An approach for improvement of the accuracy of cancer gene panel testing

BACKGROUND

Tissue-based comprehensive genomic profiling (CGP) is increasingly being employed for genotype-directed therapies in patients with advanced cancer. However, tissue availability may limit their potential applications. In Japan, the cost of cancer gene panel tests is covered by public insurance for patients diagnosed with advanced solid tumors once in their lifetime. Therefore, it is essential to improve the success rate (reportability) and accuracy of CGP tests. The purpose of this study was to identify the factors associated with efficient and accurate CGP testing using relevant information obtained from real-world data.

METHODS

This study included 159 samples analyzed using tumor-only panel FoundationOne® CDx cancer genome profiling (F1CDx) and 85 samples analyzed using matched-pair panel OncoGuide™ NCC Oncopanel system (NCCOP) at St. Marianna University Hospital. Sample characteristics (fixation conditions, storage period, histology, tumor cell ratio, and genomic tumor cell content), CGP performance, and quality control status were evaluated across all 244 tested samples.

RESULTS

In 237/244 samples (97.1%), CGP testing results were successfully obtained [F1CDx, 99.4% (158/159) and NCCOP, 92.9% (79/85)]. An increased number of fibroblasts, inflammatory cells, and necrotic tumor cells, long-term storage, and/or prolonged fixation of tissue sections were involved in the unreported results and/or qualified CGP results. In addition, a negative correlation between median insert size values and ΔΔCq was observed in the NCCOP system.

CONCLUSION

We identified various factors associated with efficient and accurate CGP testing using relevant information obtained from real-world data, suggesting that thorough selection and preparation of tissue sections could optimize CGP and maximize useful information.

Human genetics education as part of the Japanese Cancer Education Comprehensive Support Project

In Japan, cancer education has been initiated with children as a measure against cancer. Cancer genome medicine, which is a social implementation, includes aspects of genetic medicine. For this reason, it is assumed that content related to "genetics" is also necessary in cancer education. To investigate the actual situation regarding the teaching of genetics in cancer education, we conducted a questionnaire survey of schoolteachers involved in cancer education; these schoolteachers belonged to the model school of the Cancer Education Comprehensive Support Project. Regarding genetic content, we asked questions related to two aspects: "the molecular genetic mechanisms of cancer" and "the phenomenon of sharing cancer in the family." The results showed that about 60% of the teachers had experience teaching content related to the molecular genetic mechanisms of cancer and the phenomenon of sharing cancer in the family. While many teachers felt that teaching genetics in cancer education was necessary, they also felt that there were difficulties in doing so: 65.2% for content related to the molecular genetic mechanisms of cancer and 70.8% for that related to the phenomenon of sharing cancer in the family. It is important to properly treat cancer as a genetic disease, and it is necessary to examine government curriculum guidelines and establish a collaborative system among other subjects. In addition, the involvement of specialists in genetic medicine and psychosocial support is expected to improve teachers' genetic literacy as well as to communicate with students with consideration for their family history.

Caveolin-3 regulates myostatin signaling. Mini-review

Caveolins, components of the uncoated invaginations of plasma membrane, regulate signal transduction and vesicular trafflicking. Loss of caveolin-3, resulting from dominant negative mutations of caveolin-3 causes autosomal dominant limb-girdle muscular dystrophy (LGMD) 1C and autosomal dominant rippling muscle disease (AD-RMD). Myostatin, a member of the muscle-specific transforming growth factor (TGF)-beta superfamily, negatively regulates skeletal muscle volume. Herein we review caveolin-3 suppressing of activation of type I myostatin receptor, thereby inhibiting subsequent intracellular signaling. In addition, a mouse model of LGMD1C has shown atrophic myopathy with enhanced myostatin signaling. Myostatin inhibition ameliorates muscular phenotype in the model mouse, accompanied by normalized myostatin signaling. Enhanced myostatin signaling by caveolin-3 mutation in human may contribute to the pathogenesis of LGMD1C. Therefore, myostatin inhibition therapy may be a promising treatment for patients with LGMD1C. More recent studies concerning regulation of TGF-beta superfamily signaling by caveolins have provided new insights into the pathogenesis of several human diseases.

