Epidermal growth factor receptor and anaplastic lymphoma kinase mutations detected by immunohistochemistry in lung adenocarcinoma in patients from Johannesburg

A research report submitted to the Faculty of Health Sciences, University of the Witwatersrand, in partial fulfilment of the requirement for the degree of Master of Medicine in Anatomical PathologyLung cancer is the leading cause of cancer related death worldwide. Despite the availability of conventional cytotoxic chemotherapy, prognosis even with treatment is poor. Treatment targeted to specific molecular alterations called Tyrosine kinase inhibitors (TKI) has been found to be effective in certain subtypes of non small cell carcinoma (NSCC) that have the epidermal growth factor receptor (EGFR) gene mutation and the anaplastic lymphoma kinase (ALK) translocation. EGFR mutations are seen in 18-25% of lung adenocarcinomas (AC)s and are represented in more than 90% of cases by the E746_A750 deletion on exon 19 and the L858R point mutation on exon 21. The ALK translocation is seen in 2-7% of lung cancers, and involves the EML4-ALK fusion gene product. Immunohistochemistry (IHC) has the potential of being used as an initial screening tool that can facilitate a shorter diagnostic time and fast track treatment options. Little is known about the mutational status of patients with these mutations in South Africa. This study examines the use of IHC as a means of detecting the most common EGFR mutations and the ALK translocation in lung cancer. Method: Biopsies of patients from the Charlotte Maxeke Johannesburg Academic Hospital (CMJAH) and Helen Joseph Hospital (HJH) sent to the National Institute for Occupational Health (NIOH) from 1st January 2008 to 30th June 2014 were reviewed. A total of 3901 histology reports were accessed. There were 297 lung carcinomas comprising 117 (39%) ACs and 128 (46%) squamous carcinomas (SCC)s. A total of 119 biopsies comprising 107 ACs (90%), 4 (3%) adenosquamous carcinomas (ADSCC)s, 1 (1%) large cell carcinoma (LC) and 7 (6%) NSCC (nos.) comprised the cohort. One hundred and eleven biopsies were available for mutational analysis, as 8 biopsies were excluded due to insufficient tissue availability. The mutation specific antibodies, EGFR SP111 and EGFR SP125 were used to detect the E746_A750 deletion and the L858R point mutations respectively. The high affinity ALK D5F3 antibody was used for the detection of the EML4-ALK translocation. Results: The majority of patients in the study were Black males (61%). There were no Asians. The mean age was 58 years with a SD of 11.5. Most patients (76%) were younger than 65 years. The EGFR IHC stain was positive in 10/111 (9%) biopsies, of v which 8 were from Blacks, 6 were from males, 4 were from smokers and 2 were from non-smokers. There was however no significant difference between the proportions of Black or White and male or female among those who tested positive to EGFR and those who tested negative (p>0.05) and no significant association was found between the variables age, sex and smoking history (p>0.05). The ALK IHC was positive in 8 (7%) patients. All 8 patients were Black, six were male, four had a smoking history and two patients were non-smokers. A significant association was found between race and positive ALK IHC (p=0.03). There was no significant association with age (p=0.081). The acinar growth pattern was found in 80% of the EGFR IHC positive biopsies, with 10% of biopsies showing either lepidic, solid or micropapillary patterns. Although several growth patterns were seen in ALK IHC positive biopsies, there was a slight predominance of the acinar and solid growth patterns. Discussion: The EGFR IHC was positive in 9% of patients, which is half the number of cases described in literature from Western and Eastern countries, where the prevalence is usually more than 18%. There may be several reasons for the lower rate of EGFR IHC positivity. Antigen degradation, intratumoral heterogeneity and a low sensitivity of the EGFR IHC antibody may have contributed. The demographic profile of patients with positive result following EGFR IHC differs from the literature although the results were not found to be statistically significant. The sensitivity of the EGFR IHC test as described in the literature ranges from as low as 61% to 100%. A good correlation between EGFR IHC and EGFR polymerase chain reaction, in confirming the presence of the EGFR mutation, is described with biopsies that show strong positive cytoplasmic staining with IHC. Strong positive cytoplasmic staining with EGFR IHC was found in these 10 biopsies. The ALK IHC result was positive in 7% of patients, which is on the upper limit of the 2-7% rate recorded in most literature. A significant association was found with Blacks. Although an association with younger patients and the ALK mutation was found, this was not statistically significant. As ALK IHC is associated with an almost 100% sensitivity and specificity, there is a possibility that the ALK mutational rate in South African Black patients may be higher than the rate in other international populations. SCC is the more common subtype of lung cancer (46%) compared to AC vi (39%) in this group of patients from Johannesburg. This differs from studies in Cape Town and international studies, where a shift in trend from SCC to AC is observed. Conclusion: This study confirms the presence of the EGFR mutation and ALK translocation in patients with adenocarcinoma from Johannesburg using immunohistochemistry. We have proposed a diagnostic algorithm for patients with lung cancer in South Africa where EGFR IHC and ALK IHC can be used as rapid initial screening tests to identify patients with the EGFR mutation and ALK translocation respectively, provided established guidelines for IHC interpretation are followed. This approach allows patients with lung cancer who have the EGFR and ALK mutations to be fast tracked towards receiving targeted therapy.GR201

