Identification of candidate mediators of chemoresponse in breast cancer through therapy-driven selection of somatic variants

Purpose: More than a third of primary breast cancer patients are treated with cytotoxic chemotherapy, typically without guidance from predictive markers. Increased use of neoadjuvant chemotherapy provides opportunities for identification of molecules associated with treatment response, by comparing matched tumour samples before and after therapy. Our hypothesis was that somatic variants of increased prevalence after therapy promote resistance, while variants with reduced prevalence cause sensitivity. Methods: We performed systematic analyses of matched pairs of cancer exomes from primary oestrogen receptor-positive/HER2-negative breast cancers (n = 6) treated with neoadjuvant epirubicin/cyclophosphamide. We identified candidate genes as mediators of chemotherapy response by consistent subclonal changes in somatic variant prevalence through therapy, predicted variant impact on gene function, and enrichment of specific functional pathways. Influence of candidate genes on breast cancer outcome was tested using publicly available breast cancer expression data (n = 1903). Results: We identified 14 genes as the strongest candidate mediators of chemoresponse: TCHH, MUC17, ARAP2, FLG2, ABL1, CENPF, COL6A3, DMBT1, ITGA7, PLXNA1, S100PBP, SYNE1, ZFHX4, and CACNA1C. Genes contained somatic variants showing prevalence changes in up to 4 patients, with up to 3 being predicted as damaging. Genes coding for extra-cellular matrix components or related signalling pathways were significantly over-represented among variants showing prevalence changes. Expression of 5 genes (TCHH, ABL1, CENPF, S100PBP, and ZFHX4) was significantly associated with patient survival. Conclusions: Genomic analysis of paired pre- and post-therapy samples resulting from neoadjuvant therapy provides a powerful method for identification of mediators of response. Genes we identified should be assessed as predictive markers or targets in chemo-sensitization

Genomic and expression analyses define MUC17 and PCNX1 as predictors of chemotherapy response in breast cancer

Poor prognosis breast cancers are treated with cytotoxic chemotherapy, but often without any guidance from therapy predictive markers since universally-accepted markers are not currently available. Treatment failure, in the form of recurrences, is relatively common. We aimed to identify chemotherapy predictive markers and resistance pathways in breast cancer. Our hypothesis was that tumour cells remaining after neoadjuvant chemotherapy (NAC) contain somatic variants causing therapy resistance, while variants present pre-NAC but lost post-NAC cause sensitivity. Whole exome sequencing was performed on matched pre- and post-NAC cancer cells, which were isolated by laser microdissection, from 6 cancer cases, and somatic variants selected for or against by NAC were identified. Somatic variant diversity was significantly reduced after therapy (p<0.05). MUC17 variants were identified in 3 tumours and were selected against by NAC in each case, while PCNX1 variants were identified in 2 tumours and were selected for in both cases, implicating the function of these genes in defining chemoresponse. In vitro knock-down of MUC17 or PCNX1 was associated with significantly increased or decreased chemotherapy sensitivity respectively (p<0.05), further supporting their roles in chemotherapy response. Expression was tested for predictive value in two independent cohorts of chemotherapy-treated breast cancers (n=53, n=303). Kaplan-Meier analyses revealed that low MUC17 expression was significantly associated with longer survival after chemotherapy, while low PCNX1 was significantly associated with reduced survival. We concluded that therapy-driven selection of somatic variants allows identification of chemotherapy response genes. With respect to MUC17 and PCNX1, therapy-driven selection acting on somatic variants, in vitro knock-down data concerning drug sensitivity, and survival analysis of expression levels in patient cohorts all define the genes as mediators of and predictive markers for chemotherapy response in breast cancer

Medication adherence among diabetic and hypertensive patients in Al-Qassim region of Saudi Arabia

