COGNITION: a prospective precision oncology trial for patients with early breast cancer at high risk following neoadjuvant chemotherapy

BACKGROUND

COGNITION (Comprehensive assessment of clinical features, genomics and further molecular markers to identify patients with early breast cancer for enrolment on marker driven trials) is a diagnostic registry trial that employs genomic and transcriptomic profiling to identify biomarkers in patients with early breast cancer with a high risk for relapse after standard neoadjuvant chemotherapy (NACT) to guide genomics-driven targeted post-neoadjuvant therapy.

PATIENTS AND METHODS

At National Center for Tumor Diseases Heidelberg patients were biopsied before starting NACT, and for patients with residual tumors after NACT additional biopsy material was collected. Whole-genome/exome and transcriptome sequencing were applied on tumor and corresponding blood samples.

RESULTS

In the pilot phase 255 patients were enrolled, among which 213 were assessable: thereof 48.8% were identified to be at a high risk for relapse following NACT; 86.4% of 81 patients discussed in the molecular tumor board were eligible for a targeted therapy within the interventional multiarm phase II trial COGNITION-GUIDE (Genomics-guided targeted post neoadjuvant therapy in patients with early breast cancer) starting enrolment in Q4/2022. An in-depth longitudinal analysis at baseline and in residual tumor tissue of 16 patients revealed some cases with clonal evolution but largely stable genetic alterations, suggesting restricted selective pressure of broad-acting cytotoxic neoadjuvant chemotherapies.

CONCLUSIONS

While most precision oncology initiatives focus on metastatic disease, the presented concept offers the opportunity to empower novel therapy options for patients with high-risk early breast cancer in the post-neoadjuvant setting within a biomarker-driven trial and provides the basis to test the value of precision oncology in a curative setting with the overarching goal to increase cure rates.

Prognostic significance of FLT3 internal tandem duplication, nucleophosmin 1, and CEBPA gene mutations for acute myeloid leukemia patients with normal karyotype and younger than 60 years: a systematic review and meta-analysis

Diagnosis and classification of acute myeloid leukemia (AML) are based on morphology and genetics. An increasing number of gene mutations have been found, and some are used for risk classification in AML patients with normal karyotype (cytogenetically normal (CN)-AML). In this systematic review and meta-analysis, we examined three frequent mutations in CN-AML: mutations of fms-related tyrosine kinase 3 (FLT3-ITD), mutated nucleophosmin (NPM1), and mutations of the CCAAT enhancer-binding protein alpha (CEBPA) gene. A systematic literature search of publications listed in the electronic databases (Embase, Pubmed, Healthstar, BIOSIS, ISI Web of Knowledge and Cochrane) from 2000 up to March 2012 was performed (Fig. 1). Nineteen studies were included and qualitatively analyzed. Two to four studies entered the quantitative meta-analysis incorporating 1,378 to 1,942 patients with CN-AML. Meta-analysis for overall survival (OS) and relapse-free survival (RFS) showed FLT3-ITD to predict an unfavorable prognosis, with hazard ratios (HR) of 1.86 and 1.75, respectively. In contrast, meta-analysis of the impact of NPM1 and CEBPA mutations on OS yielded an HR of 0.56 for each mutation, while analysis of impact on RFS produced HRs of 0.37 and 0.42, respectively. This systematic review and meta-analysis aimed to evaluate the prognostic value of mutations in the NPM1, CEBPA, and FLT3 genes. FLT3-ITD was associated with worse prognosis, whereas mutations in NPM1 and CEBPA genes were associated with a favorable prognosis.

Beware of the ventriculogallbladder shunt

We report a case of distal end malfunction in a child with ventriculoabdominal shunt. The distal placement was in the gallbladder rather than the peritoneal cavity, as is usually the case with a ventriculoperitoneal shunt. Surgeons should be alerted to the possibility of distal terminus of a shunt to be other than the peritoneal cavity, as revision surgery in patients with ventriculogallbladder shunt requires exposure of the metal connector on the gallbladder wall to prevent biliary leakage.

