Molecular mechanisms of embryonic tail development in the self-fertilizing mangrove killifish Kryptolebias marmoratus.

Using the self-fertilizing mangrove killifish, we characterized two mutants, shorttail (stl) and balltail (btl). These mutants showed abnormalities in the posterior notochord and muscle development. Taking advantage of a highly inbred isogenic strain of the species, we rapidly identified the mutated genes, noto and msgn1 in the stl and btl mutants, respectively, using a single lane of RNA sequencing without the need of a reference genome or genetic mapping techniques. Next, we confirmed a conserved morphant phenotype in medaka and demonstrate a crucial role of noto and msgn1 in cell sorting between the axial and paraxial part of the tail mesoderm. This novel system could substantially accelerate future small-scale forward-genetic screening and identification of mutations. Therefore, the mangrove killifish could be used as a complementary system alongside existing models for future molecular genetic studies.

The 27-gene IO score is associated with efficacy of PD-1/L1 inhibitors independent of FGFR expression in a real-world metastatic urothelial carcinoma cohort.

Multiple targeted therapeutics have been approved by the FDA for mUC, including immune checkpoint inhibitors (ICIs) and more recently targeted agents for both FGFR and Nectin-4. FGFR3-aberrant and Nectin-4 expressing cells have been associated with an immunosuppressed phenotype. Given that less than half of all patients respond to these agents as monotherapies and less than 20% are eligible to receive salvage therapy, effective personalized treatment plans are critical. Typical biomarkers for ICIs such as PD-L1 and TMB have not been definitive in mUC, yet a biomarker-driven optimization of first-line therapy and subsequent sequencing have the potential to achieve higher and more durable response rates. The IO score is a 27-gene tumor immune microenvironment (TIME) classifier that has been associated with the clinical benefits of ICIs in multiple cancer types, including mUC. This study demonstrates that the IO score was associated with both progression-free survival (PFS) and overall survival (OS) in a real-world cohort of mUC patients treated with ICIs. Furthermore, the IO score was independent of and provided information incremental to TMB. Interestingly, the IO score predicted benefit in patients with high FGFR expression, despite conflicting data regarding response rates among the FGFR aberrant population. Taken together, these results demonstrate that the IO score assessment of the TIME is associated with a clinical benefit from ICI therapy and that this novel biomarker may inform therapeutic sequencing decisions in mUC, potentially improving outcomes for this notoriously difficult-to-treat disease.

Biomarkers of Airway Immune Homeostasis Differ Significantly with Generation of E-Cigarettes.

Rationale: Numerous studies have demonstrated that e-cigarettes can impact respiratory immune homeostasis; however, the extent of these effects remains an active area of investigation, and most previous studies were conducted with model systems or subjects exposed to third-generation e-cigarettes, such as vape pens and box mods. Objectives: Given the rise in popularity of nicotine-salt-containing pods and disposable e-cigarettes (fourth generation), we set out to better understand the respiratory effects of these newer e-cigarettes and compare their effects to early-generation devices. Methods: We collected induced sputum samples from a cohort of nonsmokers, smokers, third-generation e-cigarette users, and fourth-generation e-cigarette users (n = 20-30 per group) and evaluated the cellular and fluid-phase composition for markers of inflammation, host defense, and lung injury. Measurements and Main Results: Fourth-generation e-cigarette users had significantly more bronchial epithelial cells in the sputum, suggestive of airway injury. Concentrations of soluble intercellular adhesion molecule 1 (sICAM1) and soluble vascular cell adhesion molecule 1 (sVCAM1) were significantly lower in fourth-generation e-cigarette users in comparison with all other groups, and CRP (C-reactive protein), IFN-γ, MCP-1 (monocyte chemoattractant protein-1), MMP-2 (matrix metalloproteinase 2), uteroglobin, and VEGF (vascular endothelial growth factor) were significantly lower in fourth- versus third-generation e-cigarette users, suggestive of overall immune suppression in fourth-generation e-cigarette users. Predictive modeling also demonstrated clear separation between exposure groups, indicating that the overall mediator milieu is different between groups, particularly fourth-generation e-cigarette users. Conclusions: Our results indicate disrupted immune homeostasis in fourth-generation e-cigarette users and demonstrate that the biological effects of fourth-generation e-cigarette use are unique compared with those associated with previous-generation e-cigarettes.

