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\"At the center of the 2,000 mile U.S.-Mexico border, a sprawling transnational urban space has mushroomed into a metropolitan region with over two million people whose livelihoods depend on global manufacturing, cross-border trade, and border control jobs. Our volume advances knowledge on urban space, gender, education, security, and work, focusing on Ciudad Jur̀ez, the export-processing (maquiladora) manufacturing capital of the Americas and the infamous site of femicide and outlier murder rates connected with arms and drug trafficking. Given global economic trends, this transnational urban region is a likely paradigmatic future for other world regions\"--Provided by publisher.

Burkitt’s lymphoma is a rapidly proliferating lymphoma of germinal-center B cells. Most patients are cured with chemotherapy and prevention of tumor lysis. Relapse and CNS involvement carry a poor prognosis.

The Genomic Data Commons will initially house raw genomic data and diagnostic, histologic, and clinical outcome data from National Cancer Institute–funded projects. A harmonization process will align sequencing data to the genome and identify mutations and alterations. For the past 2 years, the National Cancer Institute (NCI), the University of Chicago, the Ontario Institute for Cancer Research, and Leidos Biomedical Research have been developing an information system called the NCI Genomic Data Commons (GDC) (see figure). The GDC will initially contain raw genomic data as well as diagnostic, histologic, and clinical outcome data from NCI-funded projects such as the Cancer Genome Atlas (TCGA) and the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) program. Unlike previous versions of these data sets, the genomic data will be “harmonized” using uniform analytic pipelines to align the raw sequencing data . . .

The goal of the National Cancer Institute’s (NCI’s) Genomic Data Commons (GDC) is to provide the cancer research community with a data repository of uniformly processed genomic and associated clinical data that enables data sharing and collaborative analysis in the support of precision medicine. The initial GDC dataset include genomic, epigenomic, proteomic, clinical and other data from the NCI TCGA and TARGET programs. Data production for the GDC started in June, 2015 using an OpenStack-based private cloud. By June of 2016, the GDC had analyzed more than 50,000 raw sequencing data inputs, as well as multiple other data types. Using the latest human genome reference build GRCh38, the GDC generated a variety of data types from aligned reads to somatic mutations, gene expression, miRNA expression, DNA methylation status, and copy number variation. In this paper, we describe the pipelines and workflows used to process and harmonize the data in the GDC. The generated data, as well as the original input files from TCGA and TARGET, are available for download and exploratory analysis at the GDC Data Portal and Legacy Archive ( https://gdc.cancer.gov/ ). The Genomic Data Commons repository contains genomic, epigenomic, proteomic and clinical data from the TCGA and TARGET datasets. Here, the authors describe the analysis methods for how these divergent datasets were integrated together.

The median survival of patients with mantle cell lymphoma (MCL) ranges from 3 to 5 years with current chemotherapeutic regimens. A common secondary genomic alteration detected in MCL is chromosome 13q31-q32 gain/amplification, which targets a microRNA (miRNA) cluster, miR-17∼92. On the basis of gene expression profiling, we found that high level expression of C13orf25 , the primary transcript from which these miRNAs are processed, was associated with poorer survival in patients with MCL ( P =0.021). We demonstrated that the protein phosphatase PHLPP2, an important negative regulator of the PI3K/AKT pathway, was a direct target of miR-17∼92 miRNAs, in addition to PTEN and BIM. These proteins were down-modulated in MCL cells with overexpression of the miR-17∼92 cluster. Overexpression of miR-17∼92 activated the PI3K/AKT pathway and inhibited chemotherapy-induced apoptosis in MCL cell lines. Conversely, inhibition of miR-17∼92 expression suppressed the PI3K/AKT pathway and inhibited tumor growth in a xenograft MCL mouse model. Targeting the miR-17∼92 cluster may therefore provide a novel therapeutic approach for patients with MCL.

