Nuclear Her2 contributes to paclitaxel resistance in breast cancer cells.

Translocation of full-length Her2 receptor into nucleus was reported by some studies. Here, we tested whether nuclear Her2 contributes to paclitaxel resistance in Her2-overexpressing breast cancer cells. Breast cancer cell was transfected with plasmids containing cDNA of wild-type Her2 or mutant-type Her2 lacking the nuclear localization signal (NLS) sequence which is required for Her2 nuclear transport. Cell resistance to paclitaxel was analyzed. Paclitaxel-resistant breast cancer cell was also developed and nuclear Her2 expression was tested. Then, correlation between nuclear Her2 and resistance to paclitaxel were analyzed. Expression of importin ß1 was decreased to downregulate nuclear Her2 level and cell resistance to paclitaxel was tested. We found that Her2 overexpression increases Her2 nuclear expression and cells resistance to paclitaxel in MCF-7 cells. In the paclitaxel resistant cell (SK-BR-3/R), nuclear Her2 expression is upregulated compared with parental SK-BR-3 cells. Increased expression of nuclear Her2 after short-time (48 h) treatment of paclitaxel was also observed in SK-BR-3 cells. Further downregulation of Her2 nuclear expression through blocking expression of importin ß1 sensitizes the cells to paclitaxel. The analysis showed that the Her2 nuclear expression increases the survivin expression which leads to resistance to paclitaxel. Her2 nuclear expression decreases paclitaxel-induced apoptosis. However, co-immunoprecipitation was applied, and the physical interaction of nuclear Her2 and survivin was not detected. We show for the first time that nuclear Her2 contributes to paclitaxel resistance in breast cancer cells which suggests that nuclear Her2 as a potential target to sensitize breast cancers to paclitaxel treatment.

Prognostic models for 1-year survival of NPC after radiotherapy in different ages.

PURPOSE: Previous studies have shown that approximately 10% of nasopharyngeal cancer (NPC) patients die within a year of disease onset, and that age is an independent predictor. However, no predictive model has been developed. We aimed to establish novel prognostic models to predict the 1-year cancer-specific survival (CSS) of young, middle-aged, and older patients with NPC after radiotherapy. METHODS: The data of 2822 NPC patients who underwent radiotherapy between 2004 and 2015 were reviewed from the surveillance, epidemiology, and end results database. We divided them into young, middle-aged, and older people groups according to age (< 44 years, 45-59 years, and ≥ 60 years, respectively). Multivariate analyses were performed, and prognostic models were constructed. RESULTS: Multivariate analyses indicated that age, ethnicity, histological subtype, T, and M stage were independent predictors of 1-year CSS in the older people group. In contrast, ethnicity and age were not found to have predictive value in the young and middle-aged groups, respectively. Accordingly, three prognostic models with excellent predictive values were established for the three groups (C-indices: 0.791 [95% CI 0.722-0.859], 0.763 [95% CI 0.721-0.806] and 0.723 [95% CI 0.683-0.763], respectively). These predictive values are higher than those of the eighth edition American joint committee cancer tumor-node-metastasis (TNM) classification system. CONCLUSION: Three prognostic models for predicting the 1-year CSS of young, middle-aged, and older NPC patients after radiotherapy showed better predictive power than the TNM classification system. These models may guide treatment strategies and clinical decision-making in different cohorts.

Interim results of brentuximab vedotin in combination with nivolumab in patients with relapsed or refractory Hodgkin lymphoma.

