Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28789816.fastq.gz | Fastqsanger.gz | |||
| SRR28789817.fastq.gz | Fastqsanger.gz | |||
| SRR28789818.fastq.gz | Fastqsanger.gz | |||
| SRR28789819.fastq.gz | Fastqsanger.gz | |||
| SRR28789820.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Artificial evolvable genetic information systems (AEGIS) are DNA-like molecules that can be copied, support laboratory in vitro evolution (LIVE), and evolve to give AegisBodies, analogs of antibodies. However, unlike DNA aptamers built from four different nucleotides, AegisBodies are built from six. Thus, 6-letter AEGIS-LIVE delivers AegisBodies with greater stability in biological mixtures, more folds, and enhanced binding and catalytic potential. However, AEGIS has not benefitted from four billion years of biological evolution. To learn whether AEGIS can nevertheless perform as well as natural DNA, we compare two 6-letter AegisBodies (LZH5b and LZH8) with a standard 4-letter aptamer. Both were evolved to bind cancer cells after ~10 cycles of LIVE. Both have ~ 50 nM affinities. Both discovered proteins on their cancer cell surfaces thought to function only inside of cells. Both can be internalized. Internalizing of LZH5b attached to an AEGIS nanotrain brings attached drugs into the cell. These data show that AEGIS-LIVE can do what 4-letter LIVE can do at its limits of performance after four billion years of evolution. However, synthetic biologists continue to improve AEGIS, suggesting that AEGIS not be dismissed as an avenue for future biotechnology.
2025-05-07 | PXD055115 | Pride
Project description:Artificial evolvable genetic information systems (AEGIS) are DNA-like molecules that can be copied, support laboratory in vitro evolution (LIVE), and evolve to give AegisBodies, analogs of antibodies. However, unlike DNA aptamers built from four different nucleotides, AegisBodies are built from six. Thus, 6-letter AEGIS-LIVE delivers AegisBodies with greater stability in biological mixtures, more folds, and enhanced binding and catalytic potential. However, AEGIS has not benefitted from four billion years of biological evolution. To learn whether AEGIS can nevertheless perform as well as natural DNA, we compare two 6-letter AegisBodies (LZH5b and LZH8) with a standard 4-letter aptamer. Both were evolved to bind cancer cells after ~10 cycles of LIVE. Both have ~ 50 nM affinities. Both discovered proteins on their cancer cell surfaces thought to function only inside of cells. Both can be internalized. Internalizing of LZH5b attached to an AEGIS nanotrain brings attached drugs into the cell. These data show that AEGIS-LIVE can do what 4-letter LIVE can do at its limits of performance after four billion years of evolution. However, synthetic biologists continue to improve AEGIS, suggesting that AEGIS not be dismissed as an avenue for future biotechnology.
2025-05-07 | PXD055130 | Pride
Project description:Artificial evolvable genetic information systems (AEGIS) are DNA-like molecules that can be copied, support laboratory in vitro evolution (LIVE), and evolve to give AegisBodies, analogs of antibodies. However, unlike DNA aptamers built from four different nucleotides, AegisBodies are built from six. Thus, 6-letter AEGIS-LIVE delivers AegisBodies with greater stability in biological mixtures, more folds, and enhanced binding and catalytic potential. However, AEGIS has not benefitted from four billion years of biological evolution. To learn whether AEGIS can nevertheless perform as well as natural DNA, we compare two 6-letter AegisBodies (LZH5b and LZH8) with a standard 4-letter aptamer. Both were evolved to bind cancer cells after ~10 cycles of LIVE. Both have ~ 50 nM affinities. Both discovered proteins on their cancer cell surfaces thought to function only inside of cells. Both can be internalized. Internalizing of LZH5b attached to an AEGIS nanotrain brings attached drugs into the cell. These data show that AEGIS-LIVE can do what 4-letter LIVE can do at its limits of performance after four billion years of evolution. However, synthetic biologists continue to improve AEGIS, suggesting that AEGIS not be dismissed as an avenue for future biotechnology.
2025-05-07 | PXD055107 | Pride
Project description:Nasal epithelial brushings were prospectively collected from current and former smokers with pulmonary lesions suspicious for lung cancer in the AEGIS-1 (n=375) and AEGIS-2 (n=130) clinical trials and gene expression profiled using microarrays.
