Search

Brain metastases from lung adenocarcinoma (BM-LUAD) frequently cause patient mortality. To identify genomic alterations that promote brain metastases, we performed whole-exome sequencing of 73 BM-LUAD cases. Using case-control analyses, we discovered candidate drivers of brain metastasis by identifying genes with more frequent copy-number aberrations in BM-LUAD compared to 503 primary LUADs. We identified three regions with significantly higher amplification frequencies in BM-LUAD, including MYC (12 versus 6%), YAP1 (7 versus 0.8%) and MMP13 (10 versus 0.6%), and significantly more frequent deletions in CDKN2A/B (27 versus 13%). We confirmed that the amplification frequencies of MYC, YAP1 and MMP13 were elevated in an independent cohort of 105 patients with BM-LUAD. Functional assessment in patient-derived xenograft mouse models validated the notion that MYC, YAP1 or MMP13 overexpression increased the incidence of brain metastasis. These results demonstrate that somatic alterations contribute to brain metastases and that genomic sequencing of a sufficient number of metastatic tumors can reveal previously unknown metastatic drivers.

Although lung adenocarcinomas frequently metastasize to the brain, treatment options for lung adenocarcinoma brain metastases are limited. We discovered novel candidate drivers of progression by using case-control analyses to compare whole-exome sequencing data from a cohort of 73 lung adenocarcinoma brain metastases to a control cohort of 503 primary lung adenocarcinomas. We identified 3 genomic regions with significantly more frequent amplifications in brain metastases compared to the control cohort: MYC (12% vs 6%), YAP1 (7% vs 0.8%) and MMP13 (10% vs 0.6%). We also identified CDKN2A/B as a region deleted at a significantly greater frequency in brain metastases compared to primary lung adenocarcinomas (27% vs 13%, respectively). We confirmed frequent amplifications of MYC and YAP1/MMP13 in an independent validation cohort of 105 lung adenocarcinoma brain metastasis samples using fluorescence in situ hybridization. We further validated that MYC, YAP1 and MMP13 can drive brain metastases in a patient-derived xenograft mouse model. We found a higher incidence of metastases to the brain in mice receiving intracardiac injections of tumor cells expressing the candidate drivers compared to tumor cells expressing LacZ as a control. These results indicate that somatic alterations can drive lung adenocarcinomas to metastasize to the brain. The candidate brain metastasis drivers that we identified may serve as therapeutic targets in patients with lung adenocarcinomas who develop this devastating complication.

SUMMARYUnderstanding the mechanisms controlling the invasive spread of normal and transformed cells is central to understanding diverse processes including cancer progression. Here, we report that Yes- associated protein (YAP), a central transcriptional regulator implicated in controlling organ and body size, modulates a Rho-GTPase switch that drives cellular migration by directly transactivating the Rac1-GEF protein TRIO. Additionally, YAP and TRIO activate the Rac1-STAT3 axis to promote invasive behavior. While we find this YAP-dependent infiltrative program in many cell types, it is particularly enhanced in a patient-specific way in the most common malignant brain tumor, glioblastoma (GBM), where hyperactivation of the YAP-mediated TRIO and STAT3 network also confers poor patient outcome and up-regulation of genes associated with the Mesenchymal subtype of GBM. Our analysis suggests that the YAP-TRIO-STAT3 signaling network identified in this study is a ubiquitous regulator of invasive cell spread in both normal and pathological contexts.

Summary: Molecular factors that define stem cell identity have recently emerged as oncogenic drivers. For instance, brachyury, a key developmental transcriptional factor, is also implicated in carcinogenesis, most notably of chordoma, through mechanisms that remain elusive. Here, we show that brachyury is a crucial regulator of stemness in chordoma and in more common aggressive cancers. Furthermore, this effect of brachyury is mediated by control of synthesis and stability of Yes-associated protein (YAP), a key regulator of tissue growth and homeostasis, providing an unexpected mechanism of control of YAP expression. We further demonstrate that the brachyury-YAP regulatory pathway is associated with tumor aggressiveness. These results elucidate a mechanism of controlling both tumor stemness and aggressiveness through regulatory coupling of two developmental factors. : Malignant neoplasms exhibit uninhibited and dysregulated growth coupled with acquisition of stem-like properties that are integral to the development and progression of disease. Shah et al. demonstrate a critical role of brachyury in regulating stemness and growth by activating YAP through direct transcriptional and post-transcriptional mechanisms in various cancers. Keywords: brachyury, YAP, chordoma, stremness, growth, glioblastoma, lung carcinoma

Determination of emm variations may help improve vaccine design., Group A Streptococcus (GAS) is a human-adapted pathogen that causes a variety of diseases, including pharyngitis and invasive infections. GAS strains are categorized by variation in the nucleotide sequence of the gene (emm) that encodes the M protein. To identify the emm types of GAS strains causing pharyngitis in Ontario, Canada, we sequenced the hypervariable region of the emm gene in 4,635 pharyngeal GAS isolates collected during 2002–2010. The most prevalent emm types varied little from year to year. In contrast, fine-scale geographic analysis identified inter-site variability in the most common emm types. Additionally, we observed fluctuations in yearly frequency of emm3 strains from pharyngitis patients that coincided with peaks of emm3 invasive infections. We also discovered a striking increase in frequency of emm89 strains among isolates from patients with pharyngitis and invasive disease. These findings about the epidemiology of GAS are potentially useful for vaccine research.