Identification of aminoglycoside-modifying enzymes by susceptibility testing: epidemiology of methicillin-resistant Staphylococcus aureus in Japan

A multiple-primer PCR was used to identify genes encoding aminoglycoside-modifying enzymes in 381 clinical isolates of methicillin-resistant Staphylococcus aureus (MRSA). The technique used three sets of primers delineating specific DNA fragments of the aph(3')-III, ant(4')-I, and aac(6')-aph(2") genes, which influence the MICs of gentamicin, tobramycin, and lividomycin. Isolates with none of the three genes detected were susceptible to all three agents. Isolates with the aph(3')-III gene showed resistance to lividomycin (MIC > 1,024 microg/ml), and those with the ant(4')-I gene were resistant to tobramycin (MIC > or = 8 microg/ml). Isolates with only the aac(6')-aph(2") gene were resistant to gentamicin (MIC > or = 8 microg/ml) and tobramycin in decreasing order; those with both the ant(4')-I and aac(6')-aph(2") genes also were resistant to gentamicin and tobramycin, but in increasing order. Susceptibility testing, then, could detect specific genes. In 381 Japanese MRSA isolates, the ant(4')-I, aac(6')-aph(2"), and aph(3')-III genes were prevalent in 84.5, 61.7, and 8.9%, respectively. Isolates with only the ant(4')-I gene had coagulase type II or III, but isolates with both the ant(4')-I and aac(6')-aph(2") genes included all coagulase types. Most isolates with coagulase type IV or VII carried the aac(6')-aph(2") gene. Of the MRSA isolates with ant(4')-I and/or aac(6')-aph(2") genes, 97% were resistant to aminoglycosides in clinical use, but a new aminoglycoside, arbekacin, had excellent activity against these isolates.

Plasmid-encoded metallo-beta-lactamase (IMP-6) conferring resistance to carbapenems, especially meropenem

In 1996, Serratia marcescens KU3838 was isolated from the urine of a patient with a urinary tract infection at a hospital in northern Japan and was found to contain the plasmid pKU501. Previously, we determined that pKU501 carries bla(IMP) and the genes for TEM-1-type beta-lactamases as well as producing both types of beta-lactamases (H. Yano, A. Kuga, K. Irinoda, R. Okamoto, T. Kobayashi, and M. Inoue, J. Antibiot. 52:1135-1139, 1999). pKU502 is a recombinant plasmid that contains a 1.5-kb DNA fragment, including the metallo-beta-lactamase gene, and is obtained by PCR amplification of pKU501. The sequence of the metallo-beta-lactamase gene in pKU502 was determined and revealed that this metallo-beta-lactamase gene differed from the gene encoding IMP-1 by one point mutation, leading to one amino acid substitution: 640-A in the base sequence of the IMP-1 gene was replaced by G, and Ser-196 was replaced by Gly in the mature enzyme. This enzyme was designated IMP-6. The strains that produced IMP-6 were resistant to carbapenems. The MICs of panipenem and especially meropenem were higher than the MIC of imipenem for these strains. The k(cat)/K(m) value of IMP-6 was about sevenfold higher against meropenem than against imipenem, although the MIC of meropenem for KU1917, which produced IMP-1, was lower than that of imipenem, and the MIC of panipenem was equal to that of imipenem. These results support the hypothesis that IMP-6 has extended substrate profiles against carbapenems. However, the activity of IMP-6 was very low against penicillin G and piperacillin. These results suggest that IMP-6 acquired high activity against carbapenems, especially meropenem, via the point mutation but in the process lost activity against penicillins. Although IMP-6 has reduced activity against penicillins due to this point mutation, pKU501 confers resistance to a variety of antimicrobial agents because it also produces TEM-1-type enzyme.

[Present situation of drug resistance and future prospects]

Antibiotic resistance has evolved over 60 years from a merely microbiological curiosity to a serious medical problem in hospitals. Resistance has been reported in almost all species of bacteria to various classes of antimicrobial agents including recently evaluated ones. Bacteria regulated resistance by different mechanisms. Inappropriate use of an antimicrobial agent selects resistant strains much more frequently. Since it is not expected that some epoch-making new antimicrobial agents will be developed in the near future, proper use of existing antimicrobial agents which is based on the mechanisms of action of antimicrobial agents and of resistance of bacteria, and of control of nosocomial infection are very important to reduce the further spread of resistant bacteria. With the search for natural sources of new antimicrobial substances now appearing frustrated, the genomic approach in the 21st century may be the only fruitful way to develop truly novel chemotherapeutic agents against bacterial diseases.

