PNET). Moreover, loss of IPO inhibits nuclear localization of MiT/TFE factors specifically in PDA cells. Therefore this work uncovers novel mechanisms enabling sustained activation of catabolic processes in PDA cells, that are only transiently induced by stress in normal cells, which incorporate alterations in the expression of tumorigenic transcription factors that act in concert with elevated levels of nuclear import proteins.

MiT/TFE FACTORS FUNCTION TO MAINTAIN LYSOSOME INTEGRITY IN PDA CELLS.

Having clarified the mechanisms of their constitutive nuclear import, we turned to the functional roles of MiT/TFE factors in PDA. Our transcriptional data imply contributions of the activated MiT/TFE proteins to the integrity and function of the lysosomal system in PDA cells. To test this key point, we depleted MiT/TFE proteins in PDA cells and observed striking defects in lysosome morphology, degradation of cargo protein and maturation of autophagosomes. In addition, we found that loss of MiT/TFE factors in PDA cells led to a dramatic defect in lysosomal pH. Importantly, these parameters were not altered following knockdown of MiT/TFE proteins in non-transformed control cell lines. Reciprocally, MITF or TFE3 overexpression in HPDE, HPNE, or PDA cells induced autophagy-lysosomal gene expression, LC3B foci, and lipidated LC3-II that was further enhanced following treatment with chloroquine (CQ), an inhibitor of lysosome acidification, indicating a marked augmentation of autophagic flux. Collectively, these data show that MiT/TFE proteins govern both autophagic flux and lysosome activity in PDA cells. This integrated cellular clearance program appears to enable efficient processing of cargo from autophagy as well as macropinocytosis, providing PDA cells access to critical sources of both intracellular and extracellular nutrients.

AMINO ACIDS ARE THE PRIMARY METABOLITE POOL DERIVED FROM ENHANCED AUTOPHAGY-LYSSOOME ACTIVITY IN PDA.

By degrading numerous cellular substrates, the lysosome generates metabolic intermediates that may feed into multiple pathways. We took advantage of the impaired autophagy-lysosome function caused by MiT/TFE inactivation to dissect the metabolic circuitry that sustains PDA growth. First, we conducted global metabolite profiling of PDA cells transfected with control or TFE3-targeted siRNAs. Dual gas chromatography and mass spectrometry (GC/MS) and liquid chromatography mass spectrometry (LC/MS) detected 347 known metabolites. Of these, 15.2% (53/347) showed a statistically significant change upon TFE3 inactivation in both cell lines (48/53 downregulated, 5/53 upregulated). Most prominently altered were amino acids (AA) and their breakdown products, with 31% (25/80) showing decreased abundance. No change in AA uptake was observed upon TFE3 silencing suggesting that in PDA the autophagy-lysosome system may supply a significant fraction of intracellular AA irrespective of external availability. Correspondingly, TFE3 inactivation or Bafilomycin A1 treatment (a specific inhibitor of the lysosomal V-H+ATPase), caused a significant decrease in intracellular AA levels in a multiple PDA cell lines, as did specific inactivation of autophagy by ATG5 knockdown. Importantly, these manipulations did not result in significant changes in AA levels in control non-PDA cells. Thus, the MiT/TFE factors and the autophagy-lysosome system are critical and specific regulators of intracellular AA abundance in PDA.

MiT/TFE FACTORS ARE REQUIRED FOR PDA GROWTH IN VITRO AND IN VIVO.

Consistent with their key roles in organelle function and metabolic regulation, the MiT/TFE proteins were central to PDA growth. PDA cell lines expressing high endogenous levels of MITF, TFE3, or TFEB were exceedingly sensitive to knockdown of that factor, displaying marked impairment in colony formation and reduction in proliferation, whereas non-PDA control cells were unaffected. Expression of shRNA-resistant cDNAs of MITF and TFE3 rescued proliferation in the knockdown setting, confirming the specificity of these experiments. Furthermore, PDA cells were broadly sensitive to chloroquine treatment (CQ; a well characterized autophagy inhibitor) as compared to non-PDA control cells.