The future is a zero-carbon building sector: Perspectives from Durban, South Africa

The built environment is a critical part of the climate change problem in cities, and urban buildings can act as a scaled response to mitigating anthropogenic climate change. Buildings last for well beyond a hundred years and thus have the potential to provide cities with a healthier and safer environment for urban dwellers well into the future. The role of the building sector toward reducing greenhouse gas (GHG) emissions is now better understood, and has resulted in various initiatives globally to move toward being a net-zero carbon sector. The objective of this study was to provide an assessment of the costs in achieving the emissions-reduction potential for each high-emitting sector in the eThekwini Municipality (KwaZulu-Natal, South Africa) through the determination of a marginal abatement cost curve (MACC). The MACC was developed for 2030, 2040, and 2050 across key sectors and aligned with the approach used by the eThekwini Municipality by employing the GHG Protocol’s BASIC level of reporting that excludes the Agriculture, Forestry, and Other Land-use (AFLOU) and Industrial Processes and Product Use (IPPU) sectors. We found that the building sector offers the lowest cost to mitigate each tonne of GHGs when compared to other sectors in the eThekwini Municipality. Several interventions within the building sector further display positive payback periods throughout its life cycle. The MACC produced in this study is the first of its kind for any municipality in South Africa and will provide insights into the net cost of interventions that would mitigate a tonne of carbon emissions.  Significance: The MACC produced in this study is the first of its kind for any municipality in South Africa. Developing a MACC adds to an important basket of factors that need to be considered when planning for future climates in cities and is of benefit in prioritising actions in addressing climate change. The MACC in this study demonstrates that energy efficiency interventions in the building sector offer substantial mitigation potential within the most feasible payback periods when compared to other sectors. The MACC may be replicated by other municipalities, to support the prioritisation of actions needed to address climate change

A simple micro method for determination of plasma levels of alpha tocopherol (Vitamin E) in Pakistani normal adults.

A relatively simple spectrophotometeric method has been developed for the determination of alpha tocopherol in human plasma. Method is modification of a previous micromethod base on oxidation of alpha tocopherol by ferric chloride. The complex of ferrous ions (generated in this reaction) with bathophenanthroline is determined spectrophotometrically at 536 nm. The absorbance of this colored complex is directly proportional to concentration of alpha tocopherol. The method involves extraction of alpha tocopherol from human plasma using n-hexane which is relatively less toxic than xylene. The assay is sensitive enough to detect as little as 0.2 mug of vitamin. The recovery of alpha tocopherol from the plasma using n-hexane was in the range of 75% - 100%. The mean values of intra-assay and interassy coefficient of variation were found to be 5.3% and 13%, respectively. The assay was used to monitor alpha tocopherol levels in plasma samples of 81 normal healthy adults. Mean concentration of plasma alpha tocopherol in these normal healthy adults was found to be 9.45+/-2.64 microg/ ml. Sixteen percent of adults had low levels of alpha tocopherol. The method is rapid, convenient, reproduciable and relatively less hazardous compared to methods using xylene for the extraction of vitamin E. It can be routinely used to analyze as many as 20 plasma samples in about 2 hours time

