Nasopharyngeal carriage of Streptococcus pneumoniae serotypes among sick and healthy children in northern India: A case-control study

BACKGROUND

Streptococcus pneumoniae is leading bacterial cause of community acquired pneumonia and according to World Health Organization, responsible for 14 % death in children. There is effective vaccine available against Streptococcus pneumoniae. Hence the primary objective was to isolate Streptococcus pneumoniae from nasopharyngeal swabs in children aged 2-59 months with and without community acquired pneumonia and to assess their serotypes.

METHODS

This case-control study was conducted in tertiary teaching institutes in northern India. Hospitalized children, aged 2-59 months, with World Health Organization-defined community acquired pneumonia were included as cases. Age matched healthy controls were recruited from immunization clinic. All enrolments were done after written informed parental consent. Nasopharyngeal swabs were taken from both cases and controls, and were cultured on 5 % sheep blood agar with gentamycin plate for growth of Streptococcus pneumoniae and incubated in a jar at 370 for 18-24 hrs. Quellung reaction test was used for serotyping.

RESULTS

From March 2017 to December 2022, 2693 children (1910 cases and 783 controls), were recruited. The median age of cases was 7 months and controls 10 months. Almost all the cases had received antibiotics prior to hospitalization. Streptococcus pneumoniae positivity in nasopharyngeal swab was 8.1 % in cases, of which 56.8 % were vaccine serotypes and 23.6 % in controls, of which 37.8 % were vaccine serotypes. Adjusted odds ratio of isolating vaccine serotypes among cases as compared to controls was 1.77 (95 % CI, 1.09-2.88).

CONCLUSION

Streptococcus pneumoniae isolation from nasopharyngeal was found to be in lower proportion in cases as compared to control, though colonization with vaccine serotypes was higher in cases as compared to control. Therefore, pneumococcal vaccine coverage must be increased to prevent community acquired pneumonia.

Nasopharyngeal Carriage of Streptococcus pneumoniae Serotypes Among Healthy Children in Northern India

Streptococcus pneumoniae (SP) infections cause morbidity and mortality among children worldwide. Hence India introduced 13-valent pneumococcal conjugate vaccine (PCV-13) in 2017 in a phased manner. The primary objective of this study was to assess the proportion of healthy children having nasopharyngeal colonization (NP) with SP. Secondary objective was to determine prevalent serotype of SP among the PCV13 vaccinated and non-vaccinated children. This cross-sectional study was conducted in 4 hospitals of Lucknow District, Northern India. Three hundred healthy children (2-59 months) were recruited between July and August 2019 from vaccination-clinics of hospitals. NP specimen was cultured using 5% sheep blood agar plate containing gentamicin. Pneumococcal isolates were identified by optochin sensitivity and bile-solubility tests. Serotyping was done using Quellung Method. Of the 300 healthy children, 56.7% (170/300) were males and 59.3% (181/300) had received at least one dose of PCV13 vaccine. The NP carriage rate of SP among healthy children was 37.7% (113/300). Vaccine serotypes were found in 33.3% (22/66) in PCV vaccinated children and 48.9% (23/47) in non-vaccinated children (p 0.09). Common vaccine serotypes that isolated were: 18C, 19A, 19F, 23F, 3, 4, 6A, 6B, 9 V. Thus more than one-third of healthy children had NP colonization with SP. Adjusting for age, there was a trend for significant reduction in vaccine serotypes in the NP with one doses versus two or more doses (ptrend = 0.04).

Characterization of Citrullination Sites in Neutrophils and Mast Cells Activated by Ionomycin via Integration of Mass Spectrometry and Machine Learning

Citrullination is an important post-translational modification implicated in many diseases including rheumatoid arthritis (RA), Alzheimer's disease, and cancer. Neutrophil and mast cells have different expression profiles for protein-arginine deiminases (PADs), and ionomycin-induced activation makes them an ideal cellular model to study proteins susceptible to citrullination. We performed high-resolution mass spectrometry and stringent data filtration to identify citrullination sites in neutrophil and mast cells treated with and without ionomycin. We identified a total of 833 validated citrullination sites on 395 proteins. Several of these citrullinated proteins are important components of pathways involved in innate immune responses. Using this benchmark primary sequence data set, we developed machine learning models to predict citrullination in neutrophil and mast cell proteins. We show that our models predict citrullination likelihood with 0.735 and 0.766 AUCs (area under the receiver operating characteristic curves), respectively, on independent validation sets. In summary, this study provides the largest number of validated citrullination sites in neutrophil and mast cell proteins. The use of our novel motif analysis approach to predict citrullination sites will facilitate the discovery of novel protein substrates of protein-arginine deiminases (PADs), which may be key to understanding immunopathologies of various diseases.