[In vitro antibacterial activity of prulifloxacin, a new oral quinolone, and comparative susceptibility rate at clinical breakpoint MIC]

In vitro drug sensitivity of clinically isolated bacteria against prulifloxacin (PUFX), which is a new quinolone, was investigated, and the antibacterial activity and susceptibility rate at clinical breakpoint were compared with those of norfloxacin, ofloxacin (OFLX), ciprofloxacin, tosufloxacin, fleroxacin, sparfloxacin and levofloxacin (LVFX). The following results were obtained. 1) PUFX showed a broad-spectrum antibacterial activity against both Gram-positive and Gram-negative bacteria. 2) MIC80 of PUFX was 0.25 and 1 microgram/ml, against methicillin susceptible Staphylococcus aureus and Streptococcus pneumoniae, respectively and below 0.125 microgram/ml against Gram-negative Enterobacteriaceae. MIC90 of PUFX against Pseudomonas aeruginosa, which has MIC not exceeding 4 micrograms/ml to OFLX, was 0.5 microgram/ml. 3) PUFX was judged as active against the bacteria under the criteria proposed presented by "the Sensitivity Determination Committee for Antibiotics, Japan Society of Chemotherapy: Break Point for Respiratory Infectious Diseases and Sepsis". It is suggested that the sensitivity of each bacterial species to PUFX was high. 4) From the correlation analysis of MIC, PUFX was shown to have two to eight times higher antibacterial acitivity than LVFX for Citrobacter freundii, Serratia marcescens and Pseudomonas aeruginosa. 5) PUFX showed potent short-time bactericidal activity against S. aureus and P. aeruginosa.

ampR gene mutations that greatly increase class C beta-lactamase activity in Enterobacter cloacae

The ampC and ampR genes of Enterobacter cloacae GN7471 were cloned into pMW218 to yield pKU403. Four mutant plasmids derived from pKU403 (pKU404, pKU405, pKU406, and pKU407) were isolated in an AmpD mutant of Escherichia coli ML4953 by selection with ceftazidime or aztreonam. The beta-lactamase activities expressed by pKU404, pKU405, pKU406, and pKU407 were about 450, 75, 160, and 160 times higher, respectively, than that expressed by the original plasmid, pKU403. These mutant plasmids all carried point mutations in the ampR gene. In pKU404 and pKU405, Asp-135 was changed to Asn and Val, respectively. In both pKU406 and pKU407, Arg-86 was changed to Cys. The ease of selection of AmpR mutations at a frequency of about 10(-6) in this study strongly suggests that derepressed strains, such as AmpD or AmpR mutants, could frequently emerge in the clinical setting.

Pulsed-field gel electrophoresis analysis of nasopharyngeal flora in children attending a day care center

To investigate how bacterial pathogens spread from child to child in a day care center, we monitored six children, two boys and four girls, born between August 1995 and November 1997, attending a day care center and analyzed nasopharyngeal samples from them using pulsed-field gel electrophoresis (PFGE). We obtained nasopharyngeal cultures from all of the affected children and almost all of the unaffected children between September 1998 and March 1999 after some children presented simultaneously with purulent rhinorrhea. Moreover, when a child was found to have acute otitis media, nasopharyngeal secretions from the child were independently cultured during treatment. During this period, 28 isolates of Moraxella catarrhalis, 13 of Streptococcus pneumoniae, and 4 of Haemophilus influenzae were recovered. PFGE gave 8 patterns for M. catarrhalis, 10 for S. pneumoniae, and 1 for H. influenzae. PFGE patterns demonstrated spread of M. catarrhalis between children. However, each occurrence of clusters of infection with M. catarrhalis lasted 2 to 6 weeks, with a change in PFGE pattern between occurrences of clusters. The M. catarrhalis strain infecting each child also changed. Similarly, the S. pneumoniae strain in each child also changed. In contrast, infection with H. influenzae persisted for about 3 months in an affected child.

