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Background:Limited data exist on outcomes for metastatic renal cell carcinoma (mRCC) patients treated with multiple lines of therapy. Benchmarks for survival are required for patient counselling and clinical trial design.Methods:Outcomes of mRCC patients from the International mRCC Database Consortium database treated with 1, 2, or 3+ lines of targeted therapy (TT) were compared by proportional hazards regression. Overall survival (OS) and progression-free survival (PFS) were calculated using different population inclusion criteria.Results:In total, 2705 patients were treated with TT of which 57% received only first-line TT, 27% received two lines of TT, and 16% received 3+ lines of TT. Overall survival of patients who received 1, 2, or 3+ lines of TT were 14.9, 21.0, and 39.2 months, respectively, from first-line TT (P<0.0001). On multivariable analysis, 2 lines and 3+ lines of therapy were each associated with better OS (HR=0.738 and 0.626, P<0.0001). Survival outcomes for the subgroups were as follows: for all patients, OS 20.9 months and PFS 7.2 months; for those similar to eligible patients in the first-line ADAPT trial, OS 14.7 months and PFS 5.6 months; for those similar to patients in first-line TIVO-1 trial, OS 24.8 months and PFS 8.2 months; for those similar to patients in second-line INTORSECT trial, OS 13.0 months and PFS 3.9 months; and for those similar to patients in the third-line GOLD trial, OS 18.0 months and PFS 4.4 months.Conclusions:Patients who are able to receive more lines of TT live longer. Survival benchmarks provide context and perspective when interpreting and designing clinical trials. [ABSTRACT FROM AUTHOR]

Background:A phase III trial demonstrated an overall survival advantage with the addition of vinflunine to best supportive care (BSC) in platinum-refractory advanced urothelial cancer. We subsequently examined the impact of an additional 2 years of survival follow-up and evaluated the influence of first-line platinum therapy on survival.Methods:The 357 eligible patients from the phase III study were categorised into two cohorts depending on prior cisplatin treatment: cisplatin or non-cisplatin. Survival was calculated using the Kaplan-Meier method.Results:The majority had received prior cisplatin (70.3%). Survival was higher in the cisplatin group (HR: 0.76; CI 95% 0.58-0.99; P=0.04) irrespective of treatment arm. Multivariate analysis including known prognostic factors (liver involvement, haemoglobin, performance status) and prior platinum administration did not show an independent effect of cisplatin. Vinflunine reduced the risk of death by 24% in the cisplatin-group (HR: 0.76; CI 95% 0.58-0.99; P=0.04) and by 35% in non-cisplatin patients (HR: 0.65; CI 95% 0.41-1.04; P=0.07).Interpretation:Differences in prognostic factors between patients who can receive prior cisplatin and those who cannot may explain the survival differences in patients who undergo second line therapy. Prior cisplatin administration did not diminish the subsequent benefit of vinflunine over BSC. [ABSTRACT FROM AUTHOR]

One of the persistent problems in biology is understanding how genetic variation contributes to phenotypic variation. Associations at many levels have been reported, and yet causal inference has remained elusive. We propose to rely on the knowledge of causal relationships established by molecular biology approaches. The existing molecular knowledge forms a firm backbone upon which hypotheses connecting genetic variation, transcriptional variation and phenotypic variation can be built. The sex determination pathway is a well-established molecular network, with the Yolk protein 1-3 (Yp) genes as the most downstream target. Our analyses reveal that genetic variation in expression for genes known to be upstream in the pathway explains variation in downstream targets. Relationships differ between the two sexes, and each Yp has a distinct transcriptional pattern. Yp expression is significantly negatively correlated with longevity, an important life history trait, for both males and females. [ABSTRACT FROM AUTHOR]

The occurrence of female sperm storage across taxa indicates the importance of this complex and dynamic process. Organs responsible for sperm storage (SSOs) and proteins expressed therein, are important in fundamental aspects of reproduction and could play a major role in evolutionary processes such as post-mating sexual selection. Given the essential role of SSOs, it is surprising that the process of sperm storage is so poorly understood. This study investigated the transcriptome of female Drosophila melanogaster SSOs (seminal receptacle and spermathecae). Spermathecae were enriched for proteases and metabolic enzymes while the seminal receptacle was enriched for genes involved in localization, signaling and ion transport. Differences in functional gene categories indicate that these organs play unique roles in sperm storage. [ABSTRACT FROM AUTHOR]

