Tumor immunogenomic signatures improve a prognostic model of melanoma survival

Background

Tumor mutation burden (TMB) has been associated with melanoma immunotherapy (IT) outcomes, including survival. We explored whether combining TMB with immunogenomic signatures recently identified by The Cancer Genome Atlas (TCGA) can refine melanoma prognostic models of overall survival (OS) in patients not treated by IT.

Methods

Cox proportional-hazards (Cox PH) analysis was performed on 278 metastatic melanomas from TCGA not treated by IT. In a discovery and two validation cohorts Cox PH models assessed the interaction between TMB and 53 melanoma immunogenomic features to refine prediction of melanoma OS.

Results

Interferon-γ response (IFNγRes) and macrophage regulation gene signatures (MacReg) combined with TMB significantly associated with OS (p = 8.80E−14). We observed that patients with high TMB, high IFNγRes and high MacReg had significantly better OS compared to high TMB, low IFNγRes and low MacReg (HR = 2.8, p = 3.55E−08). This association was not observed in low TMB patients.

Conclusions

We report a model combining TMB and tumor immune features that significantly improves prediction of melanoma OS, independent of IT. Our analysis revealed that patients with high TMB, high levels of IFNγRes and MacReg had significantly more favorable OS compared to high TMB patients with low IFNγRes and low MacReg. These findings may substantially improve current melanoma prognostic models.

Novel blood-based biomarker predicting severe toxicity in melanoma anti-CTLA-4 immunotherapy treatment

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Background: Immune checkpoint inhibition (ICI) has improved clinical outcomes of metastatic melanoma (MM). However, 65-80% of treated patients experience immune-related adverse events (irAEs), urging for the availability of personalized and easy-access clinical biomarkers. We have previously shown that germline genetics related to host immunity affects ICI response and MM survival. In this study, we investigated if germline immune-related expression quantitative trait loci (ieQTLs) may predict ICI-induced irAEs in MM. Methods: Through a comprehensive interrogation of a healthy twin-cohort expression dataset (MuTHER), we identified 40 ieQTLs most significantly associated with the expression of 382 immune-related genes. These germline variants were genotyped using the MassARRAY system in anti-CTLA-4-treated MM patients, collected as part of a multi-institutional collaboration. Using multivariable logistic regression models, we tested the association of 40 ieQTLs with irAEs in a discovery cohort of 97 MM patients followed by a validation in additional cohort of 97 anti-CTLA-4 treated patients. Results: We found rs7036417 significantly associated with severe anti-CTLA-4 irAEs in the discovery (OR = 6.18; 95%CI = 1.61-23.74; p = 0.007) and validation (OR = 6.73, 95%CI = 1.42-31.86; p = 0.02) cohorts. Pooled analysis showed that carriers of two rs7036417 alternate alleles (TT) have a 6-fold increased risk of developing severe irAEs (OR = 6.11; 95% = 2.26-16.56;p = 0.0003). This association was not observed with ICI response or survival. The alternate allele of rs7036417 is associated with higher expression of SYK (spleen-associated tyrosine kinase), suggesting that elevated SYK contributes to developing severe irAEs. Conclusions: We report that rs7036417, an ieQTL in SYK, associates with an increased risk of severe irAEs, independent of ICI efficacy. SYK plays an important role in B-cell/T-cell expansion and increased pSYK has been reported in patients with rheumatoid arthritis or systemic lupus erythematosus. Based on our data, the over-expression of SYK likely explains the biological mechanisms of the association between rs7036417 and anti-CTLA4 irAEs. These findings propose a novel blood-based baseline biomarker stratifying the patients at increased risk of severe irAEs, with a clinical effect substantially surpassing those observed for currently available predictors. Our ongoing studies are currently investigating SYK eQTL as a novel target in toxicity-reducing therapies.

Predicting the polyethylene wear rate in pin-on-disc experiments in the context of prosthetic hip implants: deriving a data-driven model using machine learning methods

Pin-on-disc (PoD) experiments are widely used to quantify and rank wear of different material couples for prosthetic hip implant bearings. However, polyethylene wear results obtained from different PoD experiments are sometimes difficult to compare, which potentially leaves information inaccessible. We use machine learning methods to implement several data-driven models, and subsequently validate them by quantifying the prediction error with respect to published experimental data. A data-driven model can supplement results from PoD wear experiments, and enables predicting polyethylene wear of new PoD experiments based on its operating parameters. It also reveals the relative contribution of individual PoD operating parameters to the resulting polyethylene wear, thus informing design of experiments, and potentially reducing the need for time consuming PoD wear measurements.