In this phase 1/2 study, brentuximab vedotin (BV) and nivolumab (Nivo) administered in combination were evaluated as initial salvage therapy in patients with relapsed or refractory (R/R) classical Hodgkin lymphoma (HL). Patients received up to 4 cycles of combination treatment, with BV administered on day 1 and Nivo on day 8 of the first cycle. For cycles 2 to 4, BV and Nivo were both administered on day 1. After study treatment, responses were evaluated by investigators per the 2014 Lugano classification, and patients could proceed to autologous stem cell transplantation (ASCT). Sixty-two patients were enrolled; the complete response rate among all treated patients (n = 61) was 61%, with an objective response rate of 82%. Before ASCT, adverse events (AEs) occurred in 98% of patients, mostly grades 1 and 2. Infusion-related reactions (IRRs) occurred in 44% of patients overall, with 41% of patients experiencing an IRR during at least 1 infusion of BV. Five patients (8%) were treated with systemic steroids for immune-related AEs. A reduction of peripheral T-cell subsets including regulatory T cells was observed after the first dose of BV, and reduced serum levels of thymus- and activation-regulated chemokine concurrent with an increase in proinflammatory cytokines and chemokines were seen after the first BV plus Nivo infusions. The combination of BV plus Nivo was an active and well-tolerated first salvage regimen, potentially providing patients with R/R HL an alternative to traditional chemotherapy. This trial was registered at www.clinicaltrials.gov as #NCT02572167.

Prognostic value of lymphocyte-to-C-reactive protein ratio in patients with gastric cancer after surgery: a multicentre study.

OBJECTIVE: The immune inflammation-based score is recognized as a prognostic marker for cancer. However, the most accurate prognostic marker for patients with gastric cancer remains undetermined. We aimed to evaluate the predictive value of the lymphocyte-to-C-reactive protein ratio for outcomes in gastric cancer patients after radical gastrectomy. METHODS: A total of 607 gastric cancer patients treated at three Chinese institutions were included. Receiver operating characteristic curves were generated, and the areas under the curve were calculated to compare the predictive value among the inflammation-based score, lymphocyte-to-C-reactive protein ratio, C-reactive protein/albumin and neutrophil-lymphocyte, platelet-lymphocyte and lymphocyte-monocyte ratios. Cox regression was performed to determine the prognostic factors for overall survival. RESULTS: The median follow-up time was 63 months (range: 1-84 months). The optimal cut-off value for lymphocyte-to-C-reactive protein ratio was 0.63. The patients were divided into the LCR <0.63 (LLCR, n = 294) group and the LCR ≥0.63 (HLCR, n = 313) group. LLCR was significantly correlated with poor clinical characteristics. Compared with inflammation-based score, lymphocyte-to-C-reactive protein ratio had the highest areas under the curve (0.695). Patients with LLCR experienced more post-operative complications than the HLCR group (20.4 vs. 12.1%, P = 0.006). Multivariate analysis showed that a higher lymphocyte-to-C-reactive protein ratio (HR: 0.545, 95%CI: 0.372-0.799, P = 0.002) was associated with better overall survival. The HLCR group had higher 5-year overall survival rate than the LLCR group (80.5 vs. 54.9%, P < 0.001). CONCLUSIONS: Preoperative lymphocyte-to-C-reactive protein ratio levels can effectively predict the short-term and oncological efficacy of gastric cancer patients after radical gastrectomy with a predictive value significantly better than other inflammation-based score.

Down-Regulation of EPAS1 Transcription and Genetic Adaptation of Tibetans to High-Altitude Hypoxia.

Tibetans are well adapted to the hypoxic environments at high altitude, yet the molecular mechanism of this adaptation remains elusive. We reported comprehensive genetic and functional analyses of EPAS1, a gene encoding hypoxia inducible factor 2α (HIF-2α) with the strongest signal of selection in previous genome-wide scans of Tibetans. We showed that the Tibetan-enriched EPAS1 variants down-regulate expression in human umbilical endothelial cells and placentas. Heterozygous EPAS1 knockout mice display blunted physiological responses to chronic hypoxia, mirroring the situation in Tibetans. Furthermore, we found that the Tibetan version of EPAS1 is not only associated with the relatively low hemoglobin level as a polycythemia protectant, but also is associated with a low pulmonary vasoconstriction response in Tibetans. We propose that the down-regulation of EPAS1 contributes to the molecular basis of Tibetans' adaption to high-altitude hypoxia.

Assembly errors cause false tandem duplicate regions in the chicken (Gallus gallus) genome sequence.

The complexity of eukaryote genomes makes assembly errors inevitable in the process of constructing reference genomes. Next-generation sequencing (NGS) could provide an efficient way to validate previously assembled genomes. Here, we exploited NGS data to interrogate the chicken reference genome and identified 35 pairs of nearly identical regions with >99.5 % sequence similarity and a median size of 109 kb. Several lines of evidence, including read depth, the composition of junction sequences, and sequence similarity, suggest that these regions present genome assembly errors and should be excluded from forthcoming genomic studies.