Diffuse large-B-cell lymphoma is curable, but when treatment fails, outcome is poor. Although imaging can help to identify patients at risk of treatment failure, they are often imprecise, and radiation exposure is a potential health risk. We aimed to assess whether circulating tumour DNA encoding the clonal immunoglobulin gene sequence could be detected in the serum of patients with diffuse large-B-cell lymphoma and used to predict clinical disease recurrence after frontline treatment. We used next-generation DNA sequencing to retrospectively analyse cell-free circulating tumour DNA in patients assigned to one of three treatment protocols between May 8, 1993, and June 6, 2013. Eligible patients had diffuse large-B-cell lymphoma, no evidence of indolent lymphoma, and were previously untreated. We obtained serial serum samples and concurrent CT scans at specified times during most treatment cycles and up to 5 years of follow-up. VDJ gene segments of the rearranged immunoglobulin receptor genes were amplified and sequenced from pretreatment specimens and serum circulating tumour DNA encoding the VDJ rearrangements was quantitated. Tumour clonotypes were identified in pretreatment specimens from 126 patients who were followed up for a median of 11 years (IQR 6·8–14·2). Interim monitoring of circulating tumour DNA at the end of two treatment cycles in 108 patients showed a 5-year time to progression of 41·7% (95% CI 22·2–60·1) in patients with detectable circulating tumour DNA and 80·2% (69·6–87·3) in those without detectable circulating tumour DNA (p<0·0001). Detectable interim circulating tumour DNA had a positive predictive value of 62·5% (95% CI 40·6–81·2) and a negative predictive value of 79·8% (69·6–87·8). Surveillance monitoring of circulating tumour DNA was done in 107 patients who achieved complete remission. A Cox proportional hazards model showed that the hazard ratio for clinical disease progression was 228 (95% CI 51–1022) for patients who developed detectable circulating tumour DNA during surveillance compared with patients with undetectable circulating tumour DNA (p<0·0001). Surveillance circulating tumour DNA had a positive predictive value of 88·2% (95% CI 63·6–98·5) and a negative predictive value of 97·8% (92·2–99·7) and identified risk of recurrence at a median of 3·5 months (range 0–200) before evidence of clinical disease. Surveillance circulating tumour DNA identifies patients at risk of recurrence before clinical evidence of disease in most patients and results in a reduced disease burden at relapse. Interim circulating tumour DNA is a promising biomarker to identify patients at high risk of treatment failure. National Cancer Institute and Adaptive Biotechnologies.

Activating mutations in the KRAS gene are among the most prevalent genetic changes in human cancers. To identify synthetic lethal interactions in cancer cells harbouring mutant KRAS , we performed a large-scale screen in isogenic paired colon cancer cell lines that differ by a single allele of mutant KRAS using an inducible short hairpin RNA interference library. Snail2, a zinc finger transcriptional repressor encoded by the SNAI2 gene, was found to be selectively required for the long-term survival of cancer cells with mutant KRAS that have undergone epithelial–mesenchymal transition (EMT), a transdifferentiation event that is frequently seen in advanced tumours and is promoted by RAS activation. Snail2 expression is regulated by the RAS pathway and is required for EMT. Our findings support Snail2 as a possible target for the treatment of the broad spectrum of human cancers of epithelial origin with mutant RAS that have undergone EMT and are characterized by a high degree of chemoresistance and radioresistance.

The activated B-cell–like (ABC) subtype of diffuse large B-cell lymphoma (DLBCL) relies on chronic active B-cell receptor (BCR) signaling. BCR pathway inhibitors induce remissions in a subset of ABC DLBCL patients. BCR microclusters on the surface of ABC cells resemble those generated following antigen engagement of normal B cells. We speculated that binding of lymphoma BCRs to self-antigens initiates and maintains chronic active BCR signaling in ABC DLBCL. To assess whether antigenic engagement of the BCR is required for the ongoing survival of ABC cells, we developed isogenic ABC cells that differed solely with respect to the IgH V region of their BCRs. In competitive assays with wild-type cells, substitution of a heterologous V region impaired the survival of three ABC lines. The viability of one VH4-34⁺ ABC line and the ability of its BCR to bind to its own cell surface depended on V region residues that mediate the intrinsic autoreactivity of VH4-34 to self-glycoproteins. The BCR of another ABC line reacted with self-antigens in apoptotic debris, and the survival of a third ABC line was sustained by reactivity of its BCR to an idiotypic epitope in its own V region. Hence, a diverse set of self-antigens is responsible for maintaining the malignant survival of ABC DLBCL cells. IgH V regions used by the BCRs of ABC DLBCL biopsy samples varied in their ability to sustain survival of these ABC lines, suggesting a screening procedure to identify patients who might benefit from BCR pathway inhibition.

