Dodecanoic acid & palmitic acid disarms rifampicin resistance by putatively targeting mycobacterial efflux pump Rv1218c

Background & objectives

Drug-resistant tuberculosis (TB) jeopardizes the treatment process with poor outcomes. Efflux pumps (EPs) belonging to the ABC transporter family in Mycobacterium tuberculosis confer resistance to rifampicin (RMP) besides genetic mutations thus serving as a target for a potential adjunct therapeutic inhibitory molecule. Rv1218c is one such pump that was previously reported to be active in multidrug-resistant TB clinical isolates.

Methods

In this study, the inhibition potential of Rv1218c-EP was tested on 8 molecules that were shortlisted by in silico methods. These molecules were subjected to the minimum inhibitory concentration (MIC) determination, checkerboard drug combination assay, ethidium bromide-DNA binding assay, and in vitro and ex vivo cytotoxicity assay.

Results

Based on the outcome of the study, two molecules dodecanoic acid (DA) and palmitic acid (PA) were found to be potential enough to decrease the MIC of RMP by 8 to 1000 folds against multidrug-resistant clinical isolates and Rv1218c expressing recombinant Mycobacterium smegmatis.

Interpretation & conclusions

These molecules were also found to reduce the time taken by RMP to kill these drug-resistant Mycobacteria to 48 h, unlike control isolates that survived more than 240 h of RMP exposure. The functional concentration of both molecules was non-toxic to the epithelial and blood mononuclear cells. With further comprehensive scientific validation, PA and DA could be recommended as adjunct therapeutic molecules with first-line anti-TB drugs to treat drug-resistant TB.

Changes in mitral regurgitation following acute myocardial infarction: early and long-term follow-up

Background

Mitral regurgitation (MR) is commonly observed following acute myocardial infarction (MI). Localised left ventricular (LV) remodelling in the region of papillary muscles together with impaired myocardial contractility promote MR. There is a paucity of long-term follow-up studies to determine whether the severity of MR observed post-MI, changes with time.

Purpose

This study retrospectively followed up patients with MR detected following acute MI (AMI) to investigate changes in MR severity with time and assess for pre-discharge predictors of MR regression or progression.

Methods

Clinical records of 1000 patients admitted with AMI between 2016 and 2017 to a single centre were retrospectively interrogated. One hundred and nine patients met the inclusion criteria of MR on pre-discharge transthoracic echocardiography (TTE) and follow-up TTE scans. Echocardiographic parameters were investigated to determine predictors of progression or regression at follow-up. Patients were divided according to those who had early follow-up TTE (within 1-year) and late follow-up TTE (beyond 1-year).

Results

Early follow-up TTE was performed in 73 patients at a median of 6 (IQR 3–9) months. Patients had a mean age of 69±13 years and were predominantly male 50/73 (68%). At baseline, relative MR severities were: 49/73 (67%) mild MR, 23/73 (32%) moderate MR and 1 (1%) severe MR. At follow-up, MR had completely resolved in 18/73 (23%) patients, while 39/73 (53%) had mild MR, 15/73 (21%) moderate MR and 1 (1%) severe MR. Compared to patients with no resolution of MR, those with completel resolution were younger (mean age 62±16 vs 72±11 years; p=0.015) but there were no other significant differences between the groups. Resolution at early follow-up did not significantly influence long-term mortality rates. Late follow-up TTE was performed in 69 patients at a median 2.4 (IQR 2–3.2) years. Pre-discharge, 49/69 (71%) patients had mild MR and 20/69 (29%) moderate MR. At follow-up, MR had completely resolved in 18/69 (26%), and amongst patients with persistent MR, proportion of severities were: 37/69 (54%) mild MR, 11/69 (16%) moderate MR and 3/69 (4%) severe MR. Patients with progression of mild MR were more likely to have lower left ventricular ejection fraction (LVEF: 47±15 vs 57±12%; p=0.010) and greater indexed left ventricular end-systolic volume (LVESVi: 37±23 vs 25±14 ml/m2; p<0.001) on pre-discharge TTE. Resolution of MR at late follow-up was associated with a reduction in long-term mortality [deaths: 2/55 (3%) vs 3/14 (21%); p=0.022] at a mean follow-up of 4.2 years from MI.

Conclusion

MR observed following AMI completely resolved in approximately one-quarter of patients at 6-month and 2-year follow-up. Progression of mild MR at long-term follow-up appears to be associated with increased mortality and is predicted by lower LVEF and greater LVESVi pre-discharge.