Evolutionary origin and human-specific expansion of a cancer/testis antigen gene family.

Cancer/testis (CT) antigens are encoded by germline genes and are aberrantly expressed in a number of human cancers. Interestingly, CT antigens are frequently involved in gene families that are highly expressed in germ cells. Here, we presented an evolutionary analysis of the CTAGE (cutaneous T-cell-lymphoma-associated antigen) gene family to delineate its molecular history and functional significance during primate evolution. Comparisons among human, chimpanzee, gorilla, orangutan, macaque, marmoset, and other mammals show a rapid and primate specific expansion of CTAGE family, which starts with an ancestral retroposition in the haplorhini ancestor. Subsequent DNA-based duplications lead to the prosperity of single-exon CTAGE copies in catarrhines, especially in humans. Positive selection was identified on the single-exon copies in comparison with functional constraint on the multiexon copies. Further sequence analysis suggests that the newly derived CTAGE genes may obtain regulatory elements from long terminal repeats. Our result indicates the dynamic evolution of primate genomes, and the recent expansion of this CT antigen family in humans may confer advantageous phenotypic traits during early human evolution.

STAT3 inhibitor stattic enhances radiosensitivity in esophageal squamous cell carcinoma.

The radioresistance of esophageal squamous cell carcinoma (ESCC) remains an obstacle for the effective radiotherapy of ESCC. This study aimed to investigate the radiosensitization of ESCC by signal transducer and activator of transcription 3 (STAT3) inhibitor stattic. ECA109, TE13, and KYSE150 cell lines were exposed to hypoxia and treated with stattic or radiation, alone or in combination. Cell proliferation, colony formation, apoptosis, and double-stranded DNA breaks (DSBs) were examined. In addition, ECA109 cells were xenografted into nude mice and treated with radiation and/or stattic. The levels of STAT3, p-STAT3, hypoxia-inducible factor 1α (HIF-1α), and vascular endothelial growth factor (VEGF) in ESCC cells and xenografts were detected by Western blot and immunohistochemical analysis. Our results showed that stattic efficiently radiosensitized ESCC cells and xenografts, especially under hypoxia. Moreover, stattic inhibited STAT3 activation and downregulated HIF-1α and VEGF expression. In conclusion, stattic confers radiosensitivity in ESCC cells in vitro and in vivo and is a potential adjuvant for the radiotherapy of ESCC in the clinical setting.

A house finch (Haemorhous mexicanus) spleen transcriptome reveals intra- and interspecific patterns of gene expression, alternative splicing and genetic diversity in passerines.

BACKGROUND: With its plumage color dimorphism and unique history in North America, including a recent population expansion and an epizootic of Mycoplasma gallisepticum (MG), the house finch (Haemorhous mexicanus) is a model species for studying sexual selection, plumage coloration and host-parasite interactions. As part of our ongoing efforts to make available genomic resources for this species, here we report a transcriptome assembly derived from genes expressed in spleen. RESULTS: We characterize transcriptomes from two populations with different histories of demography and disease exposure: a recently founded population in the eastern US that has been exposed to MG for over a decade and a native population from the western range that has never been exposed to MG. We utilize this resource to quantify conservation in gene expression in passerine birds over approximately 50 MY by comparing splenic expression profiles for 9,646 house finch transcripts and those from zebra finch and find that less than half of all genes expressed in spleen in either species are expressed in both species. Comparative gene annotations from several vertebrate species suggest that the house finch transcriptomes contain ~15 genes not yet found in previously sequenced vertebrate genomes. The house finch transcriptomes harbour ~85,000 SNPs, ~20,000 of which are non-synonymous. Although not yet validated by biological or technical replication, we identify a set of genes exhibiting differences between populations in gene expression (n = 182; 2% of all transcripts), allele frequencies (76 FST ouliers) and alternative splicing as well as genes with several fixed non-synonymous substitutions; this set includes genes with functions related to double-strand break repair and immune response. CONCLUSIONS: The two house finch spleen transcriptome profiles will add to the increasing data on genome and transcriptome sequence information from natural populations. Differences in splenic expression between house finch and zebra finch imply either significant evolutionary turnover of splenic expression patterns or different physiological states of the individuals examined. The transcriptome resource will enhance the potential to annotate an eventual house finch genome, and the set of gene-based high-quality SNPs will help clarify the genetic underpinnings of host-pathogen interactions and sexual selection.