Conversely, ectopic expression of MITF or TFE3 rendered control cells hypersensitive to CQ treatment, linking MiT/TFE-regulated clearance pathways to these growth phenotypes. We next sought to test the contributions of MiT/TFE to PDA tumorigenicity in vivo. Significantly, TFE3 or MITF knockdown virtually abolished xenograft tumor growth of PDA cells. In reciprocal gain-of-function studies, we investigated the impact of MITF overexpression on the tumorigenicity of primary KrasG12D-expressing mouse ductal epithelial cells. KrasG12D control cells formed only focal low-grade PanIN-like lesions by six weeks following orthotopic injection, whereas co-expression of MITF induced the expression of autophagy-lysosome genes and resulted in large orthotopic tumors in mice. In summary, our work places a new focus on lysosome regulation by MiT/TFE proteins as a nexus for metabolic reprogramming in PDA cells. Beyond serving a generic housekeeping role, lysosomes show increased activity in PDA and are critical integrators of major routes for nutrient scavenging and metabolic adaptation, providing an alternate pathway for maintaining intracellular AA stores. These studies also demonstrate activation of clearance pathways converging on the lysosome as a novel hallmark of aggressive malignancy.

Citation Format: Rushika M. Perera, Svetlana Stoykova, Brandon N. Nicolay, Kenneth N. Ross, Julien Fitamant, Myriam Boukhali, Vikram Deshpande, Martin K. Selig, Cristina R. Ferrone, Jeff Settleman, Gregory Stephanopoulos, Nicholas J. Dyson, Roberto Zoncu, Sridhar Ramaswamy, Wilhelm Haas, Nabeel M. Bardeesy. Transcriptional mechanisms for autophagy regulation and metabolic reprogramming in pancreatic cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr NG08. doi:10.1158/1538-7445.AM2015-NG08

A microfluidic device for label-free, physical capture of circulating tumor cell clusters

Cancer cells metastasize through the bloodstream either as single migratory circulating tumor cells (CTCs) or as multicellular groupings (CTC-clusters). Existing technologies for CTC enrichment are designed primarily to isolate single CTCs, and while CTC-clusters are detectable in some cases, their true prevalence and significance remain to be determined. Here, we developed a microchip technology (Cluster-Chip) specifically designed to capture CTC-clusters independent of tumor-specific markers from unprocessed blood. CTC-clusters are isolated through specialized bifurcating traps under low shear-stress conditions that preserve their integrity and even two-cell clusters are captured efficiently. Using the Cluster-Chip, we identify CTC-clusters in 30–40% of patients with metastatic cancers of the breast, prostate and melanoma. RNA sequencing of CTC-clusters confirms their tumor origin and identifies leukocytes within the clusters as tissue-derived macrophages. Together, the development of a device for efficient capture of CTC-clusters will enable detailed characterization of their biological properties and role in cancer metastasis.

The histone deacetylase SIRT6 controls embryonic stem cell fate via TET-mediated production of 5-hydroxymethylcytosine

How embryonic stem cells (ESCs) commit to specific cell lineages and yield all cell types of a fully formed organism remains a major question. ESC differentiation is accompanied by large-scale histone and DNA modifications, but the relations between these epigenetic categories are not understood. Here we demonstrate the interplay between the histone deacetylase sirtuin 6 (SIRT6) and the ten-eleven translocation enzymes (TETs). SIRT6 targets acetylated histone H3 at Lys 9 and 56 (H3K9ac and H3K56ac), while TETs convert 5-methylcytosine into 5-hydroxymethylcytosine (5hmC). ESCs derived from Sirt6 knockout (S6KO) mice are skewed towards neuroectoderm development. This phenotype involves derepression of OCT4, SOX2 and NANOG, which causes an upregulation of TET-dependent production of 5hmC. Genome-wide analysis revealed neural genes marked with 5hmC in S6KO ESCs, thereby implicating TET enzymes in the neuroectoderm-skewed differentiation phenotype. We demonstrate that SIRT6 functions as a chromatin regulator safeguarding the balance between pluripotency and differentiation through Tet-mediated production of 5hmC.