Relaparotomy after caesarean section: an analysis of the risk factors, indications and outcome

Background: Aim of this study was to establish the incidence of post caesarean laparotomy and identify the risk factors, indications and management.Methods: We conducted a retrospective observational study in a tertiary care hospital in North Kerala from January 1, 2011 to December 31, 2014 of the twenty seven cases which required relaparotomy following caesarean section.Results: In our study there were a total of 20928 caesarean deliveries and 27 cases required exploratory laparotomy following caesarean section. Majority of the cases were following emergency caesarean section, 23 cases (85.19%). The most common indication for the caesarean section was failure to progress in labour in 8 cases (29.63%). Relaparotomy was done within 24 hours after caesarean in 23 cases (85.19%). Regarding the indication of relaparotomy, 5 cases were due to atonic postpartum hemorrhage (18.52%) and 4 cases (14.81%) due to traumatic PPH. Intraperitoneal hemorrhage was seen in 12 cases (44.44%). Hysterectomy was required in a total of 21 cases (77.78%), of which 14 had total hysterectomy (66.67%). Third laparotomy following the relaparotomy was required in one case. Regarding postoperative complications, 8 cases (29.63%) required mechanical ventilation and 4 cases (14.81%) developed multiorgan failure. There were 5 cases of maternal death (18.52%).Conclusions: Decision to proceed for early reoperation after caesarean section is a real challenge. Indication of the primary surgery, patient’s preoperative condition and indication for relaparotomy will influence the outcome. Assuring meticulous hemostasis before closure is very important, as postpartum hemorrhage was the most common indication for relaparotomy. It is also important that relaparotomy should be done in centres with efficient blood transfusion facilities in order to reduce the morbidity and mortality

Cardiovascular safety of dipeptidyl peptidase-4 inhibitors in patients with type 2 diabetes mellitus

Objective: The proposed study will examine the association between the dipeptidyl peptidase-4 inhibitors (DPP-4i) drug class and the risk of major adverse cardiovascular events (MACE) in patients with diabetes. Methods: In the surveillance portion of this dissertation, we utilized the Food and Drug Administration’s Adverse Events Reporting System (FAERS) to conduct a Bayesian disproportionality analysis on reports for MACE associated with DPP-4i, to assess the association of DPP-4i with a cardiovascular subset of reports to the full database. These associations were quantified using the posterior distribution of the empirical Bayes lower bound (EB05) of the relative reporting ratio, among high- and low- risk populations. Next for the longitudinal analyses, we conducted retrospective, time to first MACE analyses of data from Truven Marketscan Commercial Claims and Encounters to compare new users of DPP-4i versus sulfonylurea and DPP-4i versus metformin. This association was measured using propensity score weighted Cox proportional hazards models, adjusted for baseline demographics, comorbidities, and concomitant medications. Propensity score weights, based on baseline clinical characteristics and concomitant medications, were calculated using a generalized boosted logistic regression model. This analysis was repeated in both individuals with established cardiovascular and/or kidney disease (high-risk cohort), as well as in individuals without these medical conditions (low-risk cohort). Results: In the surveillance study, there was a safety signal for heart failure with linagliptin (EB05=2,782.47) and saxagliptin (EB05=2.40), myocardial infarction with alogliptin (EB05=290.11), and cerebral infarction with sitagliptin (EB05=2.80) in the cardiovascular subset of reports. Eight of fourteen possible MACE events had a percent positive agreement ≥50% for a drug-event safety signal in both the cardiovascular subset and the full dataset. Overall, the cardiovascular subset elicited 11 more safety signals for DPP-4i than the full dataset. In the longitudinal analysis of low-risk individuals, DPP-4i use was associated with lower risk for MACE than sulfonylurea use (adjusted Hazard Ratio (aHR)=0.87; 95% Confidence Interval (CI): [0.78, 0.98]), and no increased risk for MACE compared to metformin use (aHR=1.07; 95% CI: [0.97, 1.18]). Risk for acute myocardial infarction (aHR=0.70; 95% CI: [0.51, 0.96]), stroke (aHR=0.57; 95%CI: [0.41, 0.79]), and heart failure (aHR=0.57; 95% CI: 0.41, 0.79) with DPP-4i was lower compared to sulfonylureas. In the longitudinal analysis of high-risk individuals, DPP-4i was associated with lower risk for MACE than sulfonylurea (aHR=0.84; 95% CI: [0.7, 0.9]), and with no increased risk for MACE compared to metformin (aHR=1.07; 95% CI: [1.0, 1.2]). Conclusions: This dissertation confirms the evidence that DPP-4i carry less risk for MACE compared to sulfonylureas in new users of antihyperglycemic therapy for type 2 diabetes. Additionally, DPP-4i and metformin are similar in risk of MACE. While the surveillance data showed a signal for heart failure with some DPP-4i, further prospective analyses of longitudinal data did not lead to evidence to support the drug label warning for increased risk of heart failure among high-risk patients with the use of DPP-4i