Evidence from a house finch (Haemorhous mexicanus) spleen transcriptome for adaptive evolution and biased gene conversion in passerine birds.

Identifying genes influenced by natural selection can provide information about lineage-specific adaptations, and transcriptomes generated by next-generation sequencing are a useful resource for identifying such genes. Here, we utilize a spleen transcriptome for the house finch (Haemorhous mexicanus), an emerging model for sexual selection and disease ecology, together with previously sequenced avian genomes (chicken, turkey, and zebra finch), to investigate lineage-specific adaptations within birds. An analysis of 4,398 orthologous genes revealed a significantly higher ratio of nonsynonymous to synonymous substitutions and significantly higher GC content in passerines than in galliforms, an observation deviating from strictly neutral expectations but consistent with an effect of biased gene conversion on the evolutionary rate in passerines. These data also showed that genes exhibiting signs of positive selection and fast evolution in passerines have functional roles related to fat metabolism, neurodevelopment, and ion binding.

Lung cancer risk and genetic variants in East Asians: a meta-analysis.

Inconsistent results are often found regarding the risk of genetic variants in lung cancer association studies. To alleviate these conflicts, we performed a large-scale meta-analysis to evaluate the effect of variants on lung cancer in East Asian population (Han Chinese, Japanese, and Korean). Forty-three genetic variants with data from at least three independent case-control studies were under investigation of which two variants (rs1800734 in hMLH1, rs2273953-rs1801173 bi-marker in P73) were first meta-analyzed in East Asians. We found that three variants in CYP1A1, GSTM1, and XRCC1 showed consistently significant associations with lung cancer in mixed analysis and stratified analysis, and several variants showed diverse effects interacting with different environmental factors in stratified analysis. Our study presents a comprehensive and systematic analysis of lung cancer association studies in East Asians and confirms the effect of three variants in lung cancer risk. Additionally, result from stratified analysis suggests the importance of inclusion of environmental factors, such as smoking and tumor histology, in the analysis.

VEGF +405G/C (rs2010963) polymorphisms and digestive system cancer risk: a meta-analysis.

Vascular endothelial growth factor (VEGF) polymorphisms, specifically +405G/C (rs2010963), reportedly influence the risk for various digestive cancers. However, the consequences of these polymorphisms remain controversial and ambiguous. Therefore, we performed a meta-analysis of 11 studies with VEGF +405G/C genotyping on 2,862 patients and 3,028 controls using the random effects model. We obtained a pooled odds ratio (OR) of 1.04 (95% confidence interval (CI) = 0.86-1.26) for the recessive genetic model, 1.07 (95% CI = 0.81-1.42) for the dominant genetic model, 1.09 (95% CI = 0.81-1.47) for the homozygote comparison, and 1.03 (95% CI = 0.83-1.27) for the heterozygote comparison. In the subgroup analysis of the recessive model, the OR was 1.20 (95% CI = 1.02-1.40) in colorectal cancer. These results show that VEGF +405G/C polymorphisms are unlikely to be a major determinant of susceptibility to digestive cancer. Furthermore, the subgroup analysis of recessive model indicates that VEGF +405G/C polymorphisms increase the risk for colorectal cancer.

HIF-1α P582S and A588T polymorphisms and digestive system cancer risk-a meta-analysis.