5-Aza-2'-deoxycytidine advances the epithelial-mesenchymal transition of breast cancer cells by demethylating Sipa1 promoter-proximal elements.

Human breast cancer cells exhibit considerable diversity in the methylation status of genomic DNA CpGs that regulate metastatic transcriptome networks. In this study, we identified human Sipa1 promoter-proximal elements that contained a CpG island and demonstrated that the methylation status of the CpG island was inversely correlated with SIPA1 protein expression in cancer cells. 5-Aza-2'-deoxycytidine (5-Aza-CdR), a DNA methyltransferase inhibitor, promoted the expression of Sipa1 in the MCF7 breast cancer cells with a low level of SIPA1 expression. On the contrary, in MDA-MB-231 breast cancer cells with high SIPA1 expression levels, hypermethylation of the CpG island negatively regulated the transcription of Sipa1 In addition, the epithelial-mesenchymal transition (EMT) was reversed after knocking down Sipa1 in MDA-MB-231 cells. However, the EMT was promoted in MCF7 cells with over-expression of SIPA1 or treated with 5-Aza-CdR. Taken together, hypomethylation of the CpG island in Sipa1 promoter-proximal elements could enhance SIPA1 expression in breast cancer cells, which could facilitate EMT of cancer cells, possibly increasing a risk of cancer cell metastasis in individuals treated with 5-Aza-CdR.

Translation of the 27-gene immuno-oncology test (IO score) to predict outcomes in immune checkpoint inhibitor treated metastatic urothelial cancer patients.

BACKGROUND: The IO Score is a 27-gene immuno-oncology (IO) classifier that has previously predicted benefit to immune checkpoint inhibitor (ICI) therapy in triple negative breast cancer (TNBC) and non-small cell lung cancer (NSCLC). It generates both a continuous score and a binary result using a defined threshold that is conserved between breast and lung. Herein, we aimed to evaluate the IO Score's binary threshold in ICI-naïve TCGA bladder cancer patients (TCGA-BLCA) and assess its clinical utility in metastatic urothelial cancer (mUC) using the IMvigor210 clinical trial treated with the ICI, atezolizumab. METHODS: We identified a list of tumor immune microenvironment (TIME) related genes expressed across the TCGA breast, lung squamous and lung adenocarcinoma cohorts (TCGA-BRCA, TCGA-LUSQ, and TCGA-LUAD, 939 genes total) and then examined the expression of these 939 genes in TCGA-BLCA, to identify patients as having high inflammatory gene expression. Using this as a test of classification, we assessed the previously established threshold of IO Score. We then evaluated the IO Score with this threshold in the IMvigor210 cohort for its association with overall survival (OS). RESULTS: In TCGA-BLCA, IO Score positive patients had a strong concordance with high inflammatory gene expression (p < 0.0001). Given this concordance, we applied the IO Score to the ICI treated IMvigor210 patients. IO Score positive patients (40%) had a significant Cox proportional hazard ratio (HR) of 0.59 (95% CI 0.45-0.78 p < 0.001) for OS and improved median OS (15.6 versus 7.5 months) compared to IO Score negative patients. The IO Score remained significant in bivariate models combined with all other clinical factors and biomarkers, including PD-L1 protein expression and tumor mutational burden. CONCLUSION: The IMvigor210 results demonstrate the potential for the IO Score as a clinically useful biomarker in mUC. As this is the third tumor type assessed using the same algorithm and threshold, the IO Score may be a promising candidate as a tissue agnostic marker of ICI clinical benefit. The concordance between IO Score and inflammatory gene expression suggests that the classifier is capturing common features of the TIME across cancer types.

Validation of an app-based portable spirometer in adolescents with asthma.