Many pathogens colonize different anatomical sites, but the selective pressures contributing to survival in the diverse niches are poorly understood. Group A Streptococcus (GAS) is a human-adapted bacterium that causes a range of infections. Much effort has been expended to dissect the molecular basis of invasive (sterile-site) infections, but little is known about the genomes of strains causing pharyngitis (streptococcal “sore throat”). Additionally, there is essentially nothing known about the genetic relationships between populations of invasive and pharyngitis strains. In particular, it is unclear if invasive strains represent a distinct genetic subpopulation of strains that cause pharyngitis. We compared the genomes of 86 serotype M3 GAS pharyngitis strains with those of 215 invasive M3 strains from the same geographical location. The pharyngitis and invasive groups were highly related to each other and had virtually identical phylogenetic structures, indicating they belong to the same genetic pool. Despite the overall high degree of genetic similarity, we discovered that strains from different host environments (i.e., throat, normally sterile sites) have distinct patterns of diversifying selection at the nucleotide level. In particular, the pattern of polymorphisms in the hyaluronic acid capsule synthesis operon was especially different between the two strain populations. This finding was mirrored by data obtained from full-genome analysis of strains sequentially cultured from nonhuman primates. Our results answer the long-standing question of the genetic relationship between GAS pharyngitis and invasive strains. The data provide previously undescribed information about the evolutionary history of pathogenic microbes that cause disease in different anatomical sites.

Understanding the fine-structure molecular architecture of bacterial epidemics has been a long-sought goal of infectious disease research. We used short-read-length DNA sequencing coupled with mass spectroscopy analysis of SNPs to study the molecular pathogenomics of three successive epidemics of invasive infections involving 344 serotype M3 group A Streptococcus in Ontario, Canada. Sequencing the genome of 95 strains from the three epidemics, coupled with analysis of 280 biallelic SNPs in all 344 strains, revealed an unexpectedly complex population structure composed of a dynamic mixture of distinct clonally related complexes. We discovered that each epidemic is dominated by micro- and macrobursts of multiple emergent clones, some with distinct strain genotype–patient phenotype relationships. On average, strains were differentiated from one another by only 49 SNPs and 11 insertion-deletion events (indels) in the core genome. Ten percent of SNPs are strain specific; that is, each strain has a unique genome sequence. We identified nonrandom temporal–spatial patterns of strain distribution within and between the epidemic peaks. The extensive full-genome data permitted us to identify genes with significantly increased rates of nonsynonymous (amino acid-altering) nucleotide polymorphisms, thereby providing clues about selective forces operative in the host. Comparative expression microarray analysis revealed that closely related strains differentiated by seemingly modest genetic changes can have significantly divergent transcriptomes. We conclude that enhanced understanding of bacterial epidemics requires a deep-sequencing, geographically centric, comparative pathogenomics strategy.

Cancer cell migration is a critical process that underlies invasion, treatment evasion, and tumor recurrence. In the complex 3D-confined microenvironments of the body, a diverse molecular machinery drives migratory behavior. In particular, the recently discovered osmotic engine plays a pivotal role in promoting cell dispersal through directed water permeation. This osmotic engine machinery is driven by solute transporters and aquaporins, collectively named the transportome. Hence, it is imperative to determine the role of this transportome and its implications for invasive gliomas. Using novel in vitro microfluidic technology, we demonstrate for the first time that human glioblastoma (GBM) cells rely on the osmotic engine to migrate in confined microenvironments. In particular, using microchannel microfluidic devices, we characterize the migratory capacity of GBM cells in 3D-confined microenvironments using real-time imaging and assess their migratory behavior upon osmotic shock treatment. Our results show that GBM cells readily migrate in high degrees of confinement (3uM). In addition, when exposed to either a hypotonic shock at the leading edge or hypertonic shock at the lagging edge, these primary GBM cells reverse their directional migration, signifying the role of the osmotic engine model in brain cancer (p < 0.05). Furthermore, we uncover the transcription factor TEAD4 as a master regulator of the transportome gene signature and the osmotic engine collectively. Genetic inhibition of TEAD4 results in reduced migratory potential through confined microchannels as well as decreased speed within these confined spaces in vitro (p < 0.05). Using TCGA (n = 528) and REMBRANDT (n = 228) GBM patient datasets, we found that the TEAD4-controlled transportome machinery is overrepresented in glioblastomas and correlates with its poor prognosis. Taken together, our results show that the osmotic engine is a crucial mechanism for GBM cell migration driven by the TEAD4-dependent transportome machinery. Targeting this TEAD4-driven osmotic engine may hold a promising alternative for management of invasive gliomas.