Funding Acknowledgement

Type of funding sources: None.

How to Achieve Therapeutic Response in Erlotinib-Resistant Head and Neck Squamous Cell Carcinoma? New Insights from Stable Isotope Labeling with Amino Acids in Cell Culture-Based Quantitative Tyrosine Phosphoproteomics

Resistance to cancer chemotherapy is a major global health burden. Epidermal growth factor receptor (EGFR) is a proven therapeutic target for multiple cancers of epithelial origin. Despite its overexpression in >90% of head and neck squamous cell carcinoma (HNSCC) patients, tyrosine kinase inhibitors such as erlotinib have shown a modest response in clinical trials. Cellular heterogeneity is thought to play an important role in HNSCC therapeutic resistance. Genomic alterations alone cannot explain all resistance mechanisms at play in a heterogeneous system. It is thus important to understand the biochemical mechanisms associated with drug resistance to determine potential strategies to achieve clinical response. We investigated tyrosine kinase signaling networks in erlotinib-resistant cells using quantitative tyrosine phosphoproteomics approach. We observed altered phosphorylation of proteins involved in cell adhesion and motility in erlotinib-resistant cells. Bioinformatics analysis revealed enrichment of pathways related to regulation of the actin cytoskeleton, extracellular matrix (ECM)-receptor interaction, and endothelial migration. Of importance, enrichment of the focal adhesion kinase (PTK2) signaling pathway downstream of EGFR was also observed in erlotinib-resistant cells. To the best of our knowledge, we present the first report of tyrosine phosphoproteome profiling in erlotinib-resistant HNSCC, with an eye to inform new ways to achieve clinical response. Our findings suggest that common signaling networks are at play in driving resistance to EGFR-targeted therapies in HNSCC and other cancers. Most notably, our data suggest that the PTK2 pathway genes may potentially play a significant role in determining clinical response to erlotinib in HNSCC tumors.

Tumescent Local Anesthesia in Parotid Abscess - Novel Application of Old Technique

Tumescent local anesthesia (TLA) is a regional anesthetic technique in which the diluted local anesthetic drug (commonly lidocaine) and epinephrine solution in large volume is injected subcutaneously around the site of incision. The main advantages of TLA are excellent bloodless field and longer duration of analgesia because of addition of epinephrine. Although TLA was used in various surgical procedures, there is no literature to date that has reported its use in the parotid region. Hence, we present an interesting case where this old technique found a novel application in avoiding general anesthesia and its sequelae. We also believe that it provides valuable information to doctors of various categories such as surgeons, Anesthesiologists and general practitioners/family physicians.

Left ventricular function and clinical heart failure after myocardial infarction revascularized with percutaneous coronary intervention - comparison between STEMI and NSTEMI in modern practice

Funding Acknowledgements

Type of funding sources: None.

Introduction

Left ventricular systolic dysfunction (LVSD) is a common consequence of myocardial infarction (MI). Data from historic series identified LVSD in up to 60% of patients post-MI. However, in modern practice, with high-sensitivity cardiac biomarkers leading to early detection of MI and widespread use of early revascularization, the prevalence of LVSD in the acute phase of MI and its impact on subsequent clinical heart failure remains unknown.

Purpose

To ascertain the prevalence of LVSD on pre-discharge echocardiography and its impact on subsequent clinical heart failure after type 1 MI treated with percutaneous coronary intervention (PCI) in a UK tertiary cardiac centre.

Methods

A retrospective electronic patient records review of consecutive patients with type 1 MI treated with PCI between January 2016 - December 2017. Patients treated conservatively or with surgical revascularization were excluded.

Results

1000 consecutive patients were identified and 948/1000 who had an inpatient echocardiogram prior to discharge were included in this analysis – 413 ST elevation MI (STEMI) and 535 non-ST elevation (NSTEMI). Median door to balloon time for STEMI was 42 minutes (IQR 28-79). Median time from symptom onset to intervention for NSTEMI was 3 days (IQR 1-6). LVSD was defined as left ventricular ejection fraction (LVEF) <50% on transthoracic echocardiogram carried out during the hospital episode. LVSD was significantly more prevalent in patients with STEMI compared to NSTEMI (37.4% vs 17.3%, p < 0.001). Median LVEF was significantly lower in the STEMI population (55%, IQR 45-60) compared to patients with NSTEMI (60%, IQR 54-65), p < 0.001. However, rates of clinical heart failure at index presentation with MI did not vary significantly between STEMI and NSTEMI patients (6.1% vs 4.9%, p = 0.414). In stepwise multivariate regression models: age, peak troponin and previous coronary artery bypass grafting were predictors of LVEF, whereas LVEF and previous MI were predictors of clinical heart failure