The WTX Tumor Suppressor Interacts with the Transcriptional Corepressor TRIM28

WTX encodes a tumor suppressor implicated in the pediatric kidney cancer Wilms tumor and in mesenchymal differentiation with potentially distinct functions in the cytoplasm, at the plasma membrane, and in the nucleus. Although modulating components of the WNT signaling pathway is a proposed function for cytoplasmic and membrane-bound WTX, its nuclear properties are not well understood. Here we report that the transcriptional corepressor TRIM28 is the major binding partner for nuclear WTX. WTX interacted with the coiled coil domain of TRIM28 required for its binding to Krüppel-associated box domains of transcription factors and for its chromatin recruitment through its own coiled coil and proline-rich domains. Knockdown of endogenous WTX reduced the recruitment of TRIM28 to a chromatinized reporter sequence and its ability to repress a target transcript. In mouse embryonic stem cells where TRIM28 plays a major role in repressing endogenous retroviruses and long interspersed elements, knockdown of either TRIM28 or WTX combined with single molecule RNA sequencing revealed a highly significant shared set of differentially regulated transcripts, including derepression of non-coding repetitive sequences and their neighboring protein encoding genes (p < 1e-20). In mesenchymal precursor cells, depletion of WTX and TRIM28 resulted in analogous β-catenin-independent defects in adipogenic and osteogenic differentiation, and knockdown of WTX reduced TRIM28 binding to Pparγ promoter. Together, the physical and functional interaction between WTX and TRIM28 suggests that the nuclear fraction of WTX plays a role in epigenetic silencing, an effect that may contribute to its function as a regulator of cellular differentiation and tumorigenesis.

RB loss in resistant EGFR mutant lung adenocarcinomas that transform to small-cell lung cancer

Tyrosine kinase inhibitors are effective treatments for non-small-cell lung cancers (NSCLCs) with epidermal growth factor receptor (EGFR) mutations. However, relapse typically occurs after an average of 1 year of continuous treatment. A fundamental histological transformation from NSCLC to small-cell lung cancer (SCLC) is observed in a subset of the resistant cancers, but the molecular changes associated with this transformation remain unknown. Analysis of tumour samples and cell lines derived from resistant EGFR mutant patients revealed that Retinoblastoma (RB) is lost in 100% of these SCLC transformed cases, but rarely in those that remain NSCLC. Further, increased neuroendocrine marker and decreased EGFR expression as well as greater sensitivity to BCL2 family inhibition are observed in resistant SCLC transformed cancers compared with resistant NSCLCs. Together, these findings suggest that this subset of resistant cancers ultimately adopt many of the molecular and phenotypic characteristics of classical SCLC.

Resistance to tyrosine kinase inhibitors occurs in treatments of non-small-cell lung cancers (NSCLCs) with EGFR mutations but the mechanisms underlying this acquired resistance are unknown. Here the authors examine the molecular changes that occur in resistant cancers that transition from NSCLC to small-cell lung cancer phenotype and implicate loss of retinoblastoma in this process.

Active viscoelastic matter: from bacterial drag reduction to turbulent solids

A paradigm for internally driven matter is the active nematic liquid crystal, whereby the equations of a conventional nematic are supplemented by a minimal active stress that violates time-reversal symmetry. In practice, active fluids may have not only liquid-crystalline but also viscoelastic polymer degrees of freedom. Here we explore the resulting interplay by coupling an active nematic to a minimal model of polymer rheology. We find that adding a polymer can greatly increase the complexity of spontaneous flow, but can also have calming effects, thereby increasing the net throughput of spontaneous flow along a pipe (a "drag-reduction" effect). Remarkably, active turbulence can also arise after switching on activity in a sufficiently soft elastomeric solid.

MAPK7 Regulates EMT Features and Modulates the Generation of CTCs

Epithelial-to-mesenchymal transition (EMT) has been implicated in models of tumor cell migration, invasion, and metastasis. In a search for candidate therapeutic targets to reverse this process, nontumorigenic MCF10A breast epithelial cells were infected with an arrayed lentiviral kinome shRNA library and screened for either suppression or enhancement of a 26-gene EMT RNA signature. No individual kinase gene knockdown was sufficient to induce EMT. In contrast, grouped epithelial markers were induced by knockdown of multiple kinases, including mitogen activated protein kinase 7 (MAPK7). In breast cancer cells, suppression of MAPK7 increased E-cadherin (CDH1) expression and inhibited cell migration. In an orthotopic mouse model, MAPK7 suppression reduced the generation of circulating tumor cells and the appearance of lung metastases. Together, these observations raise the possibility that targeting kinases that maintain mesenchymal cell properties in cancer cells, such as MAPK7, may lessen tumor invasiveness.