Susceptibility testing of macrolide and lincosamide antibiotics according to DIN guidelines. Deutsches Institut für Normung

The in-vitro activity of azithromycin, clarithromycin, erythromycin, josamycin, midekamycin, roxithromycin and clindamycin against 674 Gram-negative and Gram-positive clinical isolates, including methicillin-resistant Staphylococcus aureus, was determined by agar dilution, microdilution and agar diffusion with Mueller-Hinton medium according to the Deutsches Institut für Normung (DIN) 58940 guidelines. The results obtained by regression analysis and the error-rate-bounded method of Metzler-DeHaan indicate that common interpretative criteria (breakpoints) for test discs may be assigned to susceptible/resistant Gram-positive strains for all antibiotics tested. The following tentative DIN values are suggested for 15 microg macrolide discs: for susceptible Gram-positive and Gram-negative strains, an inhibition zone diameter (IZD) of > or = 26 mm at a corresponding MIC of < or = 2 mg/L; for resistant Gram-positive strains, an IZD of < or = 21 mm; for resistant Gram-negative strains, an IZD of < or = 19 mm at a corresponding MIC of > or = 8 mg/L. For Haemophilus influenzae only, breakpoints for azithromycin are suggested with IZDs of > or = 21 mm for susceptible and < or = 18 mm for resistant.

Design and validation of DNA probe sets for a comprehensive interphase cytogenetic analysis of acute myeloid leukemia

The objective of this study was to design DNA probe sets that enable the detection of chromosome aberrations in acute myeloid leukemia (AML) by interphase cytogenetics using fluorescence in situ hybridization (FISH) and to compare the results of interphase cytogenetics with those of conventional chromosome banding analysis. One hundred five consecutive patients with adult AML entered on a multicenter treatment trial were studied with a comprehensive set of DNA probes recognizing the most relevant AML-associated structural and numerical chromosome aberrations: translocations t(8;21), t(15;17), and t(11q23); inversion inv(16);chromosomal deletions (5q-, 7q-, 9q-, 12p-, 13q-, 17p-, and 20q-); and chromosomal aneuploidies. Interphase cytogenetics was particularly sensitive for detecting the AML-specific gene fusions: 3 additional cases of inv(16) and 1 additional case of t(8;21) were identified by FISH that were missed by banding analysis, whereas equal numbers of t(11q23) and t(15;17) were detected. Five additional cases of trisomy 8q, 3 more cases of trisomy 11q, and 2 more cases of trisomies 21q and 22q were shown by FISH. These aberrations were either masked in complex karyo-types or identified in cases in which conventional banding analysis failed. On the other hand, the DNA probes selected were not informative to detect 1 case of 5q-, 9q-, and 20q-. In 5 cases, clonal aberrations were detected on banding analysis for which no FISH probes were selected. In conclusion, interphase cytogenetics proved to be more sensitive for detecting AML-specific chimeric gene fusions and some partial trisomies. Interphase cytogenetics provides a powerful technique complementary and, with further development of diagnostic DNA probes, even an alternative to chromosome banding studies for the cytogenetic analysis of AML.

Detection of Candida albicans DNA with a yeast-specific primer system by polymerase chain reaction

The in vitro and in vivo selectivity and sensitivity of a yeast-specific primer system was investigated. A two-step polymerase chain reaction (PCR) was used: the first amplified a 245-bp fragment of the gene for cytochrome P450L1A1 and the second a product of 193 bp. This nested PCR produced an approximately 1000-fold increase in the sensitivity of the test for Candida albicans DNA compared with the first primer pair. The lower level of sensitivity of the test in physiological saline and tissue homogenate was about 10 C. albicans cells ml-1. On the other hand, the sensitivity of the nested PCR method was reduced by a factor of more than 1000 when C. albicans was fixed with 4% formalin. After i.v. injection of different doses of C. albicans into mice, the yeast could be demonstrated in blood and in six different organs. The nested PCR was to some extent more sensitive than culturing for the detection of the yeast in the specimens of organs such as lung, cardiac muscle, liver, kidneys and brain. In contrast, in blood and spleen the culture was superior to the PCR technique used. Nested PCR is thus a useful additional method for the demonstration of yeasts.