Glioblastomas are characterized by their ability to disseminate into the local brain parenchyma; thus, confounding surgical excision and radiotherapy. Hence, it is imperative to identify and decipher the signaling networks that drive invasion. Glioblastoma cells utilize molecular transporters at both their leading (inward facing) and lagging (outward facing) edge to modulate cell volume and invade the confined microenvironment of the brain. These transporters include solute transporters as well as the aquaporins, and collectively behave as an osmotic engine for cellular invasion. However, the transcriptional regulators of these transporters have not been fully identified. Here, we report that TEAD4, a transcription factor implicated in neural development, is a potent regulator of the osmotic engine through transcriptional control of solute and water transporters. In particular, our data demonstrates that loss of TEAD4 decreases glioblastoma cells ability to migrate and invade through small pores (Boyden chamber and Matrigel transwell, respectively) mimicking the confined microenvironment of the brain (p < 0.05). Additionally, we uncover the role of TEAD4 in regulating members of the Na + /H+ exchanger, chloride co-transporter and aquaporin families, as well as the volume regulated anion channel to enable water permeation (p < 0.05). Apart from regulating cell dispersal, our data also shows that TEAD4 regulates glioblastoma proliferation (p < 0.05). Using the TCGA and REMBRANDT datasets, we observed TEAD4 is selectively overexpressed and hyperactive in glioblastomas compared to non-cancer cortex and lower grade gliomas (p < 0.05). Furthermore, we found that patients with elevated TEAD4 expression have a significantly shorter progression free survival and overall survival (p < 0.05). Taken together, our results show that TEAD4 is a potent regulator of cell dispersal through transcriptional control of the osmotic engine and has relevance to clinical outcomes of glioblastoma patients. Hence, TEAD4 may be a selective and potent therapeutic target that warrants further exploration.

Glioblastoma (GBM) is a highly invasive and lethal brain tumor due to its high invasion and recurrence. The mechanisms that confer GBM cells their invasive behavior and their regulatory system have not been fully elucidated. We have shown that pharmacological inhibition and decreased expression of the electroneutral Na + -K + -Cl- cotransporter-1 (NKCC1) in GBM leads to a decreased cell migration and invasion capacity, in vitro and in vivo. We have previously reported that NKCC1 knockdown cells (NKCC1 KD) show significantly larger focal adhesions, suggesting a potential role of NKCC1 in cell adhesion. Here, we focused on the role of NKCC1 on the cytoskeleton dynamics of GBM cells. We found that glioma cells display a significant decrease on their cell spreading capacity upon NKCC1 knockdown or pharmacologic inhibition by Bumetanide (BMT) (p < 0.0001). F-actin staining showed a change in the organization of fibrillary actin of the cells, where NKCC1 KD cells displayed a ring shape actin morphology that was absent in control cells. In addition the bundled actin content was decreased by NKCC1 inhibition (GBM 612 p < 0.05; GBM 965 p < 0.001). The molecular regulation of actin dynamics can be due to the activity of RhoA acting through Cofilin, which acts as an initiator of actin polymerization. We observed that the small GTPase RhoA and Rac1 active levels decreased 40-50% in the NKCC1 KD cells. This result suggests that NKCC1 regulates cytoskeleton dynamics through multiple targets that include filament actin regulation and RhoA and Rac1 activity. Based on our results, NKCC1 modulates migration of GBM cells by at least two different mechanisms: cell volume regulation (through ion transport) and regulation of the actin cytoskeleton. Due to its essential role in cell migration and high expression in GBM, NKCC1 may serve as a specific therapeutic target to decrease GBM cell invasion.

Meningiomas frequently harbor inactivating mutations in the tumor suppressor protein Merlin (NF2), an upstream activator of the Hippo signaling pathway. This aberration drives tumor growth and aggressiveness through inactivation of this pathway and unchecked activation of its downstream effector, Yes-associated protein (YAP). The transcriptional coactivator YAP has been previously implicated in driving meningioma growth and malignant transformation of non-neoplastic arachnoid cells. YAP exerts its effect by direct binding to the TEAD family of transcription factors and transactivation of growth-related genes. However, the efficacy of pharmacologic modulation of this pathway in meningioma has yet to be explored. Verteporfin is a small molecule inhibitor of the porphyrin family, recently implicated as a direct inhibitor of YAP. Here, we report that Verteporfin modulates growth and radiation resistance in NF2 driven meningiomas through inhibition of the YAP-TEAD interaction. In particular, our data demonstrates that Verteporfin treatment in the NF2 mutant KT21MG1 human malignant meningioma cell line, results in a decreased activity of oncogenic YAP, resulting in decreased mRNA expression of YAP downstream targets (CTGF, Mcl-1 and ANKRD1) (p ≤ 0.05). Moreover, Verteporfin inhibits meningioma cell growth and proliferation in a dose dependent manner (MTT reduction and viable cell number) (p ≤ 0.05). Interestingly, pretreatment with Verteporfin results in increased sensitivity to irradiation in vitro (p ≤ 0.05). In addition, we explore the in vivo efficacy of Verteporfin treatment in a murine skull base xenograft model of human meningioma. Taken together, our results show that Verteporfin is a potent inhibitor of meningioma cell growth and radioresistance, making it an attractive drug candidate for treatment of this disease. Hence, this targeted therapy towards the NF2-YAP axis holds promising alternatives to current standard of care.