IMPLICATIONS

Suppression of MAPK7 induces epithelial markers, reduces generation of circulating tumor cells and appearance of lung metastases.

In vivo crystallography at X-ray free-electron lasers: the next generation of structural biology?

The serendipitous discovery of the spontaneous growth of protein crystals inside cells has opened the field of crystallography to chemically unmodified samples directly available from their natural environment. On the one hand, through in vivo crystallography, protocols for protein crystal preparation can be highly simplified, although the technique suffers from difficulties in sampling, particularly in the extraction of the crystals from the cells partly due to their small sizes. On the other hand, the extremely intense X-ray pulses emerging from X-ray free-electron laser (XFEL) sources, along with the appearance of serial femtosecond crystallography (SFX) is a milestone for radiation damage-free protein structural studies but requires micrometre-size crystals. The combination of SFX with in vivo crystallography has the potential to boost the applicability of these techniques, eventually bringing the field to the point where in vitro sample manipulations will no longer be required, and direct imaging of the crystals from within the cells will be achievable. To fully appreciate the diverse aspects of sample characterization, handling and analysis, SFX experiments at the Japanese SPring-8 angstrom compact free-electron laser were scheduled on various types of in vivo grown crystals. The first experiments have demonstrated the feasibility of the approach and suggest that future in vivo crystallography applications at XFELs will be another alternative to nano-crystallography.

A mechanism for asymmetric cell division resulting in proliferative asynchronicity

All cancers contain an admixture of rapidly and slowly proliferating cancer cells. This proliferative heterogeneity complicates the diagnosis and treatment of patients with cancer because slow proliferators are hard to eradicate, can be difficult to detect, and may cause disease relapse sometimes years after apparently curative treatment. While clonal selection theory explains the presence and evolution of rapid proliferators within cancer cell populations, the circumstances and molecular details of how slow proliferators are produced is not well understood. Here, a β1-integrin/FAK/mTORC2/AKT1-associated signaling pathway is discovered that can be triggered for rapidly proliferating cancer cells to undergo asymmetric cell division and produce slowly proliferating AKT1(low) daughter cells. In addition, evidence indicates that the proliferative output of this signaling cascade involves a proteasome-dependent degradation process mediated by the E3 ubiquitin ligase TTC3. These findings reveal that proliferative heterogeneity within cancer cell populations, in part, is produced through a targetable signaling mechanism, with potential implications for understanding cancer progression, dormancy, and therapeutic resistance.

IMPLICATIONS

These findings provide a deeper understanding of the proliferative heterogeneity that exists in the tumor environment and highlight the importance of designing future therapies against multiple proliferative contexts. VISUAL OVERVIEW: A proposed mechanism for producing slowly proliferating cancer cells. http://mcr.aacrjournals.org/content/early/2015/01/09/1541-7786.MCR-14-0474/F1.large.jpg.

Patient-derived models of acquired resistance can identify effective drug combinations for cancer

Targeted cancer therapies have produced substantial clinical responses, but most tumors develop resistance to these drugs. Here, we describe a pharmacogenomic platform that facilitates rapid discovery of drug combinations that can overcome resistance. We established cell culture models derived from biopsy samples of lung cancer patients whose disease had progressed while on treatment with epidermal growth factor receptor (EGFR) or anaplastic lymphoma kinase (ALK) tyrosine kinase inhibitors and then subjected these cells to genetic analyses and a pharmacological screen. Multiple effective drug combinations were identified. For example, the combination of ALK and MAPK kinase (MEK) inhibitors was active in an ALK-positive resistant tumor that had developed a MAP2K1 activating mutation, and the combination of EGFR and fibroblast growth factor receptor (FGFR) inhibitors was active in an EGFR mutant resistant cancer with a mutation in FGFR3. Combined ALK and SRC (pp60c-src) inhibition was effective in several ALK-driven patient-derived models, a result not predicted by genetic analysis alone. With further refinements, this strategy could help direct therapeutic choices for individual patients.