OBJECTIVES: Objective measurements of asthma impairment could aid teens in recognition of changes in asthma status over time. Ready access to a conventional spirometer is not realistic outside of the clinical setting. In this proof-of-concept study, we compared the performance of the VitalFlo mobile spirometer to the nSpire KoKo® sx1000 spirometer for accuracy in measuring Forced Expiratory Volume in one second (FEV1) and Forced Vital Capacity (FVC) in adolescents with asthma. METHODS: Two hundred forty pulmonary function measurements were collected from 48 adolescents with persistent asthma from the University of North Carolina's pediatric allergy and pulmonology subspecialty clinics. Participants performed spirometry with the nSpireKoKo® sx1000 spirometer and the VitalFlo spirometer during their clinic visits. 119 simulated FVC maneuvers were conducted on both devices to standardize measurements. Pearson correlations, Bland-Altman procedure, and two-sample comparison tests were performed to assess the relationship between the two spirometers. RESULTS: VitalFlo measurements were significantly highly correlated with nSpireKoKo® spirometer values for FEV1, (r2=0.721, [95% CI, 0.749 ± 0.120], P < 0.001) and moderately for FVC (r2= 0.617, [95% CI, 0.640 ± 0.130], P < 0.001) measurements. There were no statistically significant differences of the mean FEV1 (M = 0.00764, SD = 0.364, t(59)=0.16, P = 0.87) and FVC measurements (M = 0.00261, SD = 0.565, t(59)=0.036, P = 0.97.) between the VitalFlo and nSpireKoKo® systems. Both devices demonstrated significantly high correlation when comparing the automated FVC (r2 = 0.997, [95% CI, 1.00 ± 0.00974], P < 0.001) measurements. Bland-Altman plots did not demonstrate significant bias between devices for both FEV1 (0.00764 L) and FVC (0.00261 L) measurements. CONCLUSIONS: Lung function measurements from the VitalFlo mobile spirometer were comparable to a commercially-available spirometer commonly used in clinical settings. This validated app-based spirometer for home use has the potential to improve asthma self-management.

Danger in the vapor? ECMO for adolescents with status asthmaticus after vaping.

Introduction: Electronic nicotine delivery systems (ENDS) use is on the rise in the adolescent and young adult populations, especially in the wake of sweet flavored ENDS solutions and youth-targeted marketing. While the extent of effect of ENDS use and aerosolized flavorings on airway epithelium is not known, there remains significant concern that use of ENDS adversely affects airway epithelial function, particularly in populations with asthma.Case Study: In this case series, we review two cases of adolescents with history of recent and past ENDS use and asthma who required veno-venous extracorporeal membrane oxygenation (VV-ECMO) for status asthmaticus in the year 2018.Results: Both patients experienced hypercarbic respiratory failure requiring VV-ECMO secondary to their status asthmaticus, with slow recovery on extensive bronchodilator and steroid regimens. They both recovered back to respiratory baseline and were counseled extensively on cessation of ENDS use.Conclusion: While direct causation by exposure to ENDS cannot be determined, exposure likely contributed to symptoms. Based on the severity of these cases and their potential relationship with ENDS use, we advocate for increased physician screening of adolescents for ENDS use, patient and parent education on the risks of use, and family cessation counseling.

Generation of an algorithm based on minimal gene sets to clinically subtype triple negative breast cancer patients.