Identification of genes underlying complex traits is an important problem. Quantitative trait loci (QTL) are mapped using marker-trait co-segregation in large panels of recombinant genotypes. Most frequently, recombinant inbred lines derived from two isogenic parents are used. Segregation patterns are also studied in pedigrees from multiple families. Great advances have been made through creative use of these techniques, but narrow sampling and inadequate power represent strong limitations. Here, we propose an approach combining the strengths of both techniques. We established a mapping population from a sample of natural genotypes, and applied artificial selection for a complex character. Selection changed the frequencies of alleles in QTLs contributing to the selection response. We infer QTLs with dense genotyping microarrays by identifying blocks of linked markers undergoing selective changes in allele frequency. We demonstrated this approach with an experimental population composed from 20 isogenic strains. Selection for starvation survival was executed in three replicated populations with three control non-selected populations. Three individuals per population were genotyped using Affymetrix GeneChips. Two regions of the genome, one each on the left arms of the second and third chromosomes, showed significant divergence between control and selected populations. For the former region, we inferred allele frequencies in selected and control populations by pyrosequencing. We conclude that the allele frequency difference, averaging approximately 40% between selected and control lines, contributed to selection response. Our approach can contribute to the fine scale decomposition of the genetics of direct and indirect selection responses, and genotype by environment interactions.Heredity (2007) 99, 313–321; doi:10.1038/sj.hdy.6801003; published online 27 June 2007 [ABSTRACT FROM AUTHOR]

Large-scale experiments on medflies that were subjected to sterilizing doses of ionizing radiation (plus intact controls) and maintained on either sugar-only or full, protein-enriched diets revealed that, whereas the mortality trajectories of both intact and irradiated male cohorts maintained on both diets are similar, the mortality patterns of females are highly variable. Mean mortality rates at 35 days in male cohorts ranged from 0.2 to 0.3 but in female cohorts ranged from 0.09 to 0.35, depending on treatment. The study reports three main influences: (a) qualitative differences exist in the sex-mortality response of medflies subjected to dietary manipulations and irradiation; (b) the female mortality response is linked to increased vulnerability due to the nutritional demands of reproduction; and (c) female sensitivity to environmental changes underlies the dynamics of the sex-mortality differential. [ABSTRACT FROM AUTHOR]

Vitellogenic and previtellogenic oocyte stages, as well as ovariole numbers, were characterized in the selected (O) lines of D. melanogaster that have been selected for late-life reproduction and extended longevity. On day 4 post-eclosion, O females had more ovarioles than control (B) females, but this difference diminished at older ages. From days 4 to 24, O females showed a marked increase in average vitellogenic oocyte stage, whereas this parameter did not increase in B females as they aged. The previtellogenic gradient of oocyte maturation declined in both B and O females. Specifically, terminal previtellogenic stages were lost with advancing age, and this loss occurred relatively gradually in O females regardless of food regime. Among the reproductive traits assessed, differential persistence of the previtellogenic gradient of maturation is most strongly associated with selected versus control line differences in longevity. [ABSTRACT FROM AUTHOR]

The article reports on the result of the implementation of a special sterilization act in Indiana. The purpose of writing the law is to sterilize the hereditary and primary types of mentally deficient only. The influence of religious beliefs in some areas have an effect on the law. There is a tendency of certain judges never to make any authorization because they are concerned about the constitutionality of the law.