Time course and role of luteinizing hormone and follicle-stimulating hormone in the expansion of the Leydig cell population at the time of puberty in the rhesus monkey (Macaca mulatta)

In higher primates, development of the adult population of Leydig cells has received little attention. Here, the emergence of 3β-hydroxysteroid dehydrogenase (HSD3B) positive cells in the testis of the rhesus monkey was examined during spontaneous puberty, and correlated with S-phase labeling in the interstitium at this critical stage of development. In addition, the relative role of luteinizing hormone (LH) and follicle-stimulating hormone (FSH) in initiating the pubertal expansion of Leydig cells was studied by precociously stimulating the juvenile testis in vivo with pulsatile 11-day infusions of recombinant LH and FSH, either alone or in combination. At the time of castration, testes were immersion fixed in Bouin's, embedded in paraffin, and sectioned at 5 μm. Leydig cells/testis were enumerated using HSD3B as a Leydig cell marker. Leydig cell number per testis increased progressively during puberty to reach values in the adult approximately 10 fold greater than in early-pubertal animals. The rise in cell number was associated with an increase in nuclear diameter. That the pubertal expansion of Leydig cell number was driven primarily by the increase in LH secretion at this stage of development was suggested by the finding that precocious stimulation of mid-juvenile monkeys with LH, either alone or in combination with that of FSH, resulted in a 20-30 fold increase in the number of HSD3B-positive cells. Interestingly, precocious FSH stimulation, alone, also resulted in appearance of Leydig cells as indicated by the occasional HSD3B-positive cell in the interstitium. The nuclear diameter of these Leydig cells, however, was less than that of those generated in response to LH.

Bioengineered implantable scaffolds as a tool to study stromal-derived factors in metastatic cancer models

Modeling the hematogenous spread of cancer cells to distant organs poses one of the greatest challenges in the study of human metastasis. Both tumor cell-intrinsic properties as well as interactions with reactive stromal cells contribute to this process, but identification of relevant stromal signals has been hampered by the lack of models allowing characterization of the metastatic niche. Here, we describe an implantable bioengineered scaffold, amenable to in vivo imaging, ex vivo manipulation, and serial transplantation for the continuous study of human metastasis in mice. Orthotopic or systemic inoculation of tagged human cancer cells into the mouse leads to the release of circulating tumor cells into the vasculature, which seed the scaffold, initiating a metastatic tumor focus. Mouse stromal cells can be readily recovered and profiled, revealing differential expression of cytokines, such as IL1β, from tumor-bearing versus unseeded scaffolds. Finally, this platform can be used to test the effect of drugs on suppressing initiation of metastatic lesions. This generalizable model to study cancer metastasis may thus identify key stromal-derived factors with important implications for basic and translational cancer research.

Abstract 4832: Isolation and molecular characterization of circulating melanoma cells

Melanoma is a highly invasive malignancy frequently presenting with blood-borne metastases, in which recent breakthroughs in targeted and immunological therapies highlight the need for both early detection of invasion and monitoring of drug responses. We adapted a microfluidic device to capture circulating tumor cells (CTCs) in patients with melanoma and in a mouse model. In eight patients followed longitudinally, CTC numbers were correlated with response and progression on B-RAF/MEK, CDK4/6 and PDL1 inhibitors. Consistent with this trend, in a mouse model of tamoxifen-inducible B-RAF/PTEN-driven melanoma, CTCs declined within four days of treatment with a B-RAF inhibitor. In this model, CTCs are shed very early in tumorigenesis, and a four week course of B-RAF inhibition after resection of the primary tumor is sufficient to prevent the subsequent development of cutaneous metastases. Whereas primary and metastatic mouse melanomas are highly similar, RNA sequencing of CTCs identifies significant differences in expression, generating a signature that is correlated with invasiveness and motility in human melanoma.