Hypoxia-inducible factor-1 (HIF-1) influences cancer progression and metastasis through various mechanisms, and HIF-1α polymorphisms are reportedly associated with many cancers; however, the associations of HIF-1α P582S and A588T polymorphisms with the risk of digestive system cancer remain inconclusive. To understand the role of HIF-1α P582S and A588T genotypes in digestive cancer development, we conducted a comprehensive meta-analysis involving 1,517 cases and 3,740 controls. Overall, the P582S polymorphism was not significantly associated with digestive system cancers in all genotypes. By contrast, the A588T polymorphism was significantly associated with digestive system cancers in the dominant model (TT/AT vs. AA: OR = 3.17, 95% CI: 1.21, 8.25; P heterogeneity < 0.001). In subgroup analysis for cancer types, the two polymorphisms were only associated with increased risk of pancreatic cancer (P582S: SS vs. PP: OR = 2.51, 95% CI: 1.31, 4.81; SS vs. PP/PS: OR = 8.73, 95% CI: 1.33, 57.1; A588T: TT vs. AA: OR = 9.30, 95% CI: 1.12, 77.6; P heterogeneity = 0.478; TT vs. AA/AT: OR = 3.14, 95% CI: 1.99, 4.97; P heterogeneity = 0.098; TT/AT vs. AA: OR = 8.65, 95% CI: 1.05, 71.6; P heterogeneity = 0.418). According to the source of ethnicity, the P582S and the A588T polymorphisms are both significantly associated with an increased risk of cancer among Caucasians in the homozygote model (SS vs. PP: OR = 2.41, 95% CI: 1.24, 4.691; P heterogeneity = 0.010; TT vs. AA: OR = 98.6, 95% CI: 4.37, 2,224; P heterogeneity = 0.040) and the recessive model (SS vs. PP/PS: OR = 9.48, 95% CI: 1.12, 80.3; P heterogeneity < 0.001; TT vs. AA/AT: OR = 82.7, 95% CI: 3.79, 1,802; P heterogeneity = 0.041). Our findings suggest that the HIF-1α A588T polymorphism is significantly associated with higher cancer risk and the P582S polymorphism is significantly associated with pancreatic cancer risk. Furthermore, the effect of both polymorphisms on digestive system cancer is more pronounced among Caucasians than that among Asians.

STAT3 inhibitor NSC74859 radiosensitizes esophageal cancer via the downregulation of HIF-1α.

Radiotherapy is the main therapy for inoperable and locally advanced esophageal squamous cell carcinoma (ESCC). However, radioresistance in ESCC remains a challenge. The aim of this study is to investigate the radiosensitizing effects of STAT3 inhibitor NSC74859 on ESCC and explore the underlying mechanisms. ECA109 and TE13 cells were exposed to hypoxia, and treated with NSC74859 or radiation, alone or in combination. Cell proliferation, survival, apoptosis, and double-stranded DNA breaks (DSBs) were examined. Nude mice model of ECA109 xenograft was treated with radiation and/or NSC74859. The levels of STAT3, p-STAT3, HIF-1α, and VEGF were detected by Western blot analysis. NSC74859 efficiently radiosensitized ESCC cells and xenografts in nude mice, and inhibited hypoxia-/radiation-induced activation of STAT3 and upregulation of HIF-1α and VEGF expression. NSC74859 confers radiosensitivity in ESCC via the inhibition of STAT3 activation and the downregulation of HIF-1α and VEGF expression. NSC74859 may become a promising radiosensitizer for ESCC radiotherapy.

Using pseudogene database to identify lineage-specific genes and pseudogenes in humans and chimpanzees.

It has been revealed that gene content changes, or gene gains or losses, have played an important role in the evolution of modern humans. As one of the major players accounting for gene content changes, gene pseudogenization is abundant in mammalian genomes, and approximately 20000 pseudogenes have been identified in ape genomes. Therefore, it is an interesting question how to exploit rich information embedded in pseudogenes. Here, I present a bioinformatic pipeline that utilizes a pseudogene database to identify both lineage-specific genes and pseudogenes in humans and chimpanzees. I found 6 human-specific gene gains (HSGs), 1 chimpanzee-specific gene gain, and 4 chimpanzee-specific pseudogenes, most not discovered in previous studies. Further analysis showed that HSGs have been evolving under strong purifying selection and are broadly expressed, indicating strong functional constraint. This study demonstrates the usage of pseudogene information in comparative genomics and suggests that new genes during primate evolution may acquire essential functions in a short time. The pipeline developed here could also be applied to other species.