Non-adherence to medication is often an unrecognized risk factor that contributes to failure of the therapeutic plan. The purpose of the study was to identify factors related to high, medium and low medication adherence among adult Saudi patients with hypertension and diabetes mellitus. This study is designed as a descriptive cross sectional survey and was conducted in three tertiary care hospitals of Al-Qassim province of Saudi Arabia. The data was collected using the 8-item Morisky Medication Adherence Scale (MMAS-8) and analyzed by SPSS. Three levels of adherence were considered based on the following scores: 0 to <6 (low); 6 to <8 (medium); 8 (high). Of the 396 patients interviewed, 52% reported low adherence to prescribed medication. Multinomial logistic regression analysis was conducted. Gender, age, literacy level, duration of illness and type of chronic disease were negatively associated with medication adherence. The study shows very high proportion of low and medium adherence on long term medication, which may be responsible for the failure of achieving therapeutic outcome. Further investigation is required to evaluate the applicability of MMAS-8 as a tool of measuring medication adherence among Saudi patients with chronic diseases. Adherence enhancing strategies should also be evaluated in separate patients group

Global patient outcomes after elective surgery: prospective cohort study in 27 low-, middle- and high-income countries.

BACKGROUND: As global initiatives increase patient access to surgical treatments, there remains a need to understand the adverse effects of surgery and define appropriate levels of perioperative care. METHODS: We designed a prospective international 7-day cohort study of outcomes following elective adult inpatient surgery in 27 countries. The primary outcome was in-hospital complications. Secondary outcomes were death following a complication (failure to rescue) and death in hospital. Process measures were admission to critical care immediately after surgery or to treat a complication and duration of hospital stay. A single definition of critical care was used for all countries. RESULTS: A total of 474 hospitals in 19 high-, 7 middle- and 1 low-income country were included in the primary analysis. Data included 44 814 patients with a median hospital stay of 4 (range 2-7) days. A total of 7508 patients (16.8%) developed one or more postoperative complication and 207 died (0.5%). The overall mortality among patients who developed complications was 2.8%. Mortality following complications ranged from 2.4% for pulmonary embolism to 43.9% for cardiac arrest. A total of 4360 (9.7%) patients were admitted to a critical care unit as routine immediately after surgery, of whom 2198 (50.4%) developed a complication, with 105 (2.4%) deaths. A total of 1233 patients (16.4%) were admitted to a critical care unit to treat complications, with 119 (9.7%) deaths. Despite lower baseline risk, outcomes were similar in low- and middle-income compared with high-income countries. CONCLUSIONS: Poor patient outcomes are common after inpatient surgery. Global initiatives to increase access to surgical treatments should also address the need for safe perioperative care. STUDY REGISTRATION: ISRCTN5181700