An investigation of listening as a learning outcome of the literacy programme in grade one

This study investigates how listening, as part of the literacy learning programme is planned for and taught in the grade one class. The data was produced through semi-structured interviews of five participants, who were grade one educators in the urban area of Durban, Kwa Zulu Natal. Findings suggested the many factors that accounted for why some children in the grade one class do not listen and that educators need to plan for the teaching of listening. The researcher examines the use of multiple strategies, such as teaching responsively, including stimulating tasks, reading aloud, creating a purpose for listening, setting the stage for listening and modeling as strategies to teach listening. The study ends with recommendations for the Department of Education to present workshops to educators on the teaching of listening and for module courses at colleges and universities to offer specialized courses on the teaching of listening. The aim of this research which was conducted in the urban area of Durban, Kwa Zulu Natal, was to investigate how grade one educators were planning for and teaching listening. During this study, data was produced through semi-structured interviews of five participants, who were grade one educators. Findings of this study suggest that there were many factors that accounted for why some children in the grade one class do not listen. Findings also indicated that educators need to plan for the teaching of listening.Ed. (Didactics)

The role of low-frequency intraseasonal oscillations in the anomalous Indian summer monsoon rainfall of 2002

We analyze the dynamical features and responsible factors of the low-frequency intraseasonal time scales which influenced the nature of onset, intensity and duration of active/break phases and withdrawal of the monsoon during the anomalous Indian summer monsoon of 2002 - the most severe drought recorded in recent times. During that season, persistent warm sea surface temperature anomalies over the equatorial Indian Ocean played a significant role in modulating the strength of the monsoon Hadley circulation. This in turn affected the onset and intense break spells especially the long break during the peak monsoon month of July. Strong low-frequency intraseasonal modulations with significant impact on the onset and active/break phases occurred in 2002 which were manifested as a good association between low-frequency intraseasonal oscillations and the onset and active/break spells. Further, SST anomalies over the equatorial Indo-Pacific region on low-frequency intraseasonal time scales were found to affect the equatorial eastward and thereby off-equatorial northward propagations of enhanced convection over the Indian region. These propagations in turn modulated the active/break cycle deciding the consequent severity of the 2002 drought

Exploring pharmacists views, knowledge and perceptions regarding generic medicines in the Western Cape.