BACKGROUND: Recently, a gene expression algorithm, TNBCtype, was developed that can divide triple-negative breast cancer (TNBC) into molecularly-defined subtypes. The algorithm has potential to provide predictive value for TNBC subtype-specific response to various treatments. TNBCtype used in a retrospective analysis of neoadjuvant clinical trial data of TNBC patients demonstrated that TNBC subtype and pathological complete response to neoadjuvant chemotherapy were significantly associated. Herein we describe an expression algorithm reduced to 101 genes with the power to subtype TNBC tumors similar to the original 2188-gene expression algorithm and predict patient outcomes. METHODS: The new classification model was built using the same expression data sets used for the original TNBCtype algorithm. Gene set enrichment followed by shrunken centroid analysis were used for feature reduction, then elastic-net regularized linear modeling was used to identify genes for a centroid model classifying all subtypes, comprised of 101 genes. The predictive capability of both this new "lean" algorithm and the original 2188-gene model were applied to an independent clinical trial cohort of 139 TNBC patients treated initially with neoadjuvant doxorubicin/cyclophosphamide and then randomized to receive either paclitaxel or ixabepilone to determine association of pathologic complete response within the subtypes. RESULTS: The new 101-gene expression model reproduced the classification provided by the 2188-gene algorithm and was highly concordant in the same set of seven TNBC cohorts used to generate the TNBCtype algorithm (87%), as well as in the independent clinical trial cohort (88%), when cases with significant correlations to multiple subtypes were excluded. Clinical responses to both neoadjuvant treatment arms, found BL2 to be significantly associated with poor response (Odds Ratio (OR) =0.12, p=0.03 for the 2188-gene model; OR = 0.23, p < 0.03 for the 101-gene model). Additionally, while the BL1 subtype trended towards significance in the 2188-gene model (OR = 1.91, p = 0.14), the 101-gene model demonstrated significant association with improved response in patients with the BL1 subtype (OR = 3.59, p = 0.02). CONCLUSIONS: These results demonstrate that a model using small gene sets can recapitulate the TNBC subtypes identified by the original 2188-gene model and in the case of standard chemotherapy, the ability to predict therapeutic response.

Mitochondrial mutations associated with aminoglycoside ototoxicity and hearing loss susceptibility identified by meta-analysis.

BACKGROUND: Genetic variations, including mitochondrial mutations, are important contributors to hearing loss, especially in children, and newborn genetic screens for hearing loss mutations are becoming increasingly common. Mitochondrial mutations have been linked with ototoxic responses to common antibiotics, therefore understanding the association of these mutations with hearing loss is of special importance. To address the usefulness of screening for these mutations in a clinical setting, we formed a collaboration of clinicians and geneticists to analyse the association of mitochondrial mutations with non-syndromic hearing loss, including the effect of ethnicity, audiological test methods and aminoglycoside exposure. METHODS: This survey identified 122 variants in 43 studies that have been assessed for an association with hearing loss, and meta-analysis was performed on clinically relevant subsets. RNA folding and conservation analysis further explored possible relevance of these variants. RESULTS: Among all studies, eight variants were found to have significant associations with hearing loss. A partially overlapping set of six variants had significant association with hearing loss when aminoglycoside exposure was assessed. Five of these variants predictive of sensitivity to aminoglycoside spatially co-localise in an RNA folding model. There was little effect of the audiological test method used to assess hearing loss on the association with the variants. CONCLUSIONS: Our results found a small set of studied variants had reproducible association with hearing loss, which will help clarify mutations useful in genetic screens for hearing loss. Several of the aminoglycoside exposure-associated mutations may co-localise on folded 12S rRNA, suggesting a functional association between these loci and aminoglycoside-induced hearing loss.

Expression of a-Tocopherol-Associated protein (TAP) is associated with clinical outcome in breast cancer patients.

BACKGROUND: The role of vitamin E in breast cancer prevention and treatment has been widely investigated, and the different tocopherols that comprise this nutrient have been shown to have divergent associations with cancer outcome. Our previous studies have shown that α-Tocopherol-associated protein (TAP), a vitamin E binding protein, may function as a tumor suppressor-like factor in breast carcinogenesis. The current study addresses the association of TAP expression with breast cancer clinical outcomes. METHODS: Immunohistochemical stain for TAP was applied to a tissue microarray from a breast cancer cohort consisting of 271 patients with a median follow-up time of 5.2 years. The expression of TAP in tumor cells was compared with patient's clinical outcome at 5 years after diagnosis. The potential role of TAP in predicting outcome was also assessed in clinically relevant subsets of the cohort. In addition, we compared TAP expression and Oncotype DX scores in an independent breast cancer cohort consisting of 71 cases. RESULTS: We demonstrate that the expression of TAP was differentially expressed within the breast cancer cohort, and that ER+/PR ± tumors were more likely to exhibit TAP expression. TAP expression was associated with an overall lower recurrence rate and a better 5-year survival rate. This association was primarily in patients with ER+ tumors; exploratory analysis showed that this association was strongest in patients with node-positive tumors and was independent of stage and treatment with chemotherapy. TAP expression in ER/PR negative or triple negative tumors had no association with clinical outcome. In addition, we did not observe an association between TAP expression and Oncotype DX recurrence score. CONCLUSIONS: The significant positive association we found for α-Tocopherol-associated protein with outcome in breast cancer may help to better define and explain studies addressing α-tocopherol's association with cancer risk and outcome. Additionally, further studies to validate and extend these findings may allow TAP to serve as a breast-specific prognostic marker in breast cancer patients, especially in those patients with ER+ tumors.