Refractive Error Prevalence among School Children in Dadeldhura District of Nepal

Background Uncorrected refractive error is the major cause of visual impairment worldwide. There is no data on refractive error prevalence among school children in hilly region of Far West Nepal. Objective The prevalence of refractive error has been found to vary among children of different caste/ethnic groups and geographical regions. The purpose of this study is to determine the prevalence of refractive error among school children from different caste/ethnic groups in Dadeldhura district of Far West Nepal. Method This is a cross sectional study of refractive error among secondary school children from 2 schools in Dadeldhura district. All children underwent a vision screening consisting of visual acuity, ocular examination and refraction. Myopia was diagnosed for an eye with spherical equivalent refraction (SER) ≤ -0.5 D whereas an eye with SER ≥ +2.0 D was diagnosed as hyperopic. Ethnicity was reported through self administered questionnaire. Result Among children aged 12 to 16 years (14.07 ± 1.4) prevalence of myopia was 3.5%, hyperopia 0.33% and astigmatism 1%. All except three children had spherical equivalent refraction (SER) within ±2 D. Caste/ethnicity was not associated significantly with myopia in either eye (χ2 = 0.27, df= 2, p= 0.87). Conclusion The prevalence of refractive error among secondary school children in Dadeldhura district of Far West Nepal is very low in comparison to myopia prevalence reported in studies from other parts of the world, but slightly lower than myopia prevalence found in other, eastern parts of Nepal.

Abstract 4528: Quantitative mass spectrometry to interrogate proteomic heterogeneity in metastatic lung adenocarcinoma and validate a novel somatic mutation CDK12-G879V

Lung cancer is the leading cause of cancer mortality. Tumor heterogeneity is a major cause of treatment failure. Intra- and inter-metastatic tumor heterogeneity has been demonstrated by next generation sequencing (NGS) studies. However, heterogeneity in the proteome and phosphoproteome has been less studied. Integrated proteogenomics is essential to understanding the intricacies of tumor heterogeneity affecting treatment response. Here, we performed integrated mass spectrometry-based proteogenomics to characterize spatial and temporal heterogeneity of an exceptional responder lung adenocarcinoma patient who survived with metastatic disease for more than 7 years while on combination treatment with HER2-targeted and chemotherapy.

We employed Super-SILAC and TMT labeling strategies to quantify the proteome and phosphoproteome of a lung metastatic site and ten different metastatic progressive lymph nodes from our patient collected across a span of seven years, including at autopsy. To further interrogate the mass spectrometry data, patient-specific database was built to incorporate all the somatic variants identified by NGS. An extensive validation pipeline was built for confirmation of variant peptides. CRISPR-Cas9-mediated gene knockout, cell viability assays, and confocal microscopy were used for further validation of novel variants.

A total of 6214 and 4061 proteins were identified from Super-SILAC and TMT experiments, respectively. 3648 proteins were identified and quantified in both experiments. More than 2000 proteins had catalytic activity, including kinases, phosphatases and metabolic enzymes. We identified 78 and 23 mutant peptides from Super-SILAC and TMT experiments, respectively. Three somatic variants, CDK12-G879V, FASN-R1439Q and HNRNPF-A105T, were confirmed using our variant peptide detection pipeline. Multiple reaction monitoring in a triple quadrupole mass spectrometer successfully identified and relatively quantified two of the variant tryptic peptides harboring the mutations, CDK12-G879V and FASN-R1439Q from the lung and lymph node metastatic sites, respectively. We investigated the consequences of loss of CDK12 function, as predicted from the novel CDK12-G879V mutant, in chemotherapy sensitivity. A549 lung adenocarcinoma cells, upon knockdown of CDK12, exhibited greater chemotherapy sensitivity that was rescued by wild type CDK12, but not by CDK12-G879V mutant.

We demonstrate the importance of integrated proteogenomic analyses to identify variant peptides in mass spectrometry data and studying proteomic heterogeneity affecting treatment response. CDK12-G879V mutation results in a nonfunctional CDK12 kinase and chemotherapy susceptibility in lung metastatic sites, likely explaining the “cure” of lung metastatic sites in this patient.

Citation Format: Xu Xhang, Khoa Dang P. Nguyen, Paul Rudnick, Nitin Roper, Emily Kawaler, Tapan K. Maity, Shivangi Awasthi, Shaojian Gao, Romi Biswas, Abhilash Venugopalan, Constance Cultraro, David Fenyo, Udayan Guha. Quantitative mass spectrometry to interrogate proteomic heterogeneity in metastatic lung adenocarcinoma and validate a novel somatic mutation CDK12-G879V [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4528.

Quantitative Mass Spectrometry to Interrogate Proteomic Heterogeneity in Metastatic Lung Adenocarcinoma and Validate a Novel Somatic Mutation CDK12-G879V

Lung cancer is the leading cause of cancer death in both men and women. Tumor heterogeneity is an impediment to targeted treatment of all cancers, including lung cancer. Here, we sought to characterize tumor proteome and phosphoproteome changes by longitudinal, prospective collection of tumor tissue from an exceptional responder lung adenocarcinoma patient who survived with metastatic lung adenocarcinoma for over seven years while undergoing HER2-directed therapy in combination with chemotherapy. We employed "Super-SILAC" and TMT labeling strategies to quantify the proteome and phosphoproteome of a lung metastatic site and eight distinct metastatic progressive lymph nodes collected during these seven years, including five lymph nodes procured at autopsy. We identified specific signaling networks enriched in lung compared with the lymph node metastatic sites. We correlated the changes in protein abundance with changes in copy number alteration (CNA) and transcript expression. ERBB2/HER2 protein expression was higher in lung, consistent with a higher degree of ERBB2 amplification in lung compared with the lymph node metastatic sites. To further interrogate the mass spectrometry data, a patient-specific database was built by incorporating all the somatic and germline variants identified by whole genome sequencing (WGS) of genomic DNA from the lung, one lymph node metastatic site and blood. An extensive validation pipeline was built to confirm variant peptides. We validated 360 spectra corresponding to 55 germline and 6 somatic variant peptides. Targeted MRM assays revealed two novel variant somatic peptides, CDK12-G879V and FASN-R1439Q, expressed in lung and lymph node metastatic sites, respectively. The CDK12-G879V mutation likely results in a nonfunctional CDK12 kinase and chemotherapy susceptibility in lung metastatic sites. Knockdown of CDK12 in lung adenocarcinoma cells increased chemotherapy sensitivity which was rescued by wild type, but not CDK12-G879V expression, consistent with the complete resolution of the lung metastatic sites in this patient.

