Reporting of tobacco use and tobacco-related analyses in cancer cooperative group clinical trials: a systematic scoping review.

BACKGROUND: Continued smoking after a diagnosis of cancer negatively impacts cancer outcomes, but the impact of tobacco on newer treatments options is not well established. Collecting and evaluating tobacco use in clinical trials may advance understanding of the consequences of tobacco use on treatment modalities, but little is known about the frequency of reporting and analysis of tobacco use in cancer cooperative clinical trial groups. PATIENTS AND METHODS: A comprehensive literature search was conducted to identify cancer cooperative group clinical trials published from January 2017-October 2019. Eligible studies evaluated either systemic and/or radiation therapies, included ≥100 adult patients, and reported on at least one of: overall survival, disease/progression-free survival, response rates, toxicities/adverse events, or quality-of-life. RESULTS: A total of 91 studies representing 90 trials met inclusion criteria with trial start dates ranging from 1995 to 2015 with 14% involving lung and 5% head and neck cancer patients. A total of 19 studies reported baseline tobacco use; 2 reported collecting follow-up tobacco use. Seven studies reported analysis of the impact of baseline tobacco use on clinical outcomes. There was significant heterogeneity in the reporting of baseline tobacco use: 7 reported never/ever status, 10 reported never/ex-smoker/current smoker status, and 4 reported measuring smoking intensity. None reported verifying smoking status or second-hand smoke exposure. Trials of lung and head and neck cancers were more likely to report baseline tobacco use than other disease sites (83% versus 6%, P < 0.001). CONCLUSIONS: Few cancer cooperative group clinical trials report and analyze trial participants' tobacco use. Significant heterogeneity exists in reporting tobacco use. Routine standardized collection and reporting of tobacco use at baseline and follow-up in clinical trials should be implemented to enable investigators to evaluate the impact of tobacco use on new cancer therapies.

Molecular characterization of an expressed sequence tag representing the cuticle-degrading serine protease gene (PII) from the nematophagous fungus Arthrobotrys oviformis by differential display technology.

The technology of mRNA-based differential display reverse transcriptase-polymerase chain reaction (DDRT-PCR) was used to detect a 246-bp differentially expressed fragment from the nematophagous fungus Arthrobotrys oviformis when young mycelia were induced with the round worm Haemonchus contortus. The fragment was converted into an expressed sequence tag (EST) through characterization at the molecular level. Homology search indicated that the differentially expressed fragment originated from the cuticle-degrading serine protease gene, which has been previously reported to play a role in nematophagous activity in A. oligospora, Dactylaria parvispora, A. musiformis, and other potential anti-fungal biological control agents. Several single nucleotide polymorphisms found to represent both synonymous as well as non-synonymous mutations within this short sequence stretch of 246 bp suggested genetic variability within the gene in this group of nematode-trapping fungi. The cloned EST fragment has potential for use as a hybridization probe for searching full-length gene from an appropriate cDNA library of this and related fungi. This is the first report of the identification of an EST representing the cuticle-degrading serine protease gene from A. oviformis using the technique of DDRT-PCR.

Identification of an anonymous RFLP DNA probe through multiple arbitrary amplicon profiling and its use for strain differentiation in a field isolate of cellulose-degrading Aspergillus niger.

The genome of Aspergillus niger (MPS-002) was subjected to RAPD fingerprinting using none different random oligonucleotide primers. A 0.7 Kb PCR amplicon, generated by primer-3 could be used as a RFLP probe to differentiate A. niger (ATCC 16880) from A. niger (MPS-002). The probe revealed DNA polymorphism internal to two different EcoRI recognition sequences spaced apart at a distance of 0.4 Kb within a 4.0 Kb EcoRI fragment of the genome of both the strains. Localized genome mapping analysis further revealed that the 0.7 Kb RFLP probe was positioned at a distance of 2.7 Kb and 0.6 Kb from the two ends of a 4.0 Kb EcoRI fragment, respectively within the genome of the two strains of A. niger.

Dense molecular marking reveals genetic diversity in morphologically similar isolates of the nematophagous fungus Duddingtonia flagrans.

Three morphologically similar isolates of Duddingtonia flagrans [(Duddington) R. C. Cooke] viz., Df-2550, Df-2507 and Df-BJ were subjected to RAPD (Randomly Amplified Polymorphic DNA) and SRFA (Selective Fragment Length Amplification) mode of DNA fingerprinting analysis to generate 233 different anonymous DNA markers. Mean number of alleles per primer/primer pair for RAPD and SRFA primers was 13.75 and 29.66 respectively. Phylogenetic analysis through bootstrapping of 1000 simulated replicates of the data set demonstrated that Df-2550 was ancestral in the group of three and did not align with Df-2507 and Df-BJ, which appeared to diversify recently and therefore remained at the end of the phylogenetic tree. Genomic islands were also identified by three SRFA primer pairs, where Df-2550 aligned with Df-BJ, which is reverse to the master consensus-grouping pattern. Scanning image of the amplicon profiles when represented graphically generated unique molecular signature for the isolates.

Molecular cloning of a functional cis-acting, Bam HI-flanked, 1.6 Kb 'Mob' cassette for demonstrating rapid conversion of col EI origin-DNA cloning vectors into conjugal form.

A 1.6 Kb mobilization (Mob) fragment originating from broad host range IncP plasmid RP4 is effectively cloned into two different Col EI-origin based cloning vectors, pBluescript II SK+ and pT-Adv, to generate pPAR-I and pPAR-II, respectively. The vectors have different genetic markers and were demonstrated to get mobilized at significant frequency into a laboratory and an enteroroxigenic strain of Escherichia coli with all the genetic markers of the recombinant clones expressing efficiently in the recipient host cells. Important restriction endonuclease recognition sequences in the multiple cloning sites of the conjugal vector DNA molecules remained unique. Significance and relevance of the current study with regard to other gene delivery system in gram negative bacteria are discussed.

Characterization of rpo-B mutant of a strain of Escherichia coli to confirm its suitability for routine work related to recombinant DNA technology.

Rifampicin resistant spontaneous mutant of a popular laboratory strain of Escherichia coli (DH5 alpha) was isolated and found to resist high level of the drug in growth medium. The growth of the isolate was found to be slower than its wild-type counterpart. Its ability to get transformed into drug-resistant state through transformation by chemical means as tested using plasmid DNA from three different size categories, was found to be at par with the wild type. Other properties, viz., alpha-complementation and ability to express foreign gene remained unaltered. The utility of the rifampicin-resistant phenotype as a potential chromosomal genetic marker was demonstrated in a typical conjugation experiment to establish the ability of the mutant to act as recipient strain for a recombinant, mobilizable plasmid DNA molecule with the advantage of drug-mediated, high efficiency selection. Substitution of the wild strain with the mutant for routine experimentations related to recombinant DNA technology was concluded to be appropriate and of advantage.