Citation Format: Xi Luo, Devarati Mitra, Ryan J. Sullivan, Ben S. Wittner, Anya M. Kimura, Shiwei Pan, Mai P. Hoang, Brian W. Brannigan, Donald P. Lawrence, Keith T. Flaherty, Lecia V. Sequist, Shannon L. Stott, David T. Ting, Sridhar Ramaswamy, Mehmet Toner, David E. Fisher, Shyamala Maheswaran, Daniel A. Haber. Isolation and molecular characterization of circulating melanoma cells. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4832. doi:10.1158/1538-7445.AM2014-4832

Abstract LB-192: Circulating tumor cell clusters are precursors of breast cancer metastasis

The metastatic spread of breast cancer, typically to bone, lung, liver and brain, accounts for the vast majority of cancer-related deaths. Breast cancer metastases are thought to be derived primarily from individual migratory cancer cells, reaching distant sites through the bloodstream and initiating proliferation within distant organs. In addition to these single circulating tumor cells (CTCs), CTC-clusters have been detected in the blood of patients with cancer. In patients with breast cancer, we find that presence of such CTC-clusters is correlated with decreased progression-free survival. To study their functional role, we used mouse models, demonstrating that breast cancer cells injected intravascularly as clusters are more prone to survive and colonize the lungs than similarly injected single cancer cells. Primary orthotopic mammary tumors comprised of differentially tagged cells give rise to oligoclonal CTC-clusters, with 40-fold increased metastatic potential to the lung, compared with single CTCs. Using in vivo flow cytometry, we show that CTC-clusters are rapidly cleared from peripheral vessels, consistent with their trapping in small capillaries. Together, our observations suggest that primary tumor cells break off into the vasculature as CTC-clusters, and exhibit greatly enhanced metastatic propensity.

Citation Format: Nicola Aceto, Aditya Bardia, Joel A. Spencer, Ben S. Wittner, Min Yu, Maria C. Donaldson, Adam Pely, Amanda Engstrom, Huili Zhu, Brian W. Brannigan, Ravi Kapur, Shannon L. Stott, Toshi Shioda, Sridhar Ramaswamy, David T. Ting, Charles P. Lin, Mehmet Toner, Daniel A. Haber, Shyamala Maheswaran. Circulating tumor cell clusters are precursors of breast cancer metastasis. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-192. doi:10.1158/1538-7445.AM2014-LB-192

Abstract 181: Therapeutic approaches to metastasis induced by mesenchymal stem cells in the tumor microenvironment

Metastasis is the primary cause of death in non-hematological cancers yet there are no specific therapeutics against it because of a lack of validated targets. The Weinberg lab demonstrated that bone-marrow derived mesenchymal stem cells (MSCs) home to the stroma of breast tumors and induce metastasis. We verified these findings in MDA-MB-231 (MDA) xenografts in which co-injection of human MSCs increased MDA thoracic metastasis by 5-fold. In vitro, MSC co-culture induced GFP-labeled MDA cells to migrate 3-fold faster in a modified ‘wound-healing’ assay, mirroring metastasis in vivo. To identify therapeutic targets within MSC-induced metastasis, we performed gene-expression analysis of MSC-MDA co-cultures separated by flow cytometry compared with cells grown alone. The interferon pathway was found to be the most activated pathway upon co-culture, increasing mainly in MSCs. We studied the relevance of these genes in human cancers by first analyzing 3 different gene-expression datasets comparing human breast cancer stroma with normal stroma. Genes upregulated in breast cancer stroma were then studied in a meta-analysis of 19 whole tumor gene-expression datasets correlating gene-expression changes with survival. We identified 103 genes that are upregulated in MSCs by MSC-MDA interactions, are increased in human breast cancer stroma and are significantly associated with poor survival. To determine if they are necessary for MSC-induced metastatic behavior, we performed shRNA knockdown in MSC-MDA co-cultures measuring effects on in vitro migration. Knockdown of a number of interferon-associated genes significantly reduced migration supporting an unexpected functional role of interferons in metastasis. The top interferon gene, ISG15, is an attractive candidate for therapeutic targeting because it is a secreted ubiquitin-like factor that conjugates a number of cytoskeletal proteins involved in motility.