Abstract P4-16-06: Incidence of interstitial lung disease in patients with HER2-positive advanced breast cancer treated with everolimus and trastuzumab: A combined analysis of two phase 3 randomized controlled trials

Background: The human epidermal growth factor receptor 2 (HER2) protein is overexpressed in approximately one fourth of breast tumors. Trastuzumab resistance has been demonstrated via aberrant PI3K/AKT/mTOR signaling due to PTEN loss. To circumvent this resistance mechanism, everolimus, an oral mTOR inhibitor, has been employed in treatment of HER2-positive advanced breast cancer (ABC). Lung toxicity due to everolimus is well established and has been reported with trastuzumab. Yet, the incidence of interstitial lung disease (ILD), when everolimus was added to trastuzumab, has never been reported. We performed a systematic review and meta-analysis of randomized controlled trials (RCTs) to determine the incidence of ILD in patients with HER2-positive ABC treated with both everolimus and trastuzumab.

Methods: We systematically conducted a comprehensive literature search using MEDLINE, EMBASE databases and meeting abstracts through January 2018. Phase 3 RCTs that mention ILD as an adverse effect were incorporated in the analysis. The primary meta- analytic approach was a fixed effects model using the Mantel-Haenszel (MH) method. It was used to calculate the estimated pooled risk ratio (RR), and risk difference (RD) with 95% confidence interval (CI).

Results: A total of 1272 patients with HER-2 positive ABC from two phase 3 RCTs were eligible. Studies compared everolimus + paclitaxel + trastuzumab vs paclitaxel + trastuzumab and everolimus + vinorelbine + trastuzumab vs vinorelbine + trastuzumab. The initial dose of everolimus in BOLERO-1 was 10mg per day and in BOLERO-3, 5mg per day was used. The median relative dose intensity of everolimus was reduced to 0.54 in BOLERO-1 due to toxicity related dose reductions and dose interruptions. The randomization ratio of everolimus to placebo was 2 to 1 in BOLERO-1 and 1 to 1 in BOLERO-3. Everolimus was utilized in trastuzumab-resistant ABC after prior taxane therapy in the BOLERO-3 study (n= 562) and as first-line treatment in the BOLERO-1 study (n= 710). The I2 statistic for heterogeneity was 0, and the heterogeneity X2 (Cochran's Q) was 1 (P= 0), suggesting homogeneity among RCT. The incidence of all-grade ILD was 31 (4.122%) in the everolimus group vs 3 (0.577%) in control group and of high-grade ILD was 11 (1.463%) in everolimus arm vs 0 (0%) in the control arm. The pooled RR for all-grade ILD was significant at 7.258 (95% CI: 2.130 – 24.733, p = 0.002) and the absolute RD was 0.035 (95% CI: 0.019 – 0.050, P < 0.001). The pooled RR for high-grade ILD was noted at 7.930 (95% CI: 0.997 – 63.044, p = 0.050) and the absolute RD was 0.014 (95% CI: 0.004 – 0.024, P = 0.004).

Conclusions: Approximately 0.46 and 0.61% of patients on trastuzumab alone have been reported to develop ILD in previous studies. Our study showed that the addition of reduced dose of everolimus to trastuzumab, significantly contributed a higher incidence in all grades of ILD with a relative risk of 7.93 for grade 3 and 4 ILD. More randomized trials are required to determine the definitive incidence and actual relation of ILD as well as the optimal dose of everolimus, when combined with trastuzumab or other chemotherapy.

Citation Format: Thein KZ, Swarup S, Sultan A, Tijani L, D'Cunha N, Hardwicke FT, Awasthi S, Jones C. Incidence of interstitial lung disease in patients with HER2-positive advanced breast cancer treated with everolimus and trastuzumab: A combined analysis of two phase 3 randomized controlled trials [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-16-06.

Abstract P1-16-04: Risk of venous thromboembolism with abemaciclib based regimen versus other CDK 4/6 inhibitor containing regimens in patients with hormone receptor-positive HER2-negative metastatic breast cancer

Background: Approximately 70% of patients with metastatic breast cancer (MBC) are hormone receptor (HR) - positive and the cyclin dependent kinases (CDK) along with their D-type cyclin catalysts, have been shown to play a role in mediating the resistance to endocrine therapy. Several CDK-targeted agents have been recently approved by FDA. Nevertheless, the risk of venous thromboembolism (VTE) with the use of different CDK 4/6 inhibitors has never been reported. We undertook a systematic review and meta-analysis of randomized controlled trials (RCT) to determine the risk of VTE with abemaciclib based regimens versus other CDK 4/6 inhibitor containing regimens in patients with HR-positive HER2-negative MBC.

