Background Clinically-available biomarkers to identify the fraction of patients with small cell lung cancer (SCLC) who respond to immune-checkpoint inhibitors (ICIs) are lacking. High nonsynonymous tumor mutational burden (TMB), as assessed by whole exome sequencing, correlates with improved clinical outcomes for patients with SCLC treated with ICIs. Whether TMB as assessed by targeted next generation sequencing (NGS) is associated with improved efficacy of ICIs in patients with SCLC is currently unknown. Here we determined whether TMB by targeted NGS is associated with efficacy of ICIs in patients with SCLC. Methods We collected clinicopathologic data from patients with relapsed or refractory SCLC which underwent targeted NGS with TMB assessment by the Dana-Farber Cancer Institute OncoPanel platform. The relationship between TMB and clinical outcomes after treatment with ICIs was investigated. Results Among the 52 patients treated with ICIs, we found no significant difference in the objective response rate (ORR) between patients with a TMB above the 50th percentile (“TMB high”) and those with a TMB at or below the 50th percentile (“TMB low”). The median progression-free survival (mPFS) and median overall survival (mOS) were significantly longer in patients with a high TMB compared to those with a low TMB (mPFS: 3.3 versus 1.2 months, HR: 0.37 [95% CI: 0.20–0.69], P < 0.01; mOS: 10.4 versus 2.5 months, HR: 0.38 [95% CI: 0.19–0.77], P < 0.01). The one-year PFS and OS rates improved with increasing mutational load when TMB was divided into tertiles. Conclusions These findings show that targeted NGS, a readily available clinical diagnostic test, can be used to identify patients with SCLC who are most likely to benefit from treatment with immune checkpoint inhibitors. Electronic supplementary material The online version of this article (10.1186/s40425-019-0572-6) contains supplementary material, which is available to authorized users.

The MYC oncogenic transcription factor is overexpressed in most human cases of T cell acute lymphoblastic leukemia (T-ALL), often downstream of mutational NOTCH1 activation. Genetic alterations in the PTEN-PI3K-AKT pathway are also common in T-ALL. We generated a conditional zebrafish model of T-ALL in which 4-hydroxytamoxifen (4HT) treatment induces MYC activation and disease, and withdrawal of 4HT results in T-ALL apoptosis and tumor regression. However, we found that loss-of-function mutations in zebrafish pten genes, or expression of a constitutively active Akt2 transgene, rendered tumors independent of the MYC oncogene and promoted disease progression after 4HT withdrawal. Moreover, MYC suppresses pten mRNA levels, suggesting that Akt pathway activation downstream of MYC promotes tumor progression. Our findings indicate that Akt pathway activation is sufficient for tumor maintenance in this model, even after loss of survival signals driven by the MYC oncogene.

