Resource-efficient pooled sequencing expands translational impact in solid tumors.
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ABSTRACT:
SUBMITTER: DiNatale RG
PROVIDER: S-EPMC8312736 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Background and objectiveHSF1 is reported to be overexpressed in various solid tumors and play a pivotal role in cancer progression. A meta-analysis was conducted to assess the potential prognostic role of HSF1 in patients with solid tumors.MethodsAn extensive electronic search of three databases was performed for relevant articles. The pooled hazard ratios (HRs) or odds ratios with their corresponding 95% CI were calculated with a random-effects model. Heterogeneity and publication bias analyses were also conducted.ResultsA total of 3,159 patients from 10 eligible studies were included into the analysis. The results showed that positive HSF1 expression was significantly correlated with poor overall survival in all tumors (HR=2.09; 95% CI: 1.62-2.70; P<0.001). Subgroup analysis revealed that there was a significant association between HSF1 overexpression and poor prognosis in esophageal squamous cell carcinoma (ESCC) (HR=1.83; 95% CI: 1.21-2.77; P=0.004), breast cancer (BC) (HR=1.52; 95% CI: 1.24-2.86; P<0.001), hepatocellular carcinoma (HR=3.02; 95% CI: 1.77-5.18; P<0.001), non-small-cell lung cancer (HR=2.19; 95% CI: 1.20-3.99; P=0.01), and pancreatic cancer (HR=2.58; 95% CI: 1.11-6.03; P=0.03) but not in osteosarcoma (HR=1.58; 95% CI: 0.47-5.35; P=0.46). In addition, HSF1 overexpression was significantly associated with some phenotypes of tumor aggressiveness including TNM stage, histological grade, lymph node metastasis, and vascular invasion.ConclusionHSF1 overexpression may prove to be an unfavorable prognostic biomarker for solid tumor patients.
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Project description:Previous trials showed the tolerability and efficacy of a palliative radiotherapy (RT) regimen (SHARON) based on the 4 fractions delivered in 2 days in different oncological settings. In order to identify possible predictors of symptomatic response, the purpose of this study is to perform a pooled analysis of previous trials. We analyzed the impact on symptomatic response of the following parameters: tumor site, histological type, performance status (ECOG), dominant symptom, and RT dose using the Chi-square test and Fisher's exact test. One-hundred-eighty patients were analyzed. Median RT dose was 20 Gy (range: 14-20 Gy). The overall response rate was 88.8% (95% CI 83.3-92.7%) while pre- and post-treatment mean VAS was 5.3 (± 7.7) and 2.2 (± 2.2), respectively (p < 0.001). The overall response rate of pain, dyspnea, bleeding, dysphagia, and other symptoms was 86.2%, 90.9%, 100%, 87.5%, and 100%, respectively. Comparing the symptomatic effect based on the analyzed parameters no significant differences were recorded. However, patients with locally advanced disease showed a higher rate of symptomatic responses than metastatic ones (97.3% vs 83.0%; p = 0.021). Finally, the complete pain response rate was more than double in patients with mild to moderate (VAS: 4-7) compared to those with severe (VAS > 7) pain (36.0% vs 14.3%; p = 0.028). This pooled analysis showed high efficacy of the SHARON regimen in the relief of several cancer-related symptoms. The markedly and significantly higher complete pain response rate, in patients with mild-moderate pain, suggests early referral to palliative RT for patients with cancer-related pain.
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Project description:BackgroundThird-generation nanopore sequencers offer selective sequencing or "Read Until" that allows genomic reads to be analyzed in real time and abandoned halfway if not belonging to a genomic region of "interest." This selective sequencing opens the door to important applications such as rapid and low-cost genetic tests. The latency in analyzing should be as low as possible for selective sequencing to be effective so that unnecessary reads can be rejected as early as possible. However, existing methods that employ a subsequence dynamic time warping (sDTW) algorithm for this problem are too computationally intensive that a massive workstation with dozens of CPU cores still struggles to keep up with the data rate of a mobile phone-sized MinION sequencer.ResultsIn this article, we present Hardware Accelerated Read Until (HARU), a resource-efficient hardware-software codesign-based method that exploits a low-cost and portable heterogeneous multiprocessor system-on-chip platform with on-chip field-programmable gate arrays (FPGA) to accelerate the sDTW-based Read Until algorithm. Experimental results show that HARU on a Xilinx FPGA embedded with a 4-core ARM processor is around 2.5× faster than a highly optimized multithreaded software version (around 85× faster than the existing unoptimized multithreaded software) running on a sophisticated server with a 36-core Intel Xeon processor for a SARS-CoV-2 dataset. The energy consumption of HARU is 2 orders of magnitudes lower than the same application executing on the 36-core server.ConclusionsHARU demonstrates that nanopore selective sequencing is possible on resource-constrained devices through rigorous hardware-software optimizations. The source code for the HARU sDTW module is available as open source at https://github.com/beebdev/HARU, and an example application that uses HARU is at https://github.com/beebdev/sigfish-haru.
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Project description:Chemotherapeutic delivery is limited by inefficient transport across cellular membranes. Here, we harness the cellular gap junction network to release therapeutic cargos directly into the cytosol. Specifically, cell-derived vesicles, termed connectosomes, contain gap junction transmembrane proteins that open a direct passageway to the cellular interior. Connectosomes were previously shown to substantially improve chemotherapeutic delivery in vitro. Here, we test connectosomes in vivo, using a murine breast tumor model. We demonstrate that connectosomes improve chemotherapeutic delivery to cellular targets within tumors by up to 16-fold, compared to conventional drug-loaded liposomes, suggesting an efficient alternative pathway for intracellular delivery.