Methods: We systematically conducted a comprehensive literature search using MEDLINE, EMBASE databases and meeting abstracts through February 2018. The randomized controlled trials that mention deep vein thrombosis and pulmonary embolism as adverse effects of CDK 4/6 inhibitor therapy were incorporated in the analysis. The primary meta- analytic approach was a fixed effects model using the Mantel-Haenszel (MH) method. It was used to calculate the estimated pooled risk ratio (RR) and risk difference (RD) with 95% confidence interval (CI).

Results: Five phase 3 studies and one phase 2 study with a total of 3,159 patients with HR-positive HER2-negative MBC were eligible for analysis. The study arms used palbociclib-letrozole, palbociclib-fulvestrant, ribociclib-letrozole, abemaciclib-fulvestrant, and abemaciclib-nonsteroidal aromatase inhibitors (either letrozole or anastrozole) while the control arms utilized placebo in combination with letrozole or anastrozole or fulvestrant. The randomization ratio was 2 to 1 in PALOMA-2, PALOMA-3, MONARCH-2 and MONARCH-3 studies and 1 to 1 in PALOMA-1 and MONALEESA-2 trials. CDK 4/6 inhibitors were utilized as first line treatment in PALOMA-1, PALOMA-2, MONALEESA-2 and MONARCH-3. The I2 statistic for heterogeneity was 0, and the heterogeneity X2 (Cochran's Q) was 1 (P= 0.707), suggesting homogeneity among RCTs. The VTE incidence was 25 (3.255%) in the abemaciclib group vs 2 (0.520%) in the control group. The pooled relative risk for VTE was 6.222 (95% CI: 1.481 – 26.145, P = 0.013) and the absolute RD was 0.027 (95% CI: 0.013 – 0.042, P < 0.0001). In other CDK 4/6 inhibitor containing regimens, the VTE incidence was reported at 15 (1.243%) vs 2 (0.374%) in the control arm. The pooled RR for VTE was 2.312 (95% CI: 0.852 –6.272, P = 0.100) and the absolute RD was 0.008 (95% CI: - 0.000 – 0.017, P = 0.259).

Conclusion: VTE is a major cause of morbidity and mortality and is particularly common in patients with breast cancer. Our meta-analysis demonstrated that the addition of abemaciclib to endocrine therapy notably contributed to a higher incidence of VTE with a relative risk of 6.22. However, no significant increase in the risk of VTE was noted in other CDK 4/6 inhibitor-based regimen. More randomized trials are required to determine the actual relation and definitive incidence of VTE among different CDK-targeted agents when added to endocrine therapy.

Citation Format: Thein KZ, Ball S, Zaw MH, Quirch M, Hardwicke F, Awasthi S, Oo TH, Jones C. Risk of venous thromboembolism with abemaciclib based regimen versus other CDK 4/6 inhibitor containing regimens in patients with hormone receptor-positive HER2-negative metastatic breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-16-04.

Dataset describing the development, optimization and application of SRM/MRM based targeted proteomics strategy for quantification of potential biomarkers of EGFR TKI sensitivity

The data presented here describes the use of targeted proteomic assays to quantify potential biomarkers of Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) sensitivity in lung adenocarcinoma and is related to the research article: “Quantitative targeted proteomic analysis of potential markers of tyrosine kinase inhibitor (TKI) sensitivity in EGFR mutated lung adenocarcinoma” [1]. This article describes the data associated with liquid chromatography coupled to multiple reaction monitoring (LC-MRM) method development which includes selection of an optimal transition list, retention time prediction and building of reverse calibration curves. Sample preparation and optimization which includes phosphotyrosine peptide enrichment via a combination of pan-phosphotyrosine antibodies is described. The dataset also consists of figures, tables and Excel files describing the quantitative results of testing these optimized methods in two lung adenocarcinoma cell lines with EGFR mutations.

Quantitative targeted proteomic analysis of potential markers of tyrosine kinase inhibitor (TKI) sensitivity in EGFR mutated lung adenocarcinoma