[Antibacterial activity of beta-lactam antibiotics against extended-spectrum beta-lactamase producing bacteria]

MICs of various beta-lactam antibiotics by themselves and in combination with beta-lactamase inhibitor (clavulanic acid) against extended spectrum beta-lactamase (ESBL) producing strains of Escherichia coli and Klebsiella pneumoniae which were isolated from clinical materials were investigated. Furthermore, based on the results obtained, a procedure to detect ESBL producing strains was proposed. The MICs of beta-lactam antibiotics against beta-lactamase producing strains were investigated. At first, beta-lactamase was investigated by the drug sensitivity pattern (MIC) to beta-lactam antibiotics and by the substrate profiles of beta-lactamase extracted from the transconjugant of E. coli K-12 strains. After that, we classified the beta-lactamase producing gene by PCR method. Furthermore, a proposal was made for an antibiotic to be used in the confirmation of mixed type beta-lactamase. The data obtained by the above investigations were compiled and used to determine the limit concentration of each beta-lactam against beta-lactamase producing strains including ESBL. By using beta-lactam antibiotics at the following concentrations, it is considered possible to classify beta-lactamase; ampicillin (64 micrograms/ml), ampicillin/clavulanic acid (32/5 micrograms/ml), piperacillin (64 micrograms/ml), cefotaxime (1 microgram/ml), cefpodoxime (2 micrograms/ml), ceftazidime (1 microgram/ml), cefmetazole (4 micrograms/ml), cefminox (2 micrograms/ml), cefepime (0.5 microgram/ml), aztreonam (1 microgram/ml) and imipeneme (1 microgram/ml). This method may be used as a reference in investigating the prevalence of beta-lactam resistant isolates by ESBL producing E. coli and K. pneumoniae.

Why do antimicrobial agents become ineffectual?

Antibiotic resistance has evolved over the past 50 years from a merely microbiological curiosity to a serious medical problem in hospitals all over the world. Resistance has been reported in almost all species of gram-positive and -negative bacteria to various classes of antibiotics including recently developed ones. Bacteria acquire resistance by reducing permeability and intracellular accumulation, by alteration of targets of antibiotic action, and by enzymatic modification of antibiotics. Inappropriate use of an antibiotic selects resistant strains much more frequently. Once resistant bacteria has emerged, the resistance can be transferred to other bacteria by various mechanisms, resulting in multiresistant strains. MRSA is one of the typical multiresistant nosocomial pathogens. A study of the PFGE pattern of endonuclease-digested chromosomal DNA showed that MRSA of a few clones were disseminated among newborns in the NICU of a Japanese hospital. In this regard, it is important to choose appropriate antibiotics and then after some time, to change to other classes to reduce the selection of resistant strains. Since the development of epoch-making new antibiotics is not expected in the near future, it has become very important to use existing antibiotics prudently based on mechanisms of antibiotic action and bacterial resistance. Control of nosocomial infection is also very important to reduce further spread of resistant bacteria.

Detection of tet(K) and tet(M) in Staphylococcus aureus of Asian countries by the polymerase chain reaction

This study describes the use of the polymerase chain reaction (PCR) to detect the tet(K) and tet(M) tetracycline resistance genes in Staphylococcus aureus. Primers based on the DNA sequence of the tet(K) and tet(M) genes from S. aureus were used as primers in the PCR assay to detect the presence of genes for resistance to tetracycline and minocycline. Two-hundred and fifteen isolates of S. aureus from Asian countries as Japan, Indonesia, China, Korea and Thailand were examined, and the results confirm that tet(K) specifies resistance to tetracycline but not to minocycline and tet(M) specifies resistance to both tetracycline and minocycline. We observed two different types of clinical isolates of S. aureus strains resistant to minocycline and tetracycline: the first carried only the tet(M) gene, while the second carried both the tet(M) and the tet(K) genes. Almost all of the clinical isolates of S. aureus resistant to minocycline and tetracycline from Indonesia, China and Thailand carried both tet(M) and tet(K) genes, while most of clinical isolates of S. aureuss from Japan and Korea carried only tet(M) gene.