Crustal and Upper Mantle Structures Beneath the Arabian Shield and Red Sea

The Arabian Shield and Red Sea region is considered one of only a few places in the world undergoing active continental rifting and formation of new oceanic lithosphere. We determined the seismic velocity structure of the crust and upper mantle beneath this region using broadband seismic waveform data. We estimated teleseismic receiver functions from high-quality waveform data. The raw data for RF analysis consist of 3-component broadband velocity seismograms for earthquakes with magnitudes Mw > 5.8 and epicentral distances between 30° and 90°. We performed several state-of-the-art seismic analyses of the KACST and SGS data. Teleseismic P- and S-wave travel time tomography provides an image of upper mantle compressional and shear velocities related to thermal variations. We present a multi-step procedure for jointly fitting surface-wave group-velocity dispersion curves (from 7 to 100 s for Rayleigh and 20 to 70 s for Love waves) and teleseismic receiver functions for lithospheric velocity structure. The method relies on an initial grid search for a simple crustal structure, followed by a formal iterative inversion, an additional grid search for shear wave velocity in the mantle and finally forward modeling of transverse isotropy to resolve surface-wave dispersion discrepancy. Inversions of receiver functions have poor sensitivity to absolute velocities. To overcome this shortcoming we have applied the method of Julia et al. (Geophys J Int 143:99–112, 2000), which combines surface-wave group velocities with receiver functions in formal inversions for crustal and uppermost mantle velocities. The resulting velocity models provide new constraints on crustal and upper mantle structure in the Arabian Peninsula. While crustal thickness and average crustal velocities are consistent with many previous studies, the results for detailed mantle structure are completely new. Finally, teleseismic shear-wave splitting was measured to estimate upper mantle anisotropy. These analyses indicate that stations near the Gulf of Aqabah display fast orientations that are aligned parallel to the Dead Sea Transform Fault, most likely related to the strike-slip motion between Africa and Arabia. The remaining stations across Saudi Arabia yield statistically the same result, showing a consistent pattern of north-south oriented fast directions with delay times averaging about 1.4 s. The uniform anisotropic signature across Saudi Arabia is best explained by a combination of plate and density driven flow in the asthenosphere. By combining the northeast oriented flow associated with absolute plate motion with the northwest oriented flow associated with the channelized Afar plume along the Red Sea, we obtain a north-south oriented resultant that matches our splitting observations and supports models of the active rifting processes. This explains why the north-south orientation of the fast polarization direction is so pervasive across the vast Arabian Plate. Seafloor spreading in the Red Sea is non-uniform, ranging from nearly 0.8 cm/a in the north to about 2 cm/a in the south. The Moho and LAB are shallowest near the Red Sea and become deeper towards the Arabian interior. Near the coast, the Moho is at a depth of about 22–25 km. Crustal thickening continues until an average Moho depth of about 35–40 km is reached beneath the interior Arabian Shield. The LAB near the coast is at a depth of about 55 km; however, it also deepens beneath the Shield to attain a maximum depth of 100–110 km. At the Shield-Platform boundary, a step is observed in the lithospheric thickness where the LAB depth increases to about 160 km. This study supports multi plume model, which states that there are two separated plumes beneath the Arabian Shield, and that the lower velocity zones (higher temperature zones) are related to volcanic activities and topographic characteristics on the surface of the Arabian Shield. In addition, our results suggest a two-stage rifting history, where extension and erosion by flow in the underlying asthenosphere are responsible for variations in LAB depth. LAB topography guides asthenospheric flow beneath western Arabia and the Red Sea, demonstrating the important role lithospheric variations play in the thermal modification of tectonic environments

Tyrosine kinase domain mutations of EGFR gene in head and neck squamous cell carcinoma

Chittibabu Vatte,1 Ali M Al Amri,2 Cyril Cyrus,1 Shahanas Chathoth,1 Sadananda Acharya,3 Tariq Mohammad Hashim,4 Zhara Al Ali,2 Saleh Tawfeeq Alshreadah,2 Ahmed Alsayyah,4 Amein K Al-Ali5 1Department of Genetic Research, Institute for Research and Medical Consultation, University of Dammam, Dammam, 2Department of Internal Medicine, King Fahd Hospital of the University, University of Dammam, Al-Khobar, 3Department of Stemcell Research, Institute for Research and Medical Consultation, 4Department of Pathology, King Fahd Hospital of the University, University of Dammam, Al-Khobar, 5Department of Biochemistry, College of Medicine, University of Dammam, Dammam, Kingdom of Saudi Arabia Background: Epidermal growth factor receptor (EGFR) is a commonly altered gene that is identified in various cancers, including head and neck squamous cell carcinoma (HNSCC). Therefore, EGFR is a promising molecular marker targeted by monoclonal antibodies and small molecule inhibitors targeting the tyrosine kinase (TK) domain. Objective: The objective of this study was to investigate the spectrum of mutations in exons 18, 19, 20, and 21 of the EGFR gene in HNSCC patients. Materials and methods: This retrospective study included 47 confirmed HNSCC cases. Mutations in the TK domain, exons 18, 19, 20, and 21 of the EGFR gene, were detected by Scorpion&reg; chemistry and ARMS&reg; technologies on Rotor-Gene Q real-time polymerase chain reaction.Results: The tumors exhibited EGFR-TK domain mutations in 57% of cases. Four cases of T790M mutations were reported for the first time among HNSCC patients. Out of the total mutations, L861Q (exon 21), exon 20 insertions and deletions of exon 19 accounted for the majority of mutations (21%, 19%, and 17%, respectively). EGFR mutation status was correlated with the higher grade (P=0.026) and advanced stage (P=0.034) of HNSCC tumors.Conclusion: Higher frequency of EGFR-TK domain mutations together with the presence of the T790M mutation suggests that identification of these mutations might streamline the therapy and provide a better prognosis in HNSCC cases. Keywords: somatic mutations, insertions, deletions, T790M, therapy, real-time PC