Lung cancer causes the highest mortality among all cancers. Patients harboring kinase domain mutations in the epidermal growth factor receptor (EGFR) respond to EGFR tyrosine kinase inhibitors (TKIs), however, acquired resistance always develops. Moreover, 30-40% of patients with EGFR mutations exhibit primary resistance. Hence, there is an unmet need for additional biomarkers of TKI sensitivity that complement EGFR mutation testing and predict treatment response. We previously identified phosphopeptides whose phosphorylation is inhibited upon treatment with EGFR TKIs, erlotinib and afatinib in TKI sensitive cells, but not in resistant cells. These phosphosites are potential biomarkers of TKI sensitivity. Here, we sought to develop modified immuno-multiple reaction monitoring (immuno-MRM)-based quantitation assays for select phosphosites including EGFR-pY1197, pY1172, pY998, AHNAK-pY160, pY715, DAPP1-pY139, CAV1-pY14, INPPL1-pY1135, NEDD9-pY164, NF1-pY2579, and STAT5A-pY694. These sites were significantly hypophosphorylated by erlotinib and a 3rd generation EGFR TKI, osimertinib, in TKI-sensitive H3255 cells, which harbor the TKI-sensitizing EGFR^L858R mutation. However, in H1975 cells, which harbor the TKI-resistant EGFR^L858R/T790M mutant, osimertinib, but not erlotinib, could significantly inhibit phosphorylation of EGFR-pY-1197, STAT5A-pY694 and CAV1-pY14, suggesting these sites also predict response in TKI-resistant cells. We could further validate EGFR-pY-1197 as a biomarker of TKI sensitivity by developing a calibration curve-based modified immuno-MRM assay. SIGNIFICANCE: In this report, we have shown the development and optimization of MRM assays coupled with global phosphotyrosine enrichment (modified immuno-MRM) for a list of 11 phosphotyrosine peptides. Our optimized assays identified the targets reproducibly in biological samples with good selectivity. We also developed and characterized quantitation methods to determine endogenous abundance of these targets and correlated the results of the relative quantification with amounts estimated from the calibration curves. This approach represents a way to validate and verify biomarker candidates discovered from large-scale global phospho-proteomics analysis. The application of these modified immuno-MRM assays in lung adenocarcinoma cells provides proof-of concept for the feasibility of clinical applications. These assays may be used in prospective clinical studies of EGFR TKI treatment of EGFR mutant lung cancer to correlate treatment response and other clinical endpoints.

Abstract P1-17-08: Efficacy of lapatinib and capecitabine combination therapy in brain metastases from HER-2 positive metastatic breast cancer: A systematic review and meta- analysis

Background:

Brain metastases contribute to significant morbidity and mortality in breast cancer. Approximately one fourth of breast tumors overexpress the human epidermal growth factor receptor 2 (HER2) protein and are twice as likely to develop brain metastases. There are currently no systemic therapies approved. We undertook a systematic review and pooled analysis of trials to determine the efficacy of lapatinib and capecitabine combination therapy in brain metastases from HER-2 positive metastatic breast cancer (MBC).

Methods:

We performed a comprehensive literature search using MEDLINE, EMBASE databases, and meeting abstracts through December 31, 2016. Trials that utilized lapatinib and capecitabine combination therapy in brain metastases from HER-2 positive MBC were incorporated in the analysis. The pooled estimated rates were calculated using random effects model. Heterogeneity was assessed using I2 statistic.

Results:

A total of 513 patients with brain metastases from HER-2 positive MBC from 6 trials and a subgroup of another 4 trials were included in our analysis. Lapatinib and capecitabine therapy was used as second-line treatment in 9 studies (n= 468) and as first-line treatment in the LANDSCAPE study (n= 45). Three studies were retrospective evaluations of randomized trials and the rest were phase 2 trials. CNS objective response rate (ORR) was 26% (95% CI: 19 – 33, I2: 65.9%). Complete response (CR) rate was 1% (95% CI: 0 - 2, I2: 0.0%) and partial response (PR) rate was noted at 24% (95% CI: 17- 31, I2: 66.1%). Stable disease (SD) occurred in 37% (95% CI: 29- 45, I2: 66.6%) and progressive disease (PD) in 19% (95% CI: 12- 25, I2: 66.5%). The first line LANDSCAPE study had the highest PR (49%) and ORR (53%) without a significant impact on CR rate; PD was 7%.

Conclusion:

Brain metastases in breast cancer is an area of urgent unmet need. Our meta-analysis showed that lapatinib/capecitabine therapy had some first line or second line activity in brain metastases from HER-2 positive MBC. Nevertheless, further randomized controlled trials are required in this patient population.

Citation Format: Thein KZ, Zaw MH, Yendala R, Igid HP, Chai-Adisaksopha C, Hardwicke F, Awasthi S, Radhi S. Efficacy of lapatinib and capecitabine combination therapy in brain metastases from HER-2 positive metastatic breast cancer: A systematic review and meta- analysis [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-17-08.

Rapid analysis of pharmaceutical drugs using LIBS coupled with multivariate analysis

Type 2 diabetes drug tablets containing voglibose having dose strengths of 0.2 and 0.3 mg of various brands have been examined, using laser-induced breakdown spectroscopy (LIBS) technique. The statistical methods such as the principal component analysis (PCA) and the partial least square regression analysis (PLSR) have been employed on LIBS spectral data for classifying and developing the calibration models of drug samples. We have developed the ratio-based calibration model applying PLSR in which relative spectral intensity ratios H/C, H/N and O/N are used. Further, the developed model has been employed to predict the relative concentration of element in unknown drug samples. The experiment has been performed in air and argon atmosphere, respectively, and the obtained results have been compared. The present model provides rapid spectroscopic method for drug analysis with high statistical significance for online control and measurement process in a wide variety of pharmaceutical industrial applications.