Stress resistance is associated with longevity in Drosophila melanogaster and other model organisms used for genetic research. The present study tests for oxidative stress resistance in one set of lines selected for late-life reproduction and extended longevity. Both females and males from the selected lines were appreciably more resistant to oxidative stress than were flies from the control lines. A relative increase in oxidative stress resistance is a correlated response to selection in this laboratory selection experiment. Increased oxidative stress resistance appears to be a relatively robust correlated response to laboratory selection for late-life reproduction and extended longevity. [ABSTRACT FROM AUTHOR]

Abstract Background A molecular process based genotype-to-phenotype map will ultimately enable us to predict how genetic variation among individuals results in phenotypic alterations. Building such a map is, however, far from straightforward. It requires understanding how molecular variation re-shapes developmental and metabolic networks, and how the functional state of these networks modifies phenotypes in genotype specific way. We focus on the latter problem by describing genetic variation in transcript levels of genes in the InR/TOR pathway among 72 Drosophila melanogaster genotypes. Results We observe tight co-variance in transcript levels of genes not known to influence each other through direct transcriptional control. We summarize transcriptome variation with factor analyses, and observe strong co-variance of gene expression within the dFOXO-branch and within the TOR-branch of the pathway. Finally, we investigate whether major axes of transcriptome variation shape phenotypes expected to be influenced through the InR/TOR pathway. We find limited evidence that transcript levels of individual upstream genes in the InR/TOR pathway predict fly phenotypes in expected ways. However, there is no evidence that these effects are mediated through the major axes of downstream transcriptome variation. Conclusion In summary, our results question the assertion of the 'sparse' nature of genetic networks, while validating and extending candidate gene approaches in the analyses of complex traits.

Abstract Background The Y model of resource allocation predicts a tradeoff between reproduction and survival. Environmental stress could affect a tradeoff between reproduction and survival, but the physiological mechanisms underlying environmental mediation of the tradeoff are largely unknown. One example is the tradeoff between starvation resistance and early fecundity. One goal of the present study was to determine if reduced early age fecundity was indeed a robust indirect response to selection for starvation resistance, by investigation of a set of D. melanogaster starvation selected lines which had not previously been characterized for age specific egg production. Another goal of the present study was to investigate a possible relationship between ovariole number and starvation resistance. Ovariole number is correlated with maximum daily fecundity in outbred D. melanogaster. Thus, one might expect that a negative genetic correlation between starvation resistance and early fecundity would be accompanied by a decrease in ovariole number. Results Selection for early age female starvation resistance favored survival under food deprivation conditions apparently at the expense of early age egg production. The total number of eggs produced by females from selected and control lines was approximately the same for the first 26 days of life, but the timing of egg production differed such that selected females produced fewer eggs early in adult life. Females from lines selected for female starvation resistance exhibited a greater number of ovarioles than did unselected lines. Moreover, maternal starvation resulted in progeny with a greater number of ovarioles in both selected and unselected lines. Conclusion Reduced early age egg production is a robust response to laboratory selection for starvation survival. Ovariole numbers increased in response to selection for female starvation resistance indicating that ovariole number does not account for reduced early age egg production. Further, ovariole number increased in a parallel response to maternal starvation, suggesting an evolutionary association between maternal environment and the reproductive system of female progeny.

Gene interactions are emerging as central to understanding the realization of any phenotype. To probe the flexibility of interactions in a defined gene network, we isolated a set of 16 interacting genes in Drosophila, on the basis of their alteration of a quantitative behavioral phenotype—the loss of coordination in a temperature-sensitive allele of Syntaxin1A. The interactions inter se of this set of genes were then assayed in the presence and in the absence of the original Syntaxin1A mutation to ask whether the relationships among the 16 genes remain stable or differ after a change in genetic context. The pattern of epistatic interactions that occurs within this set of variants is dramatically altered in the two different genetic contexts. The results imply considerable flexibility in the network interactions of genes. [ABSTRACT FROM AUTHOR]