2022-10-25 | GSE210271 | GEO
Project description:We previously derived and validated a bronchial epithelial gene expression biomarker to detect lung cancer in current and former smokers. Given that bronchial and nasal epithelium gene expression is similarly altered by cigarette smoke exposure, we sought to determine if cancer-associated gene expression might also be detectable in more readily accessible nasal epithelium. Nasal epithelial brushings were prospectively collected from current and former smokers with pulmonary lesions suspicious for lung cancer in the AEGIS-1 (n=375) and AEGIS-2 (n=130) clinical trials and gene expression profiled using microarrays. Using the 375 AEGIS 1 samples, we identified 535 genes that were differentially expressed in the nasal epithelium of patients who were ultimately diagnosed with lung cancer vs. those with benign disease after one year of follow-up (p<0.001). Using bronchial gene expression data from 299 AEGIS-1 patients (including 157 patients with matched nasal and bronchial expression data), we found significantly concordant cancer-associated gene expression differences between the two airway sites (p<0.001). Differentially expressed genes were enriched for genes associated with the regulation of apoptosis, mitotic cell cycle, and immune system signaling. A nasal lung cancer classifier derived in the AEGIS-1 cohort that combined clinical factors and nasal gene expression had significantly higher AUC (0.80) and sensitivity (0.94) over a clinical-factor only model (p<0.05) in independent samples from the AEGIS-2 cohort (n=130). These results suggest that the airway epithelial field of lung cancer-associated injury in current and former smokers extends to the nose and demonstrates the potential of using nasal gene expression as a non-invasive biomarker for the detection of lung cancer.
2017-06-27 | GSE80796 | GEO
Project description:BACKGROUND: In patients with suspicious pulmonary lesions, bronchoscopy is frequently non-diagnostic. This often results in additional invasive testing, including surgical biopsy, although many patients have benign disease. We sought to validate an airway gene-expression classifier for lung cancer in patients undergoing diagnostic bronchoscopy. METHODS: Two multicenter prospective studies (AEGIS 1 and 2) enrolled 1357 current or former smokers undergoing bronchoscopy for suspected lung cancer. Bronchial epithelial cells were collected from normal appearing mucosa in the mainstem bronchus during bronchoscopy. Patients without a definitive diagnosis from bronchoscopy were followed for 12 months. A gene-expression classifier was used to assess the risk of lung cancer, and its performance was evaluated. RESULTS: A total of 298 patients from AEGIS 1 and 341 from AEGIS 2 met criteria for analysis. Bronchoscopy was non-diagnostic for cancer in 272 of 639 patients (43%; 95%CI, 39-46%). The gene expression classifier correctly identified 431 of 487 patients with cancer (89% sensitivity; 95%CI, 85-91%), and 72 of 152 patients without cancer (47% specificity; 95%CI, 40-55%). The combination of the classifier and bronchoscopy had a sensitivity of 97% (95%CI, 95-98%), which was independent of size, location, stage, and histological subtype of lung cancer. In patients with an intermediate pre-test risk (10-60%) of lung cancer, the NPV of the classifier was 91% (95%CI 75-98%). CONCLUSIONS: In patients with an intermediate risk of lung cancer and a non-diagnostic bronchoscopy, a gene-expression classification of “low-risk” warrants consideration of a more conservative diagnostic approach that could reduce unnecessary invasive testing in patients with benign disease. 680 CEL files from 639 BEC specimens, 152 benign and 487 malignant samples
2015-05-17 | E-GEOD-66499 | biostudies-arrayexpress
Project description:AEGIS (Ancient Environmental Genomics Initiative for Sustainability)
| PRJEB80366 | ENA
Project description:BACKGROUND: In patients with suspicious pulmonary lesions, bronchoscopy is frequently non-diagnostic. This often results in additional invasive testing, including surgical biopsy, although many patients have benign disease. We sought to validate an airway gene-expression classifier for lung cancer in patients undergoing diagnostic bronchoscopy. METHODS: Two multicenter prospective studies (AEGIS 1 and 2) enrolled 1357 current or former smokers undergoing bronchoscopy for suspected lung cancer. Bronchial epithelial cells were collected from normal appearing mucosa in the mainstem bronchus during bronchoscopy. Patients without a definitive diagnosis from bronchoscopy were followed for 12 months. A gene-expression classifier was used to assess the risk of lung cancer, and its performance was evaluated. RESULTS: A total of 298 patients from AEGIS 1 and 341 from AEGIS 2 met criteria for analysis. Bronchoscopy was non-diagnostic for cancer in 272 of 639 patients (43%; 95%CI, 39-46%). The gene expression classifier correctly identified 431 of 487 patients with cancer (89% sensitivity; 95%CI, 85-91%), and 72 of 152 patients without cancer (47% specificity; 95%CI, 40-55%). The combination of the classifier and bronchoscopy had a sensitivity of 97% (95%CI, 95-98%), which was independent of size, location, stage, and histological subtype of lung cancer. In patients with an intermediate pre-test risk (10-60%) of lung cancer, the NPV of the classifier was 91% (95%CI 75-98%). CONCLUSIONS: In patients with an intermediate risk of lung cancer and a non-diagnostic bronchoscopy, a gene-expression classification of “low-risk” warrants consideration of a more conservative diagnostic approach that could reduce unnecessary invasive testing in patients with benign disease.
2015-05-17 | GSE66499 | GEO
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
| 2533916 | ecrin-mdr-crc
Project description:To explore the symbiotic relationship in Gigantopelta aegis holobiont, the protein abundance of the symbiontic organ called oesophageal gland was identified by using metaproteomic approach.
2020-12-16 | PXD022852 | Pride