M. Pharm. University of KwaZulu-Natal, Durban 2014.BACKROUND In 1996, South Africa adopted a National Drugs Policy. An important objective of this policy focused on promoting the use of generic medicines in the country to ensure that medicines are accessible to the majority of South Africans. Pharmacists play a vital role in influencing patients’ choice of medication, thus highlighting the importance of gaining all health professionals’ support for the quality and utilization of generic medicines. OBJECTIVES This study sought to assess and evaluate the perceptions, views, knowledge and willingness to recommend generic medicines by pharmacists that are located within the Western Cape, as well as to explore pharmacists’ perceptions towards the safety, quality, and efficacy of generic medicines. In addition, the study assessed pharmacists’ views on current policy with respect to substitution of generic medicines as well as to determine if these views vary in the different practice settings. Finally the study assessed pharmacists’ views on the pricing system of generics as well as their opinion on promotion of these medications. METHOD A cross-sectional online survey, which targeted 1730 pharmacists living in the Western Cape, was conducted, using SurveyMonkey, from 7 September to 7 October 2014. Data collected included participant demographics, qualification, experience, education, knowledge and perceptions of generic medication. Survey Monkey was used to produce graphical representations of the data and data was exported onto Microsoft excel in order to make analytical comparisons. RESULTS A total of 321 pharmacists responded to the questionnaire (a response rate of 18,6%). 82% of pharmacists stated there is no difference in safety between original brand and generic medicines. Majority of respondents (74%) believed that generic medicines are therapeutically equivalent to the original medicines. However, 39% of pharmacists stated that original medicines are of a better quality than their generic counterparts. A large number (more than 60%) of pharmacists reported concerns of bioequivalence as their main problem when switching to a generic medicine. CONCLUSION Majority of Pharmacists in the Western Cape had a positive outlook on generic medication and supported and encouraged its use. Concerns were raised however, regarding quality, safety, and effectiveness of generic medicines as well as doubts in the reliability of certain generic manufacturing companies. Pharmacists’ opinions could negatively impact generic usage in South Africa, therefore continuing education and awareness campaigns should be implemented in order to re-confirm pharmacists’ knowledge of generic medicines being bioequivalent and of equal quality to branded medicines. Furthermore, pharmacists should be encouraged to report Adverse Drug Reactions in order to resolve any quality issues

Variability in lipid profile before and after coronary artery bypass grafting (CABG)

Objective: To investigate changes in total cholesterol, low density lipoprotein (LDL) cholesterol, high density lipoprotein (HDL) cholesterol, and triglycerides in serum of Pakistani patients before, immediately after and 5 days post CABG.Method: Serum samples from 31 consecutive Pakistani angina patients undergoing CABG at the Aga Khan University Hospital were analyzed for total cholesterol, LDL cholesterol, HDL cholesterol and triglycerides using kit methods.Results: Immediately after CABG, there is a significant decline in the mean levels of serum cholesterol, LDL cholesterol, HDL cholesterol and triglycerides. However, 5 days post CABG, there is a significant increase in the concentrations of total cholesterol (P = 0.01) and LDL cholesterol (P = 0.001) in nondiabetic angina patients (n = 13). Among the diabetic group of patients (n = 18), the levels of total cholesterol, LDL cholesterol, HDL cholesterol and triglycerides went back to the pre-operative levels within 5 days post CABG. Compared to European patients, Pakistani patients tend to have very low levels of HDL cholesterol (24.9 +/- 7.1 mg/dl) and high levels of triglycerides (185 +/- 50 mg/dl) on day 5 post CABG.Conclusion: Since risk of mortality following CABG increases with low level of HDL cholesterol and high level of triglycerides, close monitoring and treatment of high lipid levels of Pakistani patients following CABG is necessary to prevent further coronary events

Clinicopathological spectrum of peripheral lung tumors in resected lung specimens: a single institutional study in a tertiary care centre

Background: Lung cancer is the most common cancer and by far the leading cause of cancer death among both men and women in the world. In Kashmir, in the recent study, Lung carcinoma was found to be second common in males and sixth in females in Kashmir. This study was carried out to study the demography, clinical presentation, risk factors and histopathological pattern of peripheral lung tumours in resected specimens and to evaluate the added advantage of Immunohistochemistry for enhancing the diagnostic accuracy.Methods: It was a five-year study conducted in the Department of Pathology, SKIMS and the cases from June 2009 to April 2012 were analysed retrospectively while the cases from June 2012 to May 2014 were evaluated prospectively. A total of 97 cases with peripheral lung tumor in whom resection was done were studied.Results: Majority of the cases were seen in males (84.53%) in the fifth decade of life. Cough was the most common symptom, present in 58.76% patients. Right lung was involved in majority of the cases, 57.95% and left lung was involved in 42.04 %. Maximum growth size as seen on gross examination was 8 cm and minimum were 1 cms. Most common histopathological subtype was squamous cell carcinoma seen in 64.94% followed by adenocarcinoma seen in 19.58% of the patients. Lymph nodes were involved in 41 cases (52.56%) and were free in 37 patients (47.43%). IHC was done wherever required and was consistent with histopathology.Conclusions: To improve the therapeutic results of lung cancers efforts for early detection and treatment are essential. Timely intervention with the help of surgery, histopathology and immunohistochemistry are hence very helpful