Acute Effect of E-Cigarette Inhalation on Mucociliary Clearance in E-Cigarette Users.

Background: Recent studies show e-cigarette (EC) users have increased rates of chronic bronchitic symptoms that may be associated with depressed mucociliary clearance (MCC). Little is known about the acute or chronic effects of EC inhalation on in vivo MCC. Methods: In vivo MCC was measured in young adult vapers (n = 5 males, mean age = 21) after controlled inhalation of a radiolabeled (Tc99m sulfur colloid) aerosol. Whole-lung clearance of radiolabeled deposited particles was measured over a 90-minute period for baseline MCC and associated with controlled periodic vaping over the first 60 minutes of MCC measurements. The vaping challenge was administered from a fourth generation box mod EC containing unflavored e-liquid (65% propylene glycol/35% vegetable glycerin, 3 mg/mL freebase nicotine). The challenge was administered at the start of each 10-minute interval of MCC measurements and consisted of 1 puff every 30 seconds for 5 minutes (i.e., 10 puffs for each 10-minute period for a total of 60 puffs during the initial 60 minutes of MCC measurements). Results: Compared with baseline, peripheral lung average clearance (%) over the 90 minutes of MCC measures was enhanced, associated with EC challenge, 12 (±6) versus 24 (±6), respectively (p < 0.05 by Wilcoxon signed-rank test). Conclusions: Acute enhancement of in vivo MCC during EC challenge is contrary to recent studies showing nicotine-associated slowing of ciliary beat and mucus transport at higher nicotine levels than those used here. However, our findings are consistent with an acute increase in fluid volume and mucin secretion to the bronchial airway surface that is likely short lived. Research reported in this publication was supported by the National Institutes of Health R01HL139369 and registered with ClinicalTrials.gov (NCT03700892).

The effects of flow settings during high-flow nasal cannula oxygen therapy for neonates and young children.

BACKGROUND: During neonatal and paediatric high-flow nasal cannula therapy, optimising the flow setting is crucial for favourable physiological and clinical outcomes. However, considerable variability exists in clinical practice regarding initial flows and subsequent adjustments for these patients. Our review aimed to summarise the impact of various flows during high-flow nasal cannula treatment in neonates and children. METHODS: Two investigators independently searched PubMed, Embase, Web of Science, Scopus and Cochrane for in vitro and in vivo studies published in English before 30 April 2023. Studies enrolling adults (≥18 years) or those using a single flow setting were excluded. Data extraction and risk of bias assessments were performed independently by two investigators. The study protocol was prospectively registered with PROSPERO (CRD42022345419). RESULTS: 38 406 studies were identified, with 44 included. In vitro studies explored flow settings' effects on airway pressures, humidity and carbon dioxide clearance; all were flow-dependent. Observational clinical studies consistently reported that higher flows led to increased pharyngeal pressure and potentially increased intrathoracic airway pressure (especially among neonates), improved oxygenation, and reduced respiratory rate and work of breathing up to a certain threshold. Three randomised controlled trials found no significant differences in treatment failure among different flow settings. Flow impacts exhibited significant heterogeneity among different patients. CONCLUSION: Individualising flow settings in neonates and young children requires consideration of the patient's peak inspiratory flow, respiratory rate, heart rate, tolerance, work of breathing and lung aeration for optimal care.