Friction between a polyethylene pin and a microtextured CoCrMo disc, and its correlation to polyethylene wear, as a function of sliding velocity and contact pressure, in the context of metal-on-polyethylene prosthetic hip implants

The longevity of metal-on-polyethylene prosthetic hip implant bearings, in which a polished CoCrMo femoral head articulates with a polyethylene liner, is limited by mechanical instability or inflammation resulting from osteolysis caused by polyethylene wear debris. We use pin-on-disc experiments to measure friction and wear of a polyethylene pin that articulates with different microtextured CoCrMo surfaces, covering a wide range of operating conditions including sliding velocity and contact pressure. We determine how the lubrication regime changes as a function of operating conditions, and show that the microtexture accelerates the transition from boundary to elastohydrodynamic lubrication. Additionally, we illustrate that the microtexture could enable tailoring the hip implant to the specific patient needs based on activity level, gender, and age.

Using a patterned microtexture to reduce polyethylene wear in metal-on-polyethylene prosthetic bearing couples

The longevity of metal-on-polyethylene prosthetic hip joint bearings, in which a CoCrMo femoral head articulates with a polyethylene liner, is often limited by polyethylene wear and osteolysis caused by polyethylene wear particles. Current approaches to reduce polyethylene wear include improving the mechanical properties of the polyethylene liner, and/or manufacturing ultra-smooth articulating surfaces. In contrast, this experimental work shows that adding a patterned microtexture of concave "dimples" to a polished CoCrMo surface significantly reduces polyethylene wear by promoting the formation of an elastohydrodynamic lubricant film, which reduces contact between the CoCrMo and polyethylene bearing surfaces. Using a gravimetric method to measure polyethylene pin wear during pin-on-disc experiments, it was demonstrated that microtextured CoCrMo caused reduced polyethylene wear compared to polished CoCrMo surfaces. Wear was quantified for different polyethylene materials currently used in commercial prosthetic hip joint bearings, and for several microtexture geometries. It was also documented by correlating polyethylene wear with surface topography measurements that the patterned microtexture reduced contact between the articulating bearing surfaces.

Co-treatment with a C1B5 peptide of protein kinase Cγ and a low dose of gemcitabine strongly attenuated pancreatic cancer growth in mice through T cell activation

Although gemcitabine is an effective chemotherapeutic for pancreatic cancer, severe side effects often accompany its use. Since we have discovered that locally administered C1B domain peptides effectively control tumor growth without any side effects, the efficacy of co-treatment with this peptide and a low dose of gemcitabine on the growth of pancreatic cancer was examined. Two- and three-dimensional cell culture studies clarified that a co-treatment with C1B5 peptide and gemcitabine significantly attenuated growth of PAN02 mouse and PANC-1 human pancreatic cancer cells in 2D and 3D cultures. Although treatment with the low dose of gemcitabine alone (76%) or the C1B5 peptide alone (39%) inhibited tumor growth moderately, a co-treatment with C1B5 peptide and a low dose of gemcitabine markedly inhibited the growth of PAN02 autografts in the mouse peritoneal cavity (94% inhibition) without any noticeable adverse effect. The number of peritoneal cavity-infiltrating neutrophils and granzyme B⁺ lymphocytes was significantly higher in the co-treatment group than in the control group. A significant increase of granzyme B mRNA expression was also detected in human T cells by the co-treatment. Taken together, the current study suggests that C1B5 peptide offers a remarkably effective combination treatment strategy to reduce side effects associated with gemcitabine, without losing its tumoricidal effect.

Implications of subcutaneous or intravenous delivery of trastuzumab; further insight from patient interviews in the PrefHer study

BACKGROUND

The 2 Cohort randomised PrefHer trial examined the preferences of HER2+ve primary breast cancer patients for intravenous (IV) or subcutaneous (SC) delivery of trastuzumab via a Single Injectable Device (SID) or hand-held syringe (HHS). The novel approach and design of the study permitted an in-depth exploration of patients' experiences, the impact that different modes of delivery had on patients' well-being and implications for future management.

METHODS

The preferences, experiences and general comments of patients in the PrefHer study were collected via specific semi-structured interview schedules. Exploratory analyses of data were conducted using standard methodology. The final question invited patients to make further comments, which were divided into 9 thematic categories - future delivery, compliments, time/convenience, practical considerations, pain/discomfort, study design, side-effects, psychological impact, and perceived efficacy.

RESULTS

267/467 (57%) patients made 396 additional comments, 7 were neutral, 305 positive and 86 negative. The three top categories generating the largest number of comments were compliments and gratitude about staff and being part of PrefHer (75/396; 19%), the potential future delivery of SC trastuzumab (73/396; 18%), and practical considerations about SC administration (60/396; 15%).