Patients with LVSD on pre-discharge echocardiography had significantly higher rates of 30-day readmission with heart failure (2.9% vs 0.7%, p = 0.017), 30-day all-cause mortality (6.1% vs 2%, p = 0.001), 30-day cardiac mortality (5.7% vs 1%, p < 0.001) and 2-year all-cause mortality (5.7% vs 1.6%, p = 0.001). However, at 2-years, there was no difference in hospital readmission with heart failure (0.8% vs 0.3%, p = 0.276). There were no significant differences between STEMI and NSTEMI patients for these endpoints.

Conclusions

Early revascularisation with PCI has led to a reduction in the prevalence of early LVSD post-MI compared to historical data. However, the presence of LVSD remains a powerful predictor of adverse clinical outcomes. Despite lower rates of LVSD on pre-discharge echocardiography in patients with NSTEMI compared with STEMI, the incidence of subsequent clinical heart failure is similar. This however may be underestimated due to survival bias.

Anaemia and coronary microvascular dysfunction in end-stage renal disease

Funding Acknowledgements

Type of funding sources: Private grant(s) and/or Sponsorship. Main funding source(s): (1) University Hospitals Birmingham Charity (2) Metchley Park Medical Society

Introduction

 

Coronary microvascular dysfunction (CMD) is common among patients with end-stage renal disease (ESRD) and confers poor prognosis. Coronary flow velocity reserve (CFVR) is a marker of coronary microvascular function and can be reliably measured using Doppler echocardiography. Reduced CFVR in ESRD has been attributed to factors such as hypertension and left ventricular hypertrophy (LVH). Anaemia is prevalent in ESRD but the association between haemoglobin and CFVR in ESRD has not been studied. 

Purpose

 

To assess if CFVR is related to haemoglobin among patients with ESRD. 

Methods

 

22 subjects with ESRD and awaiting kidney transplant (8 pre-dialysis and 14 on peritoneal dialysis) were studied with adenosine myocardial contrast echocardiography, Doppler CFVR assessment and serum multiplex immunoassay analysis. Individuals with diabetes, uncontrolled hypertension or ischaemic heart disease were excluded.

Results 

7/22 (32%) of subjects had CMD (defined as CFVR <2). Age (47 years ± 15 vs 55 ± 10, p = 0.177), estimated glomerular filtration rate [7ml/min/1.73m² (5-11) vs 9 (7-10), p = 0.837], systolic blood pressure (129mmHg ± 25 vs 137 ± 20, p = 0.398) and left ventricular mass index (98g/m² ± 31 vs 98 ± 28, p = 0.936) did not significantly differ between subjects with or without CMD. There were no significant differences in other demographic, haemodynamic, laboratory or echocardiographic variables between the two groups.  A panel of biomarkers of inflammation, myocardial stretch, cardiac fibrosis and LVH studied by multiplex immunoassay also did not show any significant differences between the two groups. No subjects had wall motion abnormalities or perfusion defects on myocardial contrast echocardiography.

CFVR was significantly lower in subjects with CMD (1.6 ± 0.2 vs 3.2 ± 0.9, p < 0.001). Subjects with CMD had significantly lower haemoglobin than subjects without CMD (102g/L ± 12 vs 117g/L ± 11, p = 0.008). There was a moderate positive correlation between haemoglobin and CFVR (r = 0.65, p = 0.001) – figure 1. In a stepwise multiple regression model with CFVR as the dependent variable and age, haemoglobin, systolic blood pressure, left ventricular mass index and estimated glomerular filtration rate as independent variables, only haemoglobin was an independent predictor of CFVR (β=0.051 95%CI 0.023-0.079, p = 0.001). 

Conclusions 

Among our cohort of ESRD patients awaiting kidney transplant, there was a high prevalence of CMD despite well controlled blood pressure and no significant LVH. Subjects with CMD had significantly lower haemoglobin than subjects without CMD. Reduced haemoglobin causes impaired oxygen carrying capacity to the