Feasibility and value of genomic profiling in cancer of unknown primary: real-world evidence from prospective profiling study

Real-world evidence regarding the value of integrating genomic profiling (GP) in managing cancer of unknown primary (CUP) is limited. We assessed this clinical utility using a prospective trial of 158 patients with CUP (October 2016-September 2019) who underwent GP using next-generation sequencing designed to identify genomic alterations (GAs). Only 61 (38.6%) patients had sufficient tissue for successful profiling. GAs were seen in 55 (90.2%) patients of which GAs with US Food and Drug Administration-approved genomically matched therapy were seen in 25 (40.9%) patients. A change in therapy was recommended and implemented (primary endpoint of the study) in 16 (10.1%) and 4 (2.5%) patients of the entire study cohort, respectively. The most common reason for inability to implement the profiling-guided therapy was worsening of performance status (56.3%). Integrating GP in management of CUP is feasible but challenging because of paucity of tissue and aggressive natural history of the disease and requires innovative precision strategies.

The Salivary Mycobiome Contains 2 Ecologically Distinct Mycotypes

A broad range of fungi has been detected in molecular surveys of the oral mycobiome. However, knowledge is still lacking on interindividual variability of these communities and the ecologic and clinical significance of oral fungal commensals. In this cross-sectional study, we use internal transcribed spacer 1 amplicon sequencing to evaluate the salivary mycobiome in 59 subjects, 36 of whom were scheduled to receive cancer chemotherapy. Analysis of the broad population structure of fungal communities in the whole cohort identified 2 well-demarcated genus-level community types (mycotypes), with Candida and Malassezia as the main taxa driving cluster partitioning. The Candida mycotype had lower diversity than the Malassezia mycotype and was positively correlated with cancer and steroid use in these subjects, smoking, caries, utilizing a removable prosthesis, and plaque index. Mycotypes were also associated with metabolically distinct bacteria indicative of divergent oral environments, with aciduric species enriched in the Candida mycotype and inflammophilic bacteria increased in the Malassezia mycotype. Similar to their fungal counterparts, coexisting bacterial communities associated with the Candida mycotype showed lower diversity than those associated with the Malassezia mycotype, suggesting that common environmental pressures affected bacteria and fungi. Mycotypes were also seen in an independent cohort of 24 subjects, in which cultivation revealed Malassezia as viable oral mycobiome members, although the low-abundance Malassezia sympodialis was the only Malassezia species recovered. There was a high degree of concordance between the molecular detection and cultivability of Candida, while cultivation showed low sensitivity for detection of the Malassezia mycotype. Overall, our work provides insights into the oral mycobiome landscape, revealing 2 community classes with apparently distinct ecologic constraints and specific associations with coexisting bacteria and clinical parameters. The utility of mycotypes as biomarkers for oral diseases warrants further study.

Prospective study for comprehensive genomic profiling (GP) in cancer of unknown primary (CUP): Feasibility, molecular landscape, and clinical utility in current era

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Background: CUP presents a unique niche and challenge for application of GP. Absence of a primary limits consensus regarding site-directed and availability of tissue specific targeted therapy. We evaluated the real time feasibility and clinical utility of GP in CUP. Methods: Treatment eligible CUP pts were prospectively enrolled. A novel next-gen targeted sequencing (NGS) assay (ActionSeq/FusionSeq) was used to find genomic alterations (GAs) (somatic mutations in 212 and fusions in 53 cancer-associated genes). The primary objective was to determine prevalence of GAs and to assess the clinical impact via change in pre-test planned therapy (either referral to biomarker pertinent clinical trial (CT) or off label use of FDA approved drugs). With 54 pts we achieved 80% power (α 0.05) to a treatment change in 10% (5% to 15%) pts. Results: Between 9/2016 and 8/2019, 150 pts were consented. Tissue for GP was available in 59 (39%) pts (for 91 pts, samples had exhausted or insufficient tissue). Test was successfully performed on 54 (92%) pts. Cohort characteristics include: median age: 58 yr, male 43%, ECOG PS ≤1 96%, median IHC 8 (range 2-26), median survival 33 m (95% CI 18-47). Median reporting time was 23 days. Four (7%) pts had no identifiable GAs. A fusion ( PTRPK) was seen in 1 (2%) pt. Among 50 pts, total number of GAs were 487; 123 (26%) were “clinically relevant” (median 2.5/pt, range 1-11) while 364 (76%) were variants of unknown significance. Of the 123 GAs, 94 were mutations and 29 were amplifications. The 5 most common mutations were TP53, KRAS, PIK3CA, ARID1A, and NRAS and amplifications were CCND1, FGFR3, ERBB2, EGFR, and MYC. Planned therapy change post ActionSeq occurred in 13 pts (22%, 95% CI 13-34) (2 received an off-label drug; 9 were CT eligible [2 enrolled, 5 had PS decline, 2 pending]; 2 were lost to follow-up). Responses were seen in 2 of 4 pts who received GP based treatment. Conclusions: Comprehensive GP should be offered early to CUP pts. GP can help identify novel therapy and clinical trial options. Given the high rate of insufficient tissue cases, integrating a tissue sensitive algorithm involving IHC and GP in therapeutic management of CUP is merited.