[Computerized tomography diagnosis of a secondary extramedullary situated, non-secreting plasmacytoma of the right plica ventricularis]

We report the case of a 62-year-old male patient with an extramedullary non-secreting plasmacytoma of the right plica ventricularis. Although his skeletal lesions remained stable, the patient developed hoarseness. This was interpreted as mycotic laryngitis and computed tomography showed a tumor of the right plica ventricularis. Differential diagnosis included neoplasms of the larynx, thyroid gland or a lymphoma. After biopsy, however, histology revealed the rare diagnosis of a secondary extramedullary non-secreting plasmacytoma.

p53 gene deletion predicts for poor survival and non-response to therapy with purine analogs in chronic B-cell leukemias

Conventional cytogenetic analysis in B-cell chronic lymphocytic leukemia (B-CLL) has been very difficult, and the prognostic significance of specific chromosome aberrations is under discussion. Recent improvements in fluorescence in situ hybridization (ISH) techniques have provided an alternative approach for the detection of chromosome aberrations. Here, an interphase cytogenetic study was performed to analyze the incidence and prognostic significance of a p53 gene deletion in B-CLL and related disorders. We studied mononuclear cells from 100 patients with chronic B-cell leukemias [B-CLL, 90 patients; B-prolymphocytic leukemia (B-PLL), 7; Waldenström's macroglobulinemia (WM), 3] by fluorescence ISH with a genomic p53 DNA probe. In a subset of patients, additional G-banding analysis and single strand conformation polymorphism (SSCP) analysis was performed. Seventeen of the 100 patients [17%; B-CLL, 11 of 90 (12%); WM, 1 of 3; B-PLL, 5 of 7] exhibited a monoallelic p53 gene deletion by ISH. G-banding analysis demonstrated abnormalities of chromosome 17 in 13 of these 17 patients, all leading to loss of band 17p13. SSCP analysis showed aberrant bands in 9 of 14 patients with a p53 gene deletion. None of 12 patients with a p53 gene deletion compared with 20 of 36 patients (56%) without a deletion responded to therapy with fludarabine or pentostatin (P < .001). The difference in survival probabilities from the time of diagnosis and from the start of treatment with purine analogs between the two groups was highly significant (P < .001). In multivariate analysis, p53 gene deletion was the strongest prognostic factor for survival. In conclusion, p53 gene deletion predicts for non-response to therapy with purine analogs and for poor survival in chronic B-cell leukemias.

Prediction of phenotype for dextromethorphan O-demethylation by using polymerase chain reaction in healthy volunteers

The polymorphism of dextromethorphan (CAS 125-71-3) metabolism is dependent on hepatic cytochrom P4502D6 (CYP2D6) activity. The relationship between the CYP2D6 genotype and the dextromethorphan phenotype was studied in 83 healthy unrelated subjects. Genotype was determined by allele-specific polymerase chain reaction (PCR). Phenotyping was performed by administration of 25 mg dextromethorphan hydrobromide and determination of the urinary metabolic ratio of dextromethorphan and its O-demethylated metabolite dextrorphan (DEM/DOR). Six subjects (7.2%) were homozygous for mutant alleles (95% confidence interval 2.7%-14.7%), 18 subjects (22%) were heterozygous carriers, and 59 were homozygous for the wild-type allele. Six subjects were classified as poor metabolizers (PM) of dextromethorphan, 77 as extensive metabolizers (EM). Genotyping correctly predicted all PMs and EMs. The CYP2D6-B mutation was most frequently found, being present in 83% of PM and 8% of EM alleles. Heterozygous EMs (22% of the total population studied) were significantly underrepresented compared to the expected genotype frequency of 31% (p < 0.05). The extensive metabolizers who were heterozygous for the wild-type allele had a significantly higher metabolic ratio, compared to the homozygous EMs (log10DEM/DOR [95% = -1.99 [(-2.30)-(-1.69)] vs. -2.55 [(-2.67)-(-2.43)]; p < 0.001), indicating a gene-dose effect for CYP2D6.