In parallel, we conducted a small-molecule screen with 1600 compounds on the migration of MSC-MDA co-cultures to identify small-molecule inhibitors of metastasis. Counter screens on highly motile endothelial cells excluded compounds that non-specifically inhibit normal cell migration. Only 1 compound, RSL3, specifically blocked MSC-induced MDA migration with cytotoxicity at &gt;10-fold higher concentrations. RSL3 inhibits the glutathione peroxidase 4 (GPX4) enzyme that metabolizes lipid peroxides including arachidonic acid metabolites participating in inflammatory cascades like interferon gamma signaling. RSL3 activity was completely abrogated by co-treatment with the 5-lipoxygenase inhibitor zileuton consistent with the role of arachidonic acid metabolites in MSC-MDA migration.

In summary, targeting components of interferon and arachidonic acid pathways have been discovered as novel therapeutic approaches against microenvironment-induced breast cancer metastasis.

Citation Format: Shrikanta Chattopadhyay, Cherrie Huang, Siddhartha Mukherjee, Rushdia Z. Yusuf, Vasanthi Viswanathan, Ben S. Wittner, Jeff Gentry, Alykhan Shamji, Sridhar Ramaswamy, David T. Scadden, Stuart L. Schreiber. Therapeutic approaches to metastasis induced by mesenchymal stem cells in the tumor microenvironment. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 181. doi:10.1158/1538-7445.AM2014-181

Small molecules facilitate rapid and synchronous iPSC generation

The reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) upon overexpression of OCT4, KLF4, SOX2, and c-MYC (OKSM) provides a powerful system to interrogate basic mechanisms of cell fate change. However, iPSC formation with standard methods is protracted and inefficient, resulting in heterogeneous cell populations. Here we show that exposure of OKSM-expressing cells to both ascorbic acid and a GSK3-beta inhibitor (termed “AGi”) facilitates more synchronous and rapid iPSC formation from a variety of mouse cell types. AGi treatment restored the ability of refractory cell populations to yield iPSC colonies, and it attenuated the activation of developmental regulators commonly observed during the reprogramming process. Moreover, AGi supplementation gave rise to chimera-competent iPSCs after as little as 48 hours of OKSM expression. Our results offer a simple modification to the reprogramming protocol, facilitating iPSC induction at unparalleled efficiencies and enabling dissection of the underlying mechanisms in more homogeneous cell populations.

Single-cell RNA sequencing identifies extracellular matrix gene expression by pancreatic circulating tumor cells

Circulating tumor cells (CTCs) are shed from primary tumors into the bloodstream, mediating the hematogenous spread of cancer to distant organs. To define their composition, we compared genome-wide expression profiles of CTCs with matched primary tumors in a mouse model of pancreatic cancer, isolating individual CTCs using epitope-independent microfluidic capture, followed by single-cell RNA sequencing. CTCs clustered separately from primary tumors and tumor-derived cell lines, showing low-proliferative signatures, enrichment for the stem-cell-associated gene Aldh1a2, biphenotypic expression of epithelial and mesenchymal markers, and expression of Igfbp5, a gene transcript enriched at the epithelial-stromal interface. Mouse as well as human pancreatic CTCs exhibit a very high expression of stromal-derived extracellular matrix (ECM) proteins, including SPARC, whose knockdown in cancer cells suppresses cell migration and invasiveness. The aberrant expression by CTCs of stromal ECM genes points to their contribution of microenvironmental signals for the spread of cancer to distant organs.

Yeast alcohol dehydrogenase structure and catalysis

Yeast (Saccharomyces cerevisiae) alcohol dehydrogenase I (ADH1) is the constitutive enzyme that reduces acetaldehyde to ethanol during the fermentation of glucose. ADH1 is a homotetramer of subunits with 347 amino acid residues. A structure for ADH1 was determined by X-ray crystallography at 2.4 Å resolution. The asymmetric unit contains four different subunits, arranged as similar dimers named AB and CD. The unit cell contains two different tetramers made up of "back-to-back" dimers, AB:AB and CD:CD. The A and C subunits in each dimer are structurally similar, with a closed conformation, bound coenzyme, and the oxygen of 2,2,2-trifluoroethanol ligated to the catalytic zinc in the classical tetrahedral coordination with Cys-43, Cys-153, and His-66. In contrast, the B and D subunits have an open conformation with no bound coenzyme, and the catalytic zinc has an alternative, inverted coordination with Cys-43, Cys-153, His-66, and the carboxylate of Glu-67. The asymmetry in the dimeric subunits of the tetramer provides two structures that appear to be relevant for the catalytic mechanism. The alternative coordination of the zinc may represent an intermediate in the mechanism of displacement of the zinc-bound water with alcohol or aldehyde substrates. Substitution of Glu-67 with Gln-67 decreases the catalytic efficiency by 100-fold. Previous studies of structural modeling, evolutionary relationships, substrate specificity, chemical modification, and site-directed mutagenesis are interpreted more fully with the three-dimensional structure.