Abstract 2203: A SRM/MRM based targeted proteomics strategy for absolute quantification of potential biomarkers of TKI sensitivity in EGFR mutated lung adenocarcinoma

Lung cancer remains the leading cause of cancer-related deaths worldwide. Epidermal growth factor receptor(EGFR) is the primary driver oncogene in 10-30% lung adenocarcinoma. Kinase domain mutations in EGFR (L858R and E746-A750 deletion) provide sensitivity to EGFR-specific tyrosine kinase inhibitors (TKIs). Despite good tumor inhibitory effects, after approximately a year, patients acquire resistance to EGFR TKIs. We have carried out a stable isotope labeling with amino acids in cell culture (SILAC)-based quantitative mass spectrometry (MS) on a Thermo Orbitrap Elite to identify and characterize the dynamics of tyrosine phosphorylation upon TKI treatment of human lung adenocarcinoma cell lines. The degree of inhibition of phosphorylation of several phospho-sites correlated with the extent of TKI-sensitivity. Several kinases and adaptor proteins that were significantly differentially phosphorylated include AHNAK-Y160, -Y715, STAT5A-Y694, DAPP1-Y139, ERRFI1-Y394, NEDD9-Y164, NF1-Y2579, INNPL1-Y1135, suggesting that these are a subset of potential biomarkers of TKI response. To corroborate our results, the next logical step is to carry out clinical validation of these phospho-sites in human lung adenocarcinoma patients, however no absolute quantification assay is currently available for these tyrosine phosphorylated peptides in human samples. The MS method most often used to complement shotgun methods is selected/multiple reaction monitoring (SRM/MRM) because of its high sensitivity, speed and dynamic range. We have performed SRM/MRM-MS using a nano-flow high performance liquid chromatography instrument coupled to a nano-electrospray ionization source attached to a Triple Quadrupole MS (Agilent 6495). In this method, digested proteins are chromatographically separated and ionized. The resulting precursor ions are m/z filtered in the first quadrupole(Q1) and collision induced dissociation is carried out in Q2 and the resultant product ions are m/z filtered in Q3. Each precursor-product pair is termed as a transition. For absolute quantification, heavy isotope labelled versions of the target peptides are spiked in biological samples to build a calibration curve. For the robust assay development, we have carried out the initial empirical refinement process using the heavy labelled versions of the target peptides, including selection of optimal transitions, normalizing retention times of peptides, running peptide stability assays and digestion time course experiments. We are currently validating these assays in human lung adenocarcinoma cell lines with known EGFR mutations with or without treatment with 1st and 3rd generation EGFR TKIs. The overall goal of these targeted studies is to develop absolute quantitation assays to precisely and accurately quantify these potential biomarkers in clinical samples.

Citation Format: Shivangi Awasthi, Xu Zhang, Tapan Maity, Benjamin L. Oyler, David R. Goodlett, Udayan Guha. A SRM/MRM based targeted proteomics strategy for absolute quantification of potential biomarkers of TKI sensitivity in EGFR mutated lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2203. doi:10.1158/1538-7445.AM2017-2203

Genome-wide association study of borderline personality disorder reveals genetic overlap with bipolar disorder, major depression and schizophrenia

Borderline personality disorder (BOR) is determined by environmental and genetic factors, and characterized by affective instability and impulsivity, diagnostic symptoms also observed in manic phases of bipolar disorder (BIP). Up to 20% of BIP patients show comorbidity with BOR. This report describes the first case-control genome-wide association study (GWAS) of BOR, performed in one of the largest BOR patient samples worldwide. The focus of our analysis was (i) to detect genes and gene sets involved in BOR and (ii) to investigate the genetic overlap with BIP. As there is considerable genetic overlap between BIP, major depression (MDD) and schizophrenia (SCZ) and a high comorbidity of BOR and MDD, we also analyzed the genetic overlap of BOR with SCZ and MDD. GWAS, gene-based tests and gene-set analyses were performed in 998 BOR patients and 1545 controls. Linkage disequilibrium score regression was used to detect the genetic overlap between BOR and these disorders. Single marker analysis revealed no significant association after correction for multiple testing. Gene-based analysis yielded two significant genes: DPYD (P=4.42 × 10-7) and PKP4 (P=8.67 × 10-7); and gene-set analysis yielded a significant finding for exocytosis (GO:0006887, PFDR=0.019; FDR, false discovery rate). Prior studies have implicated DPYD, PKP4 and exocytosis in BIP and SCZ. The most notable finding of the present study was the genetic overlap of BOR with BIP (rg=0.28 [P=2.99 × 10-3]), SCZ (rg=0.34 [P=4.37 × 10-5]) and MDD (rg=0.57 [P=1.04 × 10-3]). We believe our study is the first to demonstrate that BOR overlaps with BIP, MDD and SCZ on the genetic level. Whether this is confined to transdiagnostic clinical symptoms should be examined in future studies.