The use of culture-independent diagnostic tests (CIDTs), such as stool antigen tests, as standalone tests for the detection of Campylobacter in stool is increasing. We conducted a prospective, multicenter study to evaluate the performance of stool antigen CIDTs compared to culture and PCR for Campylobacter detection. Between July and October 2010, we tested 2,767 stool specimens from patients with gastrointestinal illness with the following methods: four types of Campylobacter selective media, four commercial stool antigen assays, and a commercial PCR assay. Illnesses from which specimens were positive by one or more culture media or at least one CIDT and PCR were designated "cases." A total of 95 specimens (3.4%) met the case definition. The stool antigen CIDTs ranged from 79.6% to 87.6% in sensitivity, 95.9 to 99.5% in specificity, and 41.3 to 84.3% in positive predictive value. Culture alone detected 80/89 (89.9% sensitivity) Campylobacter jejuni/Campylobacter coli-positive cases. Of the 209 noncases that were positive by at least one CIDT, only one (0.48%) was positive by all four stool antigen tests, and 73% were positive by just one stool antigen test. The questionable relevance of unconfirmed positive stool antigen CIDT results was supported by the finding that noncases were less likely than cases to have gastrointestinal symptoms. Thus, while the tests were convenient to use, the sensitivity, specificity, and positive predictive value of Campylobacter stool antigen tests were highly variable. Given the relatively low incidence of Campylobacter disease and the generally poor diagnostic test characteristics, this study calls into question the use of commercially available stool antigen CIDTs as standalone tests for direct detection of Campylobacter in stool. Campylobacter infection continues to be a major public health problem. Campylobacter jejuni and Campylobacter coli are pathogens transmitted commonly through food, causing an estimated 1.3 million cases of illness per year in the United States (1), and yet diagnosis can be challenging because the organism is difficult to isolate, grow, and identify. Recent reports describing clinical laboratory practices for Campylobacter diagnostics in Pennsylvania (2) and the Foodborne Diseases Active Surveillance Network (FoodNet) sites (3) highlight the wide range of testing practices in use; currently, no best-practice clinical or public health laboratory guidelines exist for laboratory diagnosis of Campylobacter infections. Direct plating onto a Campylobacter selective medium, followed by incubation at 42°C under microaerobic conditions for 72 h, has long been considered the "gold standard" for diagnosis (4).The use of culture-independent diagnostic tests (CIDTs) for Campylobacter testing on stool samples is increasing, which may have important implications for both patient management and public health surveillance efforts (5). Stool antigen tests to directly detect Campylobacter in fecal samples are fast and generate sameday results, but concerns regarding speci...

The smear of a clinical specimen provides essential laboratory information that is used to make therapeutic decisions. For this study, smears were made by centrifugation in a Beckman Microfuge 11 (Beckman Instruments, Palo Alto, Calif.) and in parallel by using a Cytospin 2 apparatus (Shandon Inc., Pittsburgh, Pa.). Of 350 consecutive body fluid specimens examined, 50 (14.0%) grew bacteria. Both methods were culture and smear positive for 24 (6.9%) specimens; 18 (5.1%) specimens were cytocentrifuge smear positive, culture positive, and high-speed centrifugation (HSC) negative; 3 (0.8%) were culture negative and positive by both smear methods; and 1 (0.2%) was HSC smear positive, culture positive, and cytocentrifuge negative. Seven (2.0%) specimens were culture positive and negative by both smear methods. Clinically, cytocentrifuge preparations showed greater sensitivity for culture-positive specimens and a closer correlation with the CFU per milliliter than HSC did, resulting in a greater ability to treat patients with specific therapies. In addition, analysts needed to examine only a 6-mm-diameter area on the slide, cells and microbes were somewhat larger and more regular in appearance, and smears stained more uniformly. Because of the increased clinical and laboratory utility of the cytocentrifuge, its use is recommended in clinical microbiology laboratories for all sterile body fluid specimens.Rapid diagnosis by Gram staining for a suspected infectious organism from a sterile body fluid is a major responsibility of our Clinical Microbiology Laboratory. In addition to suggesting a diagnosis, it guides clinicians in the choice of antibiotics. This is especially critical in patients with lifethreatening diseases such as meningitis, peritonitis, and obstetric infections, in which the clinical efficacy is dependent on the therapeutic intervention that is used. Because the concentration of microorganisms in body fluid specimens may be low and/or the volume of specimen submitted for study may be extremely low, a technique for concentrating body fluids is recommended for body fluids that are to be used in smears and cultures (5,6,9). In the Hematology and Cytology laboratories, a cytocentrifuge technique is commonly used to prepare body fluid specimen smears when the intent is to observe the morphologies of the cells (2,4,8). These methods sometimes demonstrate organisms that were not observed in the smears prepared from the same specimens by the Clinical Microbiology laboratory. Because of this phenomenon, we undertook an investigation into the sensitivity and specificity of smears prepared with the cytocentrifuge compared with those of smears prepared by the high-speed centrifugation (HSC) method currently used in our laboratory. Both methods were evaluated for laboratory and clinical utility. MATERIALS AND METHODSSpecimens. Three hundred fifty consecutive sterile body fluids from sterile body sites submitted to the Clinical Microbiology Laboratory for evaluation were included in this study. Specimens were processed...

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