Pan cancer patterns of allelic imbalance from chromosomal alterations in 33 tumor types

Somatic copy number alterations (SCNAs) serve as hallmarks of tumorigenesis and often result in deviations from one-to-one allelic ratios at heterozygous loci, leading to allelic imbalance (AI). The Cancer Genome Atlas (TCGA) reports SCNAs identified using a circular binary segmentation algorithm, providing segment mean copy number estimates from single-nucleotide polymorphism DNA microarray total intensities (log R ratio), but not allele-specific intensities (“B allele” frequencies) that inform of AI. Our approach provides more sensitive identification of SCNAs by modeling the “B allele” frequencies jointly, thereby bolstering the catalog of chromosomal alterations in this widely utilized resource. Here we present AI summaries for all 33 tumor sites in TCGA, including those induced by SCNAs and copy-neutral loss-of-heterozygosity (cnLOH). We identified AI in 94% of the tumors, higher than in previous reports. Recurrent events included deletions of 17p, 9q, 3p, amplifications of 8q, 1q, 7p, as well as mixed event types on 8p and 13q. We also observed both site-specific and pan-cancer (spanning 17p) cnLOH, patterns which have not been comprehensively characterized. The identification of such cnLOH events elucidates tumor suppressors and multi-hit pathways to carcinogenesis. We also contrast the landscapes inferred from AI- and total intensity-derived SCNAs and propose an automated procedure to improve and adjust SCNAs in TCGA for cases where high levels of aneuploidy obscured baseline intensity identification. Our findings support the exploration of additional methods for robust automated inference procedures and to aid empirical discoveries across TCGA.     

Interaction between GSTM1 genotype and IL-6 on mortality in older adults: results from the ilSIRENTE study

Background and aimsThe inflammatory process is related to oxidative stress and inflammation was proven to be a strong determinant of the aging process and to ultimately lead to death. The aim of the present study was to assess if, in a population of older adults, the effect of antioxidant genes GSTM1 and GSTT1 genotypes on mortality may differ depending on levels of inflammation.MethodsData are from 353 older persons aged ?80 years enrolled in the ilSIRENTE study. Study population was divided into two groups computed based on the median value of serum IL-6 (low IL-6, n = 177 and high IL-6, n = 176). All participants were followed up for 48 months.ResultsMean age of study participants was 85.8 years (Standard Deviation 4.8), 235 (66.6%) were women. Overall 48/177 participant (27.1%) in the low IL-6 group died during the study period, compared with 97/176 (55.1%) in the high IL-6 group (p < 0.001). After adjusting for potential confounders, GSTM1 wildtype had no effect on mortality in the low IL-6 group (RR = 1.07; 95% CI 0.46–2.47), but it was associated with a significant lower mortality rate in the high IL-6 level (RR = 0.33; 95% CI 0.15–0.69). Testing the interaction between IL-6 and GSTM1 genotype, we found a significant result (p = 0.02). No significant effect of GSTT1 genotype on mortality was shown in participants with low and high IL-6 level.ConclusionGSTM1 wildtype is associated with reduced mortality among older adults with high levels of inflammation, but not among those with low levels of inflammation.     

IFN-gamma and Fas ligand are required for graft-versus-tumor activity against renal cell carcinoma in the absence of lethal graft-versus-host disease

To determine the mechanisms of graft-versus-tumor (GVT) activity in the absence of graft-versus-host disease (GVHD) against a solid tumor, we established two allogeneic bone marrow transplantation models with a murine renal cell carcinoma (RENCA). The addition of 0.3 x 10(6) donor CD8(+) T cells to the allograft increased the survival of tumor-bearing mice without causing GVHD. The analysis of CD8(+) T cells deficient in cytotoxic molecules demonstrated that anti-RENCA activity is dependent on IFN-gamma and Fas ligand (FasL), but does not require soluble or membrane-bound TNF-alpha, perforin, or TRAIL. Recipients of IFN-gamma(-/-) CD8(+) T cells are unable to reject RENCA compared with recipients of wild-type CD8(+) T cells and, importantly, neither group develops severe GVHD. IFN-gamma(-/-) CD8(+) T cells derived from transplanted mice are less able to kill RENCA cells in vitro, while pretreatment of RENCA cells with IFN-gamma enhances class I and FasL expression and rescues the lytic capacity of IFN-gamma(-/-) CD8(+) T cells. These results demonstrate that the addition of low numbers of selected donor CD8(+) T cells to the allograft can mediate GVT activity without lethal GVHD against murine renal cell carcinoma, and this GVT activity is dependent on IFN-gamma and FasL.     