Impact of Breathing Pattern and Nebulization on Expelled Viral Content During Mechanical Ventilation Using an Ex Vivo Porcine Lung System.

BACKGROUND: Little is known about the fate of expelled viral particulates during the aerosolization of inhaled medications during mechanical ventilation. We hypothesized that breathing patterns that generate a greater degree of shear stress and turbulent air flow will produce a greater concentration of exhaled viral RNA with the presence of a nebulizer during mechanical ventilation. METHODS: Eight ex vivo pig lungs were utilized as the physiological model. Each lung was dedicated to a specific breathing pattern that consisted of tidal breathing, respiratory distress, cough, and sneeze. Breath simulations were carried out through a commercial mechanical ventilator. Ninety mL of a bacteriophage stock at a concentration of 108 PFU/mL were introduced into the lungs during a 10-min sample collection session. The number of viral particles collected in exhalate was measured using quantitative polymerase chain reaction. The impact of breathing pattern on measured viruses was analyzed through two-way analysis of variance. RESULTS: The interaction effect between nebulization and breath pattern on exhaled viral quantity was not statistically significant P = .80, partial η2 = 0.167. The analysis of the main effects indicated that the effects of the breathing pattern and nebulization phase were not statistically significant P = .26, partial η2 = 0.519; P = .98, partial η2 = 0, respectively. There were no statistically significant differences among the breathing patterns related to measurable viral RNA. Coughing produced the most measurable increase in measured viral quantity during the nebulization phase and non-nebulization phase with a mean exhaled viral quantity (3.5 × 105 ng/µL [95% CI 1.6 × 105-5.5 × 105] and 2.7 × 105 ng/µL [95% CI 7.1 × 103-5.5 × 105], respectively). Tidal breathing with the presence of a nebulizer and respiratory distress without a nebulizer produced the lowest measured viral quantities (M = 1.1 × 105 ng/µL [95% CI -1.7 × 105 to 3.9 × 105]; M = 1.2 × 105 ng/µL [95% CI -1.6 × 105 to 4.0 × 105]). CONCLUSIONS: In this ex vivo porcine model, the introduction of a nebulizer did not increase the mean viral RNA captured throughout all of the breathing patterns.

The selection and use of sorghum (Sorghum propinquum) bacterial artificial chromosomes as cytogenetic FISH probes for maize (Zea mays L.).

The integration of genetic and physical maps of maize is progressing rapidly, but the cytogenetic maps lag behind, with the exception of the pachytene fluorescence in situ hybridization (FISH) maps of maize chromosome 9. We sought to produce integrated FISH maps of other maize chromosomes using Core Bin Marker loci. Because these 1 Kb restriction fragment length polymorphism (RFLP) probes are below the FISH detection limit, we used BACs from sorghum, a small-genome relative of maize, as surrogate clones for FISH mapping. We sequenced 151 maize RFLP probes and compared in silico BAC selection methods to that of library filter hybridization and found the latter to be the best. BAC library screening, clone verification, and single-clone selection criteria are presented along with an example of transgenomic BAC FISH mapping. This strategy has been used to facilitate the integration of RFLP and FISH maps in other large-genome species.

Angiosarcoma: a study of 98 cases with immunohistochemical evaluation of TLE3, a recently described marker of potential taxane responsiveness.