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Project description:BACKGROUND:Further advances of targeted cancer therapy require comprehensive in-depth profiling of somatic mutations that are present in subpopulations of tumor cells in a clinical tumor sample. However, it is unclear to what extent such intratumor heterogeneity is present and whether it may affect clinical decision-making. To study this question, we established a deep targeted sequencing platform to identify potentially actionable DNA alterations in tumor samples. METHODS:We assayed 515 formalin-fixed paraffin-embedded (FFPE) tumor samples and matched germline DNA (475 patients) from 11 disease sites by capturing and sequencing all the exons in 201 cancer-related genes. Mutations, indels, and copy number data were reported. RESULTS:We obtained a 1000-fold mean sequencing depth and identified 4794 nonsynonymous mutations in the samples analyzed, of which 15.2% were present at <10% allele frequency. Most of these low level mutations occurred at known oncogenic hotspots and are likely functional. Identifying low level mutations improved identification of mutations in actionable genes in 118 (24.84%) patients, among which 47 (9.8%) otherwise would have been unactionable. In addition, acquiring ultrahigh depth also ensured a low false discovery rate (<2.2%) from FFPE samples. CONCLUSIONS:Our results were as accurate as a commercially available CLIA-compliant hotspot panel but allowed the detection of a higher number of mutations in actionable genes. Our study reveals the critical importance of acquiring and utilizing high sequencing depth in profiling clinical tumor samples and presents a very useful platform for implementing routine sequencing in a cancer care institution.
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Project description:Next-generation sequencing has proven an extremely effective technology for molecular counting applications where the number of sequence reads provides a digital readout for RNA-seq, ChIP-seq, Tn-seq and other applications. The extremely large number of sequence reads that can be obtained per run permits the analysis of increasingly complex samples. For lower complexity samples, however, a point of diminishing returns is reached when the number of counts per sequence results in oversampling with no increase in data quality. A solution to making next-generation sequencing as efficient and affordable as possible involves assaying multiple samples in a single run. Here, we report the successful 96-plexing of complex pools of DNA barcoded yeast mutants and show that such 'Bar-seq' assessment of these samples is comparable with data provided by barcode microarrays, the current benchmark for this application. The cost reduction and increased throughput permitted by highly multiplexed sequencing will greatly expand the scope of chemogenomics assays and, equally importantly, the approach is suitable for other sequence counting applications that could benefit from massive parallelization.
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Project description:Genome-wide association studies (GWAS) have identified >500 common variants associated with quantitative metabolic traits, but in aggregate such variants explain at most 20-30% of the heritable component of population variation in these traits. To further investigate the impact of genotypic variation on metabolic traits, we conducted re-sequencing studies in >6,000 members of a Finnish population cohort (The Northern Finland Birth Cohort of 1966 [NFBC]) and a type 2 diabetes case-control sample (The Finland-United States Investigation of NIDDM Genetics [FUSION] study). By sequencing the coding sequence and 5' and 3' untranslated regions of 78 genes at 17 GWAS loci associated with one or more of six metabolic traits (serum levels of fasting HDL-C, LDL-C, total cholesterol, triglycerides, plasma glucose, and insulin), and conducting both single-variant and gene-level association tests, we obtained a more complete understanding of phenotype-genotype associations at eight of these loci. At all eight of these loci, the identification of new associations provides significant evidence for multiple genetic signals to one or more phenotypes, and at two loci, in the genes ABCA1 and CETP, we found significant gene-level evidence of association to non-synonymous variants with MAF<1%. Additionally, two potentially deleterious variants that demonstrated significant associations (rs138726309, a missense variant in G6PC2, and rs28933094, a missense variant in LIPC) were considerably more common in these Finnish samples than in European reference populations, supporting our prior hypothesis that deleterious variants could attain high frequencies in this isolated population, likely due to the effects of population bottlenecks. Our results highlight the value of large, well-phenotyped samples for rare-variant association analysis, and the challenge of evaluating the phenotypic impact of such variants.
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Project description:BackgroundTargeted sequencing of cytologic samples has significantly increased in recent years. With increasing numbers of clinical trials for variant specific therapeutics, validating a comprehensive assay for cytologic samples has become clinically important.AimFor this study, a retrospective review of cytologic cell blocks from fine needle aspirations and fluid specimens was performed.MethodsTwo hundred twenty six total cases of solid tumor malignancies were identified, of which 120 cases and 20 lymph node negative controls were sequenced for the Oncomine Comprehensive Assay. Cytology and surgical specimen correlation was performed in a subset of cases. Statistical analysis to determine variant concordance was performed.ResultsWithin the 117 cases sequenced, a total of 347 pathogenic variants were detected. Of the 117 cases, 32 cases (27.4%) would qualify for FDA approved targeted therapy according to the current guidelines, and an additional 23 cases (19.7%) would qualify for clinical trial based on pathogenic variants detected.DiscussionWith over 27% of cases in our cohort qualifying for some form of targeted therapy, our study shows the importance of providing comprehensive molecular diagnostic options. Despite only half of the cytology cases in the review period having enough material to be sequenced, overall approximately 27% of patients in this cohort would have benefitted from this service.
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