Integrated Analysis of Clinical and Microbiome Risk Factors Associated with the Development of Oral Candidiasis during Cancer Chemotherapy

Oral candidiasis is a common side effect of cancer chemotherapy. To better understand predisposing factors, we followed forty-five subjects who received 5-fluorouracil- or doxorubicin-based treatment, during one chemotherapy cycle. Subjects were evaluated at baseline, prior to the first infusion, and at three additional visits within a two-week window. We assessed the demographic, medical and oral health parameters, neutrophil surveillance, and characterized the salivary bacteriome and mycobiome communities through amplicon high throughput sequencing. Twenty percent of all subjects developed oral candidiasis. Using multivariate statistics, we identified smoking, amount of dental plaque, low bacteriome and mycobiome alpha-diversity, and the proportions of specific bacterial and fungal taxa as baseline predictors of oral candidiasis development during the treatment cycle. All subjects who developed oral candidiasis had baseline microbiome communities dominated by Candida and enriched in aciduric bacteria. Longitudinally, oral candidiasis was associated with a decrease in salivary flow prior to lesion development, and occurred simultaneously or before oral mucositis. Candidiasis was also longitudinally associated with a decrease in peripheral neutrophils but increased the neutrophil killing capacity of Candida albicans. Oral candidiasis was not found to be associated with mycobiome structure shifts during the cycle but was the result of an increase in Candida load, with C. albicans and Candida dubliniensis being the most abundant species comprising the salivary mycobiome of the affected subjects. In conclusion, we identified a set of clinical and microbiome baseline factors associated with susceptibility to oral candidiasis, which might be useful tools in identifying at risk individuals, prior to chemotherapy.

Chemotherapy-induced oral mucositis is associated with detrimental bacterial dysbiosis

BACKGROUND

Gastrointestinal mucosal injury (mucositis), commonly affecting the oral cavity, is a clinically significant yet incompletely understood complication of cancer chemotherapy. Although antineoplastic cytotoxicity constitutes the primary injury trigger, the interaction of oral microbial commensals with mucosal tissues could modify the response. It is not clear, however, whether chemotherapy and its associated treatments affect oral microbial communities disrupting the homeostatic balance between resident microorganisms and the adjacent mucosa and if such alterations are associated with mucositis. To gain knowledge on the pathophysiology of oral mucositis, 49 subjects receiving 5-fluorouracil (5-FU) or doxorubicin-based chemotherapy were evaluated longitudinally during one cycle, assessing clinical outcomes, bacterial and fungal oral microbiome changes, and epithelial transcriptome responses. As a control for microbiome stability, 30 non-cancer subjects were longitudinally assessed. Through complementary in vitro assays, we also evaluated the antibacterial potential of 5-FU on oral microorganisms and the interaction of commensals with oral epithelial tissues.