Quantitative Tyrosine Phosphoproteomics of Epidermal Growth Factor Receptor (EGFR) Tyrosine Kinase Inhibitor-treated Lung Adenocarcinoma Cells Reveals Potential Novel Biomarkers of Therapeutic Response

Mutations in the Epidermal growth factor receptor (EGFR) kinase domain, such as the L858R missense mutation and deletions spanning the conserved sequence ⁷⁴⁷LREA⁷⁵⁰, are sensitive to tyrosine kinase inhibitors (TKIs). The gatekeeper site residue mutation, T790M accounts for around 60% of acquired resistance to EGFR TKIs. The first generation EGFR TKIs, erlotinib and gefitinib, and the second generation inhibitor, afatinib are FDA approved for initial treatment of EGFR mutated lung adenocarcinoma. The predominant biomarker of EGFR TKI responsiveness is the presence of EGFR TKI-sensitizing mutations. However, 30-40% of patients with EGFR mutations exhibit primary resistance to these TKIs, underscoring the unmet need of identifying additional biomarkers of treatment response. Here, we sought to characterize the dynamics of tyrosine phosphorylation upon EGFR TKI treatment of mutant EGFR-driven human lung adenocarcinoma cell lines with varying sensitivity to EGFR TKIs, erlotinib and afatinib. We employed stable isotope labeling with amino acids in cell culture (SILAC)-based quantitative mass spectrometry to identify and quantify tyrosine phosphorylated peptides. The proportion of tyrosine phosphorylated sites that had reduced phosphorylation upon erlotinib or afatinib treatment correlated with the degree of TKI-sensitivity. Afatinib, an irreversible EGFR TKI, more effectively inhibited tyrosine phosphorylation of a majority of the substrates. The phosphosites with phosphorylation SILAC ratios that correlated with the TKI-sensitivity of the cell lines include sites on kinases, such as EGFR-Y1197 and MAPK7-Y221, and adaptor proteins, such as SHC1-Y349/350, ERRFI1-Y394, GAB1-Y689, STAT5A-Y694, DLG3-Y705, and DAPP1-Y139, suggesting these are potential biomarkers of TKI sensitivity. DAPP1, is a novel target of mutant EGFR signaling and Y-139 is the major site of DAPP1 tyrosine phosphorylation. We also uncovered several off-target effects of these TKIs, such as MST1R-Y1238/Y1239 and MET-Y1252/1253. This study provides unique insight into the TKI-mediated modulation of mutant EGFR signaling, which can be applied to the development of biomarkers of EGFR TKI response.

Glycosylation characterization of therapeutic mAbs by top- and middle-down mass spectrometry

A reference monoclonal antibody IgG1 and a fusion IgG protein were analyzed by top- and middle-down mass spectrometry with multiple fragmentation techniques including electron transfer dissociation (ETD) and matrix-assisted laser desorption ionization in-source decay (MALDI-ISD) to investigate heterogeneity of glycosylated protein species. Specifically, glycan structure, sites, relative abundance levels, and termini structural conformation were investigated by use of Fourier transform ion cyclotron resonance (FT-ICR) or high performance liquid chromatography electrospray ionization (HPLC-ESI) linked to an Orbitrap. Incorporating a limited enzymatic digestion by immunoglobulin G-degrading enzyme Streptococcus pyogenes (IdeS) with MALDI-ISD analysis extended sequence coverage of the internal region of the proteins without pre-fractionation. The data in this article is associated with the research article published in Journal of Proteomics (Tran et al., 2015) [1].

Fallopian tube papilloma--case report of a rare tumor

Fallopian tube neoplasms are rare. We report a rare case of fallopian tube papilloma discovered incidentally in a 45 year old female, operated for procidentia. Right tube was dilated at the infundibular region, with friable grey white tissue in the lumen. Microscopy showed delicate branching papillae lined by a single layer of epithelium resembling tubal lining. There were no features to suggest a reactive hyperplasia in response to inflammation or of aggressive behaviour.

Regulation of tamoxifen sensitivity by a PAK1-EBP1 signalling pathway in breast cancer

Background:

EBP1, an ErbB3-binding protein, sensitises breast cancer cells to tamoxifen in part by decreasing ErbB2 protein levels. The p21-regulated serine/threonine kinase PAK1, implicated in tamoxifen resistance, phosphorylates EBP1 in vitro and in vivo at T261. Phosphorylation of EBP1 at this site induces tamoxifen resistance. We thus postulated that inhibition of PAK1 activity, by restoring EBP1 function, could ameliorate the hormone refractory phenotype of ErbB2-overexpressing breast cancer cells.

Methods:

Effects of EBP1 on ErbB2 levels were measured by western blotting. Effects of EBP1 and IPA-3 on tamoxifen sensitivity were measured using a tetrazolium based cell viability assay.

Results:

Transient transfection studies indicated that an EBP1 T261E mutant, which mimics EPB1 phosphorylated by PAK1, increased ErbB2 protein levels. An EBP1 T261A mutant, unable to be phosphorylated by PAK1, ameliorated PAK1-induced tamoxifen resistance, suggesting that phosphorylation of EBP1 by PAK1 contributes to tamoxifen resistance. We then tested if pharmacological inhibition of PAK1 activity might render hormone resistant cells, which endogenously overexpress PAK1, tamoxifen sensitive. IPA-3, a specific small MW PAK1 inhibitor, sensitised cells to tamoxifen only when EBP1 was ectopically expressed. IPA had no effect on tamoxifen resistance in T47D cells in which EBP1 protein had been ablated by shRNA. The IPA-induced increase in tamoxifen sensitivity was accompanied by a decrease in ErbB2 levels only in EBP1-overexpressing cells.

Conclusion:

These studies suggest that phosphorylation of EBP1 may be one mechanism of PAK1-induced hormone resistance and that PAK1 inhibitors may be useful in cells in which EBP1 is overexpressed.