Mitochondrial complex I and III mutations and neutral-lipid storage in activated mononuclear macrophages and neutrophils: a case presenting with necrotizing myopathy, poikiloderma atrophicans vasculare, and xanthogranulomatous bursitis

We report the case of a 57-year-old woman suffering from xanthogranulomatous bursitis, necrotizing myopathy, and poikiloderma atrophicans vasculare, which are associated with marked accumulation of neutral-lipid storage phagocytes. The observed lipid storage was restricted to activated phagocytes independent of the presence of tissue necrosis and was not seen either in circulating blood leukocytes or in muscle fibers. The patient's daughter disclosed xanthomatous inflammatory reaction with profound delay of wound healing secondary to pelviscopy. Examination of the mitochondrial DNAs of the patient, her daughter, and her two grandchildren revealed two homoplasmic mutations at positions 13708 and 15257 of the mitochondrial genome. We discuss the involvement of these mutations in the pathogenesis of xanthomatous and xanthogranulomatous inflammation. Further investigations are required to test whether impairment of aerobic energy production independent from mitochondrial DNA mutations (eg, by hypoxia or microbial toxins) similarly can cause the accumulation of lipid-laden macrophages and explain the persistency of xanthogranulomatous inflammation.

In situ autolysis of mouse brain: ultrastructure of mitochondria and the function of oxidative phosphorylation and mitochondrial DNA

The effect of in situ autolysis on cerebral mitochondrial structure and function has been investigated. Mice (n = 9) were sacrificed and stored for up to 24 h under unfavorable post-mortem conditions at 25 degrees C. At different time intervals groups of three animals were submitted to post-mortem dissection and tissue from different regions of the brain was used for the preparation of "free" and synaptosomal mitochondria. On electron microscopic examination, the post-mortem period had no significant influence on mitochondrial morphology and enzymatic activities of complexes I-V of the mitochondrial oxidative phosphorylation system were still present in all the mitochondrial preparations from different regions of the brain, albeit at a reduced levels. Degradation of mitochondrial DNA was virtually absent from mitochondrial preparations during the 24-h period of autolysis, as shown by the presence of intact DNA by Southern blot and PCR analysis. Based on these results, alterations in mitochondrial DNA and deficiencies of mitochondrial respiratory complexes I-V can be recognized in cerebral tissue even after 24 h of unfavorable post-mortem storage conditions.

Identification of Legionella pneumophila in various specimens by the polymerase chain reaction

Amplification of the mip sequence with polymerase chain reaction (PCR) proved to be specific for Legionella pneumophila. With nested PCR, the sensitivity of the test was markedly increased. The lower limit of detection for nested PCR in the aqueous medium for live and heat-inactivated dead L. pneumophilia was approximately 1-10 bacteria/ml. The sensitivity of the method, however, was reduced by a factor of 10 to 100 when the bacteria were added to homogenised pulmonary tissue. Fixing the bacteria in aqueous suspension or in tissue homogenate with buffered 4% formalin (pH 7.3) reduced the sensitivity of the PCR by a factor of about 100. After intravenous injection of heat-inactivated bacteria in mice L. pneumophila was detected in deep-frozen samples of plasma and various tissues. The molecular biological technique of nested PCR is proposed as an additional method for the diagnosis of legionella.

[Infantile and late-onset type of globoid cell leucodystrophy in one family (author's transl)]

Globoid cells leucodystrophy was diagnosed by specific enzyme assays in two siblings of one family. A male infant presented the typical symptoms of hyperirritability and progressive loss of psychomotor functions beginning at the age of 4 months. The progression of the disease lead to decerebration and death at 19 months of age. The elder sister had a normal development until her third year, when she developed exclusively symptoms of peripheral neuropathy. Up to the moment there are no symptoms of cortical function loss.

[Long-term artificial respiration in the treatment of neonatal tetanus (author's transl)]

A case of severe neonatal tetanus is reported which developed seven days after birth. The child was transferred to the intensive care unit where she was artificially ventilated for 25 days via a naso-tracheal catheter. The temperature and humidity of the inspired air were carefully controlled. Muscle relaxants and sedatives were given at 2-4 hours' interval.