To classify cancer specimens by their gene expression profiles, we created a statistical method based on Bayes' rule that estimates the probability of membership in one of two cancer subgroups. We used this method to classify diffuse large B cell lymphoma (DLBCL) biopsy samples into two gene expression subgroups based on data obtained from spotted cDNA microarrays. The germinal center B cell-like (GCB) DLBCL subgroup expressed genes characteristic of normal germinal center B cells whereas the activated B cell-like (ABC) DLBCL subgroup expressed a subset of the genes that are characteristic of plasma cells, particularly those encoding endoplasmic reticulum and golgi proteins involved in secretion. We next used this predictor to discover these subgroups within a second set of DLBCL biopsies that had been profiled by using oligonucleotide microarrays [Shipp, M. A., et al. (2002) Nat. Med. 8, 68-74]. The GCB and ABC DLBCL subgroups identified in this data set had significantly different 5-yr survival rates after multiagent chemotherapy (62% vs. 26%; P = 0.0051), in accord with analyses of other DLBCL cohorts. These results demonstrate the ability of this gene expression-based predictor to classify DLBCLs into biologically and clinically distinct subgroups irrespective of the method used to measure gene expression.

Surface-active compounds present in aerosols can increase their cloud condensation nuclei (CCN) activation efficiency by reducing the surface tension (σ) in the growing droplets. However, the importance of this effect is poorly constrained by measurements. Here we present estimates of droplet surface tension near the point of activation derived from direct measurement of droplet diameters using a continuous flow streamwise thermal gradient chamber (CFSTGC). The experiments used sea spray aerosol (SSA) mimics composed of NaCl coated by varying amounts of (i) oleic acid, palmitic acid or myristic acid, (ii) mixtures of palmitic acid and oleic acid, and (iii) oxidized oleic acid. Significant reductions in σ relative to that for pure water were observed for these mimics at relative humidity (RH) near activation (∼ 99.9 %) when the coating was sufficiently thick. The calculated surface pressure (π = σH2O − σobserved) values for a given organic compound or mixture collapse onto one curve when plotted as a function of molecular area for different NaCl seed sizes and measured RH. The observed critical molecular area (A0) for oleic acid determined from droplet growth was similar to that from experiments conducted using macroscopic solutions in a Langmuir trough. However, the observations presented here suggest that oleic acid in microscopic droplets may exhibit larger π values during monolayer compression. For myristic acid, the observed A0 compared well to macroscopic experiments on a fresh subphase, for which dissolution has an important impact. A significant kinetic limitation to water uptake was observed for NaCl particles coated with pure palmitic acid, likely as a result of palmitic acid (with coating thicknesses ranging from 67 to 132 nm) being able to form a solid film. However, for binary palmitic-acid–oleic-acid mixtures there was no evidence of a kinetic limitation to water uptake. Oxidation of oleic acid had a minor impact on the magnitude of the surface tension reductions observed, potentially leading to a slight reduction in the effect compared to pure oleic acid. A CCN counter was also used to assess the impact on critical supersaturations of the substantial σ reductions observed at very high RH. For the fatty-acid-coated NaCl particles, when the organic fraction (εorg) was > 0.90 small depressions in critical supersaturation were observed. However, when εorg < 0.90 the impact on critical supersaturation was negligible. Thus, for the fatty acids considered here, the substantial σ reductions observed at high RH values just below activation have limited impact on the ultimate critical supersaturation. A surface film model is used to establish the properties that surface-active organic molecules must have if they are to ultimately have a substantial impact on the activation efficiency of SSA. To influence activation, the average properties of surface-active marine-derived organic molecules must differ substantially from the long-chain fatty acids examined, having either smaller molecular volumes or larger molecular areas. The model results also indicate that organic-compound-driven surface tension depression can serve to buffer the critical supersaturation against changes to the organic-to-salt ratio in particles in which the organic fraction is sufficiently large.