CONCLUSIONS

Eliciting patient preferences about routes of administration of drugs via comprehensive interviews within a randomised cross-over trial yielded rich and important information. The few negative comments made demonstrated a need for proper staff training in SC administration Patients were grateful to have been part of the trial, and would have liked to continue with SC delivery. The possibility of home administration in the future also seemed acceptable.

EUDRACT NUMBER

2010-024099-25.

ARIX: a randomised trial of acupuncture v oral care sessions in patients with chronic xerostomia following treatment of head and neck cancer

BACKGROUND

Radiation treatment of head and neck cancer can cause chronic xerostomia which impairs patients' quality of life. The study reported here examined the efficacy of acupuncture in alleviating xerostomia symptoms especially dry mouth.

PATIENTS AND METHODS

A total of 145 patients with chronic radiation-induced xerostomia >18 months after treatments were recruited from seven UK cancer centres. The study employed a randomised crossover design with participants receiving two group sessions of oral care education and eight of acupuncture using standardised methods. Patient-reported outcome (PROs) measures were completed at baseline and weeks 5, 9, 13, 17, and 21. The primary outcome was improvement in dry mouth.

OBJECTIVE

saliva measurements were also carried out.

RESULTS

Acupuncture compared with oral care, produced significant reductions in patient reports of severe dry mouth (OR = 2.01, P = 0.031) sticky saliva (OR = 1.67, P = 0.048), needing to sip fluids to swallow food (OR = 2.08, P = 0.011) and in waking up at night to drink (OR = 1.71, P = 0.013). There were no significant changes in either stimulated or unstimulated saliva measurements over time.

CONCLUSION

Eight sessions of weekly group acupuncture compared with group oral care education provide significantly better relief of symptoms in patients suffering from chronic radiation-induced xerostomia.

A method for the automated mapping of laboratory results to LOINC

LOINC is emerging as the standard for laboratory result names, and there is great interest in mapping legacy terms from laboratory systems to it. However, the mapping task is non-trivial, requiring significant resource commitment and a good understanding of the LOINC identifying attributes for the laboratory result names. Because the number of results in a laboratory system may range from around 500 to 2000 or more, manual, one-by-one matching, even with the aid of the RELMA matching tool provided by LOINC, is time consuming and laborious. Moreover, human variation may introduce mapping inconsistencies or errors. Through our experience mapping the results from a variety of laboratory systems to LOINC, an automated mapping method has been developed and is described in this paper. This method allows for data from the laboratory information system to be provided in a manner familiar to the submitting technician, and makes use of parsing and logic rules, combined with synonyms, attribute relationships and mapping frequency data, to perform automated matching to LOINC.

Quantitative high-performance liquid chromatography determination of ICI 125,211 in plasma

A rapid, specific and quantitative high-performance liquid chromatography assay procedure is described for the determination of ICI 125, 211, (I), a guanidino-thiazole H2-receptor antagonist, in small samples of animal plasma. A 0.2 mL aliquot of plasma is extracted at pH 9 with ethyl acetate. After reconstitution in mobile phase, the sample is run on a silica column using ultraviolet detection at 280 nm. The procedure utilizes ICI 125, 253, (II), an analogous compound as the internal standard. The assay is linear (r2 = 0.99) and the recovery is 97.6 +/- 6.38% over a concentration range of 0.050-5.00 microgram/mL. Detection of levels as low as 0.025 microgram/mL has been documented in some animal study samples. Typical day-to-day precision is 3-9%, relative, for triplicate determinations of four concentrations in the 0.050-0.500 microgram/mL concentration range. Compound (I) is stable in whole blood for at least two hours at room temperature. Plasma concentrations remain constant for at least 48 hours at room temperature and six months at -5 degrees C. The whole blood/plasma ratio averages 0.97 +/- .073 for dog blood (N = 5). Pharmacokinetic data gathered for two dogs dosed orally with an HPMC-TWEEN 80 suspension of (I) at 40 mg/kg gave elimination half-life values of 4.3 and 7.4 hours. The specificity of the HPLC procedure has been confirmed by mass spectrometry.

Electron-capture GLC determination of nanogram to picogram amounts of isosorbide dinitrate

A GLC method for the determination of plasma isosorbide dinitrate using electron-capture detection is described. The organic nitrates are especially suited for electron-capture detection if the detector temperature is optimized for maximum sensitivity, e.g., 175 degrees. Proper maintenance of the detector and column assures reproducible data in the low nanogram range. The extraction procedure described is simple, efficient, and expedient for processing large numbers of samples. The method was used to study plasma levels in four human volunteers after a single dose of a 5-mg chewable isosorbide dinitrate tablet. Concentration levels of isosorbide dinitrate as low as 0.5 ng/ml of plasma can be measured by this procedure.