Angiosarcomas may be primary in the skin, primary in soft tissue or viscera, or secondary to irradiation. All angiosarcomas have a poor prognosis. Taxanes may have efficacy in the treatment of angiosarcoma. Expression of TLE3 has been associated with improved outcome in taxane-treated breast cancers. We studied a series of angiosarcoma with TLE3 immunohistochemistry. Cases of angiosarcoma (98 total cases; 37 cutaneous, 48 soft tissue/visceral and 13 post-irradiation) were retrieved and follow up was obtained. Tumors were classified as 'vasoformative', 'spindled', 'epithelioid' and 'mixed'. TLE3 immunohistochemistry was performed. Statistical analyses were performed. Patients (50 males and 48 females) had a median age of 60.2 years. Tumors had a median size 7.5 cm and were vasoformative (N = 43, 44%), spindled (N = 21, 21%), epithelioid (N = 16, 16%) and mixed (N = 18, 18%). Follow up was available for 89/98 patients (91%): 32 (36%) were dead due to disease, 36 (41%) were dead due to other causes and 21 (24%) remained alive. The median time to death was 2.1 years. TLE3 reactivity was observed in 0/37 (0%) cutaneous angiosarcomas, in 28/48 (58%) cases from soft tissue/viscera and in 4/13 (31%) post-irradiation angiosarcomas. (p = <0.0001). Improved 5-year survival was seen in vasoformative angiosarcomas (p = 0.03). TLE3 expression was not associated with taxane response. However, only a subset of patients was treated with taxane. Our study confirms the poor prognosis of angiosarcoma. Vasoformative angiosarcoma may have a more favorable prognosis. A lack of TLE3 expression in cutaneous angiosarcoma may reflect differing pathogenesis.

A novel immuno-oncology algorithm measuring tumor microenvironment to predict response to immunotherapies.

Immune checkpoint inhibitor (ICI) therapies can improve clinical outcomes for patients with solid tumors, but relatively few patients respond. Because ICI therapies support an adaptive immune response, patients with an active tumor microenvironment (TME) may be more likely to respond, and thus biomarkers capable of discerning an active from a quiescent TME may be useful in patient selection. We developed an algorithm optimized for genes expressed in the mesenchymal and immunomodulatory subtypes of a 101-gene triple negative breast cancer model (Ring, BMC Cancer, 2016, 16:143) as a means to capture the immunological state of the TME. We compared the outcome of the algorithm (IO score) with the 101-gene model and found 88% concordance, indicating the models are correlated but not identical, and may be measuring different TME features. We found 92.5% correlation between IO scores of matched tumor epithelial and adjacent stromal tissues, indicating the IO score is not specific to these tissues, but reflects the TME as a whole. We observed a significant difference in IO score (p = 0.0092) between samples with high tumor-infiltrating lymphocytes and samples with increased neutrophil load, demonstrating agreement between IO score and these two prognostic markers. Finally, among non-small cell lung cancer patients receiving immunotherapy, we observed a significant difference in IO score (p = 0.0035) between responders and non-responders, and a significant odds ratio (OR = 5.76, 95% CI 1.30-25.51, p = 0.021), indicating the IO score can predict patient response. The immuno-oncology algorithm may offer independent and incremental predictive value over current biomarkers in the clinic.

Intron 3 16 bp duplication polymorphism of TP53 contributes to cancer susceptibility: a meta-analysis.

A few genetic polymorphisms of TP53 are known to have a significant effect on cancer susceptibility. Intron 3 16 bp duplication polymorphism of TP53 has been reported to be associated with breast cancer, colorectal cancer, lung cancer and other cancers, but the reported results remain inconclusive. The present study, a meta-analysis including a total of 9801 cases and 10,391 controls from 26 studies, revealed that the 16 bp insertion (Ins) allele is significantly associated with an increased cancer risk in overall analysis [Ins/Ins + deletion (Del)/Ins versus Del/Del: odds ratio (OR) = 1.14, 95% confidence interval (CI) = 1.02-1.27, P = 0.02; Ins/Ins versus Del/Del: OR = 1.35, 95% CI = 1.11-1.63, P = 0.002; Del/Ins versus Del/Del: OR = 1.10, 95% CI = 0.98-1.23, P = 0.11.), particularly in breast cancer subgroup (Ins/Ins + Del/Ins versus Del/Del: OR = 1.16, 95% CI = 1.03-1.31, P = 0.02; Ins/Ins versus Del/Del: OR = 1.81, 95% CI = 1.30-2.52, P < 0.001; Del/Ins versus Del/Del: OR = 1.10, 95% CI = 0.97-1.25, P = 0.13). The relative risks to the colorectal and lung cancers increased but their association power was relatively weak, which may result from a limited number of studies of these two cancer types. These results suggest that intron 3 16 bp duplication polymorphism of TP53 is potentially an important and clinically relevant genetic marker contributing to cancer susceptibility.