dREAM co-operates with insulator-binding proteins and regulates expression at divergently paired genes

dREAM complexes represent the predominant form of E2F/RBF repressor complexes in Drosophila. dREAM associates with thousands of sites in the fly genome but its mechanism of action is unknown. To understand the genomic context in which dREAM acts we examined the distribution and localization of Drosophila E2F and dREAM proteins. Here we report a striking and unexpected overlap between dE2F2/dREAM sites and binding sites for the insulator-binding proteins CP190 and Beaf-32. Genetic assays show that these components functionally co-operate and chromatin immunoprecipitation experiments on mutant animals demonstrate that dE2F2 is important for association of CP190 with chromatin. dE2F2/dREAM binding sites are enriched at divergently transcribed genes, and the majority of genes upregulated by dE2F2 depletion represent the repressed half of a differentially expressed, divergently transcribed pair of genes. Analysis of mutant animals confirms that dREAM and CP190 are similarly required for transcriptional integrity at these gene pairs and suggest that dREAM functions in concert with CP190 to establish boundaries between repressed/activated genes. Consistent with the idea that dREAM co-operates with insulator-binding proteins, genomic regions bound by dREAM possess enhancer-blocking activity that depends on multiple dREAM components. These findings suggest that dREAM functions in the organization of transcriptional domains.

Cancer therapy. Ex vivo culture of circulating breast tumor cells for individualized testing of drug susceptibility

Circulating tumor cells (CTCs) are present at low concentrations in the peripheral blood of patients with solid tumors. It has been proposed that the isolation, ex vivo culture, and characterization of CTCs may provide an opportunity to noninvasively monitor the changing patterns of drug susceptibility in individual patients as their tumors acquire new mutations. In a proof-of-concept study, we established CTC cultures from six patients with estrogen receptor-positive breast cancer. Three of five CTC lines tested were tumorigenic in mice. Genome sequencing of the CTC lines revealed preexisting mutations in the PIK3CA gene and newly acquired mutations in the estrogen receptor gene (ESR1), PIK3CA gene, and fibroblast growth factor receptor gene (FGFR2), among others. Drug sensitivity testing of CTC lines with multiple mutations revealed potential new therapeutic targets. With optimization of CTC culture conditions, this strategy may help identify the best therapies for individual cancer patients over the course of their disease.

Bacterial periplasmic sialic acid-binding proteins exhibit a conserved binding site

Sialic acids are a family of related nine-carbon sugar acids that play important roles in both eukaryotes and prokaryotes. These sialic acids are incorporated/decorated onto lipooligosaccharides as terminal sugars in multiple bacteria to evade the host immune system. Many pathogenic bacteria scavenge sialic acids from their host and use them for molecular mimicry. The first step of this process is the transport of sialic acid to the cytoplasm, which often takes place using a tripartite ATP-independent transport system consisting of a periplasmic binding protein and a membrane transporter. In this paper, the structural characterization of periplasmic binding proteins from the pathogenic bacteria Fusobacterium nucleatum, Pasteurella multocida and Vibrio cholerae and their thermodynamic characterization are reported. The binding affinities of several mutations in the Neu5Ac binding site of the Haemophilus influenzae protein are also reported. The structure and the thermodynamics of the binding of sugars suggest that all of these proteins have a very well conserved binding pocket and similar binding affinities. A significant conformational change occurs when these proteins bind the sugar. While the C1 carboxylate has been identified as the primary binding site, a second conserved hydrogen-bonding network is involved in the initiation and stabilization of the conformational states.