Enhanced immune reconstitution by sex steroid ablation following allogeneic hemopoietic stem cell transplantation

Delayed immune reconstitution in adult recipients of allogeneic hemopoietic stem cell transplantations (HSCT) is related to age-induced thymic atrophy. Overcoming this paucity of T cell function is a major goal of clinical research but in the context of allogeneic transplants, any strategy must not exacerbate graft-vs-host disease (GVHD) yet ideally retain graft-vs-tumor (GVT) effects. We have shown sex steroid ablation reverses thymic atrophy and enhances T cell recovery in aged animals and in congenic bone marrow (BM) transplant but the latter does not have the complications of allogeneic T cell reactivity. We have examined whether sex steroid ablation promoted hemopoietic and T cell recovery following allogeneic HSCT and whether this benefit was negated by enhanced GVHD. BM and thymic cell numbers were significantly increased at 14 and 28 days after HSCT in castrated mice compared with sham-castrated controls. In the thymus, the numbers of donor-derived thymocytes and dendritic cells were significantly increased after HSCT and castration; donor-derived BM precursors and developing B cells were also significantly increased. Importantly, despite restoring T cell function, sex steroid inhibition did not exacerbate the development of GVHD or ameliorate GVT activity. Finally, IL-7 treatment in combination with castration had an additive effect on thymic cellularity following HSCT. These results indicate that sex steroid ablation can profoundly enhance thymic and hemopoietic recovery following allogeneic HSCT without increasing GVHD and maintaining GVT.     

The Effects of Leptin on Rat Brain Development; An Experimental Study

International Journal of Peptide Research and Therapeutics -     

Are black flies of the subgenus Wilhelmia (Diptera: Simuliidae) multiple species or a single geographical generalist? Insights from the macrogenome

Organisms with vast distributions often represent geographical mosaics of cryptic species. The black fly Simulium (Wilhelmia) lineatum is among the most widely distributed members of the family Simuliidae, ranging from the British Isles to eastern China. Rather than viewing S. lineatum as a possible aggregate of multiple species, taxonomists have suggested a more inclusive taxon with additional synonyms. Accordingly, S. lineatum is an ideal candidate for testing the hypothesis that a wide geographical distribution signals the presence of more than one species. A cytogenetic approach was used to probe the macrogenome of S. lineatum and other taxa proposed by taxonomists as conspecific. The banding patterns in the polytene chromosomes of 480 larvae from 15 countries across the Palearctic Region revealed 128 rearrangements of the complement. All rearrangements were autosomal and 89% were inversions nonrandomly distributed among species and among chromosome arms. The analyses clarify long‐standing confusion over previously proposed names and reveal a longitudinal succession of four species sequentially replacing one another from west to east: Simulium lineatum s.s., Simulium balcanicum, Simulium turgaicum, and Simulium takahasii. Thus, S. turgaicum is recalled from synonymy and the other three species are validated. Within the most‐represented species, S. balcanicum, the frequency of inversions follows a longitudinal gradient with a north–south bias; as the distance between the sites increases along this north‐west–south‐east axis, the similarity of inversion frequencies between sites decreases. Validation of the concept that broadly distributed black flies are composites of structurally similar species provides a framework for guiding discovery of additional biodiversity. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 114 , 163–183.     

The interrelations of radiologic findings and mechanical ventilation in community acquired pneumonia patients admitted to the intensive care unit: a multicentre retrospective study

Background

Burkholderia cepacia complex (BCC) bacteria are highly virulent, typically multidrug-resistant, opportunistic pathogens in cystic fibrosis (CF) patients and other immunocompromised individuals. B. vietnamiensis is more often susceptible to aminoglycosides than other BCC species, and strains acquire aminoglycoside resistance during chronic CF infection and under tobramycin and azithromycin exposure in vitro, apparently from gain of antimicrobial efflux as determined through pump inhibition. The aims of the present study were to determine if oxidative stress could also induce aminoglycoside resistance and provide further observations in support of a role for antimicrobial efflux in aminoglycoside resistance in B. vietnamiensis.

Findings

Here we identified hydrogen peroxide as an additional aminoglycoside resistance inducing agent in B. vietnamiensis. After antibiotic and hydrogen peroxide exposure, isolates accumulated significantly less [³H] gentamicin than the susceptible isolate from which they were derived. Strains that acquired aminoglycoside resistance during infection and after exposure to tobramycin or azithromycin overexpressed a putative resistance-nodulation-division (RND) transporter gene, amrB. Missense mutations in the repressor of amrB, amrR, were identified in isolates that acquired resistance during infection, and not in those generated in vitro.

Conclusions

These data identify oxidative stress as an inducer of aminoglycoside resistance in B. vietnamiensis and further suggest that active efflux via a RND efflux system impairs aminoglycoside accumulation in clinical B. vietnamiensis strains that have acquired aminoglycoside resistance, and in those exposed to tobramycin and azithromycin, but not hydrogen peroxide, in vitro. Furthermore, the repressor AmrR is likely just one regulator of the putative AmrAB-OprM efflux system in B. vietnamiensis.     

Cisplatin resistance induced by decreased apoptotic activity in non-small-cell lung cancer cell lines

We have investigated defective steps in apoptosis that might account for the development of resistance. For this purpose, A549 and Calu1 NSCLC (non-small-cell lung cancer) cell lines were treated with cisplatin to obtain resistant sub-lines. Gene expression profiles and the phosphorylation status of the BAD (Bcl-2/Bcl-XL-antagonist, causing cell death) protein were determined for each cell line. Cell death and cytochrome c release were analysed after treating cell lines with their appropriate cisplatin doses. Gene expression of BAD, Bid, caspases 4 and 6 were clearly decreased in the resistant cell lines, and the differential phosphorylation status of BAD also seemed to play a role in the development of cisplatin resistance. Since this is a new cisplatin-resistant Calu1 cell line, it is noteworthy that DNA fragmentation, apoptotic cell ratio and cytochrome c levels were most decreased in the CR-Calu1 cell line.