RESULTS

Oral mucositis severity was associated with 5-FU, increased salivary flow, and higher oral granulocyte counts. The oral bacteriome was disrupted during chemotherapy and while antibiotic and acid inhibitor intake contributed to these changes, bacteriome disruptions were also correlated with antineoplastics and independently and strongly associated with oral mucositis severity. Mucositis-associated bacteriome shifts included depletion of common health-associated commensals from the genera Streptococcus, Actinomyces, Gemella, Granulicatella, and Veillonella and enrichment of Gram-negative bacteria such as Fusobacterium nucleatum and Prevotella oris. Shifts could not be explained by a direct antibacterial effect of 5-FU, but rather resembled the inflammation-associated dysbiotic shifts seen in other oral conditions. Epithelial transcriptional responses during chemotherapy included upregulation of genes involved in innate immunity and apoptosis. Using a multilayer epithelial construct, we show mucositis-associated dysbiotic shifts may contribute to aggravate mucosal damage since the mucositis-depleted Streptococcus salivarius was tolerated as a commensal, while the mucositis-enriched F. nucleatum displayed pro-inflammatory and pro-apoptotic capacity.

CONCLUSIONS

Altogether, our work reveals that chemotherapy-induced oral mucositis is associated with bacterial dysbiosis and demonstrates the potential for dysbiotic shifts to aggravate antineoplastic-induced epithelial injury. These findings suggest that control of oral bacterial dysbiosis could represent a novel preventive approach to ameliorate oral mucositis.

Transient bacteremia induced by dental cleaning is not associated with infection of central venous catheters in patients with cancer

OBJECTIVE

The aim of this study was to determine the incidence of bacteremia resulting from dental cleaning and of subsequent established bloodstream infection (BSI) caused by oral microorganisms in patients with cancer with central venous catheters (CVCs).

STUDY DESIGN

Twenty-six patients with cancer with CVCs and absolute neutrophil count over 1000 cells/µL received dental cleaning without antibiotic prophylaxis. Periodontal status was assessed at baseline by using the Periodontal Screening and Recording (PSR) score. Blood cultures were drawn via the CVCs at baseline, 20 minutes into cleaning, and 30 minutes and 24 hours after cleaning. Medical records were monitored for 6 months.

RESULTS

Baseline blood culture results were negative in 25 patients. Nine of 25 patients (36%) had positive blood culture 20 minutes into cleaning, all associated with at least 1 microorganism typically found in the mouth. These 9 patients had significantly higher mean PSR score (3.22) compared with the other 16 (2.56; P = .035). These expected bacteremias did not persist, with blood culture results (0/25) at 30 minutes and 24 hours after cleaning showing no positivity (P = .001). There were no cases of CVC-related infection or BSI attributable to dental cleaning.

CONCLUSIONS

Bacteremia resulting from dental cleaning is transient and unlikely to cause CVC-related infection or BSI in patients with absolute neutrophil count greater than 1000 cells/µL.

Ultrasensitive microfluidic array for serum pro-inflammatory cytokines and C-reactive protein to assess oral mucositis risk in cancer patients

In addition to disease diagnostics, there is a need for biomarkers to predict severity of cancer therapy side effects such as oral mucositis. Oral mucositis is an inflammatory lesion of oral mucosa caused by high-dose chemotherapy and/or radiation that is especially prevalent during oral cancer treatment. We describe here a semi-automated, modular microfluidic immunoarray optimized for ultrasensitive detection of pro-inflammatory cytokines involved in pathobiology of oral mucositis. Our goal is to methodologically identify risk of mucositis early in oral cancer treatment, before the onset of lesions. Biomarkers include tumor necrosis factor alpha (TNF-α), interleukin-6 (IL-6), interleukin-1β (IL-1β), and C-reactive protein (CRP). Protein analytes were captured from serum in a capture chamber by 1-μm magnetic beads coated with antibodies and enzyme labels. Beads are then transported downstream to a detection chamber containing an eight-sensor array coated with glutathione-coated gold nanoparticles (GSH-AuNP) and a second set of antibodies to capture the beads with analyte proteins. In this first application of the immunoarray to four-protein multiplexed measurements, ultralow detection limits of 10-40 fg mL(-1) in 5 μL serum were achieved for simultaneous detection in 30 min. Mass detection limits were 2.5-10 zmol, as few as 1500 molecules. Accuracy and diagnostic utility of the arrays were demonstrated by correlation of levels of the four biomarker proteins in serum from head and neck cancer patients with results from standard ELISA. This approach may lead to rapid, low-cost estimates of projected risk for severity of oral mucositis in cancer patients to enable improved therapeutic management.

Using high throughput sequencing to explore the biodiversity in oral bacterial communities

High throughput sequencing of 16S ribosomal RNA gene amplicons is a cost-effective method for characterization of oral bacterial communities. However, before undertaking large-scale studies, it is necessary to understand the technique-associated limitations and intrinsic variability of the oral ecosystem. In this work we evaluated bias in species representation using an in vitro-assembled mock community of oral bacteria. We then characterized the bacterial communities in saliva and buccal mucosa of five healthy subjects to investigate the power of high throughput sequencing in revealing their diversity and biogeography patterns. Mock community analysis showed primer and DNA isolation biases and an overestimation of diversity that was reduced after eliminating singleton operational taxonomic units (OTUs). Sequencing of salivary and mucosal communities found a total of 455 OTUs (0.3% dissimilarity) with only 78 of these present in all subjects. We demonstrate that this variability was partly the result of incomplete richness coverage even at great sequencing depths, and so comparing communities by their structure was more effective than comparisons based solely on membership. With respect to oral biogeography, we found inter-subject variability in community structure was lower than site differences between salivary and mucosal communities within subjects. These differences were evident at very low sequencing depths and were mostly caused by the abundance of Streptococcus mitis and Gemella haemolysans in mucosa. In summary, we present an experimental and data analysis framework that will facilitate design and interpretation of pyrosequencing-based studies. Despite challenges associated with this technique, we demonstrate its power for evaluation of oral diversity and biogeography patterns.

Effect of stressful life events on the onset and duration of recurrent aphthous stomatitis

BACKGROUND

Recurrent aphthous stomatitis (RAS) is a common and painful oral mucosal disease. Possible etiologies include genetics, vitamin deficiencies, trauma, immune dysfunction, and stress. The goal of this study was to examine the relationship between the occurrence, type, and magnitude of stressful events and the onset and duration of RAS episodes.

METHODS

One hundred and sixty subjects with a history of RAS completed a weekly phone survey for up to 1 year, providing data on the occurrence of RAS episodes and details of any stressful events they experienced during the previous week. During RAS episodes, subjects also completed daily paper diaries that recorded incidence and duration of the RAS episode. Stressful events were quantified using the validated Recent Life Changes Questionnaire (RLCQ) and were classified as mental or physical stressors.

RESULTS

Stressful life events were significantly associated with the onset of RAS episodes (P < 0.001), however, not with the duration of the RAS episodes. Experiencing a stressful life event increased the odds of an RAS episode by almost three times (OR = 2.72; 95% CI = 2.04-3.62). When controlled for each other, mental stressors had a larger effect (OR = 3.46, 95% CI = 2.54-4.72) than physical stressors (OR = 1.44; 95% CI = 1.04-1.99) on the occurrence of RAS episodes. RAS episodes did not occur more frequently or last longer with increasing stress severity.

CONCLUSIONS

In patients with a history of RAS, stressful events may mediate changes involved in the initiation of new RAS episodes. Mental stressors are more strongly associated with RAS episodes than physical stressors.

Calcium and magnesium utilization in rats: effect of dietary butterfat and calcium and of age

This factorial study was designed to examine the effect of short- and long-term ingestion of dietary calcium (0.25% and 1.0%) and butterfat (5% and 20%) and treatment with dimethylhydrazine (DMH) in rats. Calcium, magnesium and phosphorus absorption and, to a lesser extent, total diet digestibility decreased as the rats aged from 2 to 8 mo. Increased ingestion of butterfat had no effect on apparent absorption of calcium among young rats but tended to decrease calcium absorption in mature rats. The weak effect (P less than 0.05) of butterfat on calcium absorption reflected the small amount of calcium (less than 2% of fecal calcium) associated with lipids in feces. Ingestion of 10 vs. 2.5 mg Ca/g diet reduced the efficiency of apparent absorption of calcium, magnesium and phosphorus of young and mature rats and resulted in slightly, but significantly, greater retention of calcium in bone after 27 wk. The total amounts of calcium retained in tibias were correlated with the amounts of calcium absorbed by rats after 4, but not after 27, wk of dietary treatments. Rats dosed with DMH exhibited improved efficiency of calcium absorption, but the incidence of intestinal tumors did not affect mineral utilization.