Assessment of Health-Related Quality of Life in school-going adolescents: validation of PedsQL instrument and comparison with WHOQOL-BREF

BACKGROUND

Health-Related Quality of Life (HRQoL) studies are gaining importance. Yet there is a dearth of crossculturally validated generic HRQoL instruments for Indian adolescents. Two HRQoL instruments, namely World Health Organization Quality of Life-Brief (WHOQOL-BREF) and Pediatric Quality of Life inventory™ 4.0 (PedsQL), are widely used internationally, with both measuring four domains (physical, psychological/emotional, social relations and environment/school) but each having different questions with 26 in the former and 23 in the latter. This study was done among adolescents in the city of Lucknow to evaluate the psychometric properties of PedsQL and compare its performance with previously validated and culturally revised WHOQOL-BREF.

METHODS

This cross-sectional study was conducted in February 2010 after institutional ethical approval. Data were collected by a self-administered, redesigned questionnaire in which items of PedsQL and revised WHOQOL-BREF were intermingled. Reliability, content and construct validity were evaluated for PedsQL. Convergent validity of PedsQL with revised WHOQOL-BREF was calculated for domains with similar questions.

RESULTS

Parents of 76.5% adolescents (385/503) provided consent. Mean age of adolescents was 13.6 years (1.6 SD and 44.7% were girls). PedsQL showed substantial reliability (Cronbach alpha=0.82, p<0.00001) but poor to fair validity as compared to revised WHOQOL-BREF.

CONCLUSIONS

For Indian adolescents, PedsQL is a reliable and valid instrument. However, on comparison with revised WHOQOL-BREF, PedsQL has poor to fair validity. We conclude that revised WHOQOL-BREF is a better HRQoL instrument for Indian adolescents.

A cross-sectional pilot study to determine the prevalence of testosterone deficiency syndrome in working population of Indian men

Aim:

To determine the prevalence of testosterone deficiency syndrome (TDS) in healthy Indian men employed in a hospital aged above 40 years.

Materials and Methods:

A general medical health check-up camp was organized for all male employees above 40 years age working in surgical departments. After clinical history and systemic inquiry, subjects were requested to fill the St. Louis University's ADAM Questionnaire based on which the total and free-serum testosterone estimation was then done.

Results:

One hundred fifty seven healthy volunteers enrolled for the study (mean age 53.1 years; range 40–60). The androgen decline in the aging male (ADAM) Questionnaire detected 106 men (67.5%) to be symptomatic for TDS. Serum testosterone estimation in these subjects revealed 41/106 to have low free-serum testosterone levels and 32/106 to have low total-serum testosterone. In 11 and 6 cases, respectively, the serum free- and total-testosterone levels were found to be low although the subjects were asymptomatic for TDS.

Conclusions:

The prevalence of symptomatic biochemical hypogonadism was 26.1%. The higher prevalence of symptoms alone of TDS was unusual. It could be because of the nature of the questionnaire. Free-serum testosterone may be a better single test to diagnose symptomatic hypogonadism than total-serum testosterone.

Efficiency assessment of Common Effluent Treatment Plant (CETP) treating tannery effluents

The efficacy of Common Effluent Treatment Plant (CETP) based on activated sludge process employed for treatment of tannery effluent was analyzed for the efficiency to reduce chromium and other contaminants. Physico-chemical parameters of treated effluent were found within permissible levels of statutory limits. A significant reduction in COD and BOD levels were achieved during the course of treatment in CETP. A reduction of 98.46%, 87.5%, and 96.15% in bacterial counts especially in pathogens like Escherichia coli, Vibrio spp., and Pseudomonas spp. were observed after treatment. Pathogens were not detected in the dried sludge. Complete elimination of fecal streptococci was observed in treated effluent. Around 10.8% of microbial isolates from the effluent showed ability to reduce chromate >90%. In treated effluent chromium level was 5.48 mg/L, which exceeds the statutory limit of Indian standards. Cleaner production options to reduce chromium levels before discharging into water bodies is discussed.

Reduced vision and refractive errors, results from a school vision screening program in Kanchanpur District of far western Nepal

BACKGROUND

At present there is no data available on reduced vision and refractive errors in school children of far western Nepal. So, school screening records were used to obtain data useful for planning of refractive services.

METHODS

Data are provided from school screening conducted by Geta Eye Hospital during February/March 2008. The cases with complete data sets on visual acuity, refractive error and age were included and analyzed using computer software.

RESULTS

Of 1165 children (mean age 11.6 ± 2.5 years) examined, 98.8% (n = 1151) had uncorrected visual acuity of 6/9 and better in at least one eye whereas 1.2% (n = 14) had acuity 6/12 and worse in both eyes. Among them, either eye of 9 children improved to 6/9 and better with correction. However, visual acuity was 6/12 and worse in both eyes of 5 children even after correction. There were 24 children with refractive errors (myopia, 1.54%; n = 18 and hypermetropia, 0.51%; n = 6) in at least one eye. The spherical equivalent refraction was not significantly different with age and gender.

CONCLUSIONS

The incidence of reduced vision and refractive errors among school children of this semi rural district were low.