Several evolutionary models of linked selection (e.g., genetic hitchhiking, background selection, and random environment) predict a reduction in polymorphism relative to divergence in genomic regions where the rate of crossing over per physical distance is restricted. We tested this prediction near the telomere of the Drosophila melanogaster and D. simulans X chromosome at two loci, erect wing (ewg) and suppressor of sable [su(s)]. Consistent with this prediction, polymorphism is reduced at both loci, while divergence is normal. The reduction is greater at ewg; the more distal of the two regions. Two models can be discriminated by comparing the observed site frequency spectra with those predicted by the models. The hitchhiking model predicts a skew toward rare variants in a sample, while the spectra under the background-selection model are similar to those of the neutral model of molecular evolution. Statistical tests of the fit to the predictions of these models require many sampled alleles and segregating sites. Thus we used SSCP and stratified DNA sequencing to cover a large number of randomly sampled alleles (∼50) from each of three populations. The result is a clear trend toward negative values of Tajima's D, indicating an excess of rare variants at ewg, the more distal of the two loci. One fixed difference among the populations and high FST values indicate strong population subdivision among the three populations at ewg. These results indicate genetic hitchhiking at ewg, in particular, geographically localized hitchhiking events within Africa. The reduction of polymorphism at su(s) combined with the excess of high-frequency variants in D. simulans is inconsistent with the hitchhiking and background-selection models. [ABSTRACT FROM AUTHOR]

Variation in vein position and wing shape of Drosophila melanogaster depends on many genes. In the following, we report the results of a QTL analysis of wing shape in D. melanogaster. We identified QTL responsible for natural variation for wing shape and analyzed their interactions with developmental genetic signaling pathways important for vein positioning. The QTL analysis indicated that the total number of QTL segregating in this population is likely to be very large. The locations of putative QTL identified in this study were compared to those identified in previous studies and, while there is more correspondence across studies than expected by chance on the third chromosome, the studies appear to have identified different QTL. Using a complementation design, we tested for interactions among these QTL with the Hedgehog and Decapentaplegic signaling pathways, which are important for the development and position of vein pairs L3-L4 and L2-L5. Three QTL showed strong interactions with these two pathways, supporting the hypothesis that these QTL are involved in these pathways. Naturally segregating variation can therefore act through known signaling pathways to produce variation in vein position. [ABSTRACT FROM AUTHOR]

Linkage disequilibrium mapping has been used extensively in medical and evolutionary genetics to map causal polymorphisms within genes associated with disease status or phenotypic variation for a trait. However, the initial findings of most nonhuman studies have not been replicated in subsequent studies, due in part to false positives, as well as additional factors that can render true positives unreplicable. These factors may be more severe when the initial study is performed using an experimental population of organisms reared under controlled lab conditions. We demonstrate that despite considerable phenotypic differences for wing shape between a lab-reared experimental population and a wild-caught cohort of Drosophila melanogaster, an association between a putative regulatory polymorphism in Egfr and wing shape can be replicated. These results are discussed both within the framework of future association-mapping studies and within the context of the evolutionary dynamics of alleles in populations. [ABSTRACT FROM AUTHOR]

Spermatogenesis is a complex process that can be disrupted by genetic and epigenetic changes, potentially leading to male infertility. Recent research has rapidly increased the number of protein coding mutations causally linked to impaired spermatogenesis in humans and mice. However, the role of non-coding mutations remains largely unexplored. As a case study to evaluate the effects of non-coding mutations on spermatogenesis, we first identified an evolutionarily conserved topologically associated domain (TAD) boundary near two genes with important roles in mammalian testis function: Dmrtb1 and Lrp8. We then used CRISPR-Cas9 to generate a mouse line where 26 kb of the boundary was removed including a strong and evolutionarily conserved CTCF binding site. ChIP-seq and Hi-C experiments confirmed the removal of the CTCF site and a resulting mild increase in the DNA-DNA interactions across the domain boundary. Mutant mice displayed significant changes in testis gene expression, higher frequency of histological abnormalities, a drop of 47-52% in efficiency of meiosis, a 15-18% reduction in efficiency of spermatogenesis, and consistently, a 12-28% decrease in daily sperm production compared to littermate controls. Despite these quantitative changes in testis function, mutant mice show no significant changes in fertility. This suggests that non-coding deletions affecting testis gene regulation may have smaller effects on fertility compared to coding mutations of the same genes. Our results demonstrate that disruption of a TAD boundary can have a negative impact on sperm production and highlight the importance of considering non-coding mutations in the analysis of patients with male infertility., (© The Author(s) 2025. Published by Oxford University Press on behalf of Society for the Study of Reproduction. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)