Mammostrat as a tool to stratify breast cancer patients at risk of recurrence during endocrine therapy.

INTRODUCTION: Patients with early-stage breast cancer, treated with endocrine therapy, have approximately 90% 5-year disease-free survival. However, for patients at higher risk of relapse despite endocrine therapy, additional adjuvant therapy, such as chemotherapy, may be indicated. The challenge is to prospectively identify such patients. The Mammostrat® test uses five immunohistochemical markers to stratify patients on tamoxifen therapy into risk groups to inform treatment decisions. We tested the efficacy of this panel in a mixed population of cases treated in a single center with breast-conserving surgery and long-term follow-up. METHODS: Tissue microarrays from a consecutive series (1981 to 1998) of 1,812 women managed by wide local excision and postoperative radiotherapy were collected following appropriate ethical review. Of 1,390 cases stained, 197 received no adjuvant hormonal or chemotherapy, 1,044 received tamoxifen only, and 149 received a combination of hormonal therapy and chemotherapy. Median age at diagnosis was 57, 71% were postmenopausal, 23.9% were node-positive and median tumor size was 1.5 cm. Samples were stained using triplicate 0.6 mm2 tissue microarray cores, and positivity for p53, HTF9C, CEACAM5, NDRG1 and SLC7A5 was assessed. Each case was assigned a Mammostrat risk score, and distant recurrence-free survival (DRFS), relapse-free survival (RFS) and overall survival (OS) were analyzed by marker positivity and risk score. RESULTS: Increased Mammostrat scores were significantly associated with reduced DRFS, RFS and OS in estrogen receptor (ER)-positive breast cancer (P < 0.00001). In multivariate analyses the risk score was independent of conventional risk factors for DRFS, RFS and OS (P < 0.05). In node-negative, tamoxifen-treated patients, 10-year recurrence rates were 7.6 ± 1.5% in the low-risk group versus 20.0 ± 4.4% in the high-risk group. Further, exploratory analyses revealed associations with outcome in both ER-negative and untreated patients. CONCLUSIONS: This is the fifth independent study providing evidence that Mammostrat can act as an independent prognostic tool for ER-positive, tamoxifen-treated breast cancer. In addition, this study revealed for the first time a possible association with outcome regardless of node status and ER-negative tumors. When viewed in the context of previous results, these data provide further support for this antibody panel as an aid to patient management in early-stage breast cancer.

Three common TP53 polymorphisms in susceptibility to breast cancer, evidence from meta-analysis.

The association of polymorphisms of tumor suppressor gene TP53 with breast cancer has widely been reported; however, the results are inconsistent. Here, we selected three commonly studied TP53 polymorphisms: codon 72 Arg > Pro, IVS3 16 bp Del/Ins, and IVS6 + 62A > G to explore their association with breast cancer risk by meta-analysis of published case-control studies. The results showed that codon 72 was not associated with breast cancer risk among 37 combined case-control studies (23,567 cases and 25,995 controls). However, a significant association with decreased risk of breast cancer was found in the Mediterranean studies (PP + PR vs. RR: OR = 0.32, 95% CI = 0.24-0.44, P < 0.001; PP vs. RR: OR = 0.35, 95% CI = 0.21-0.60, P < 0.001). IVS3 16 bp Del/Ins was significantly associated with an increased risk of developing breast cancer in a pooled 8 study dataset (2,470 cases and 2,825 controls; Ins/Ins + Del/Ins vs. Del/Del: OR = 1.15, 95% CI = 1.01-1.30, P = 0.04; Ins/Ins vs. Del/Del: OR = 1.75, 95% CI = 1.20-2.37, P = 0.003). No significant association was observed between IVS6 + 62A > G and breast cancer risk in a total of 10 studies (8,537 cases and 9,586 controls). These results suggest that IVS3 16 bp Del/Ins is likely an important genetic marker contributing to susceptibility of breast cancer, and codon 72 has a potential role in association with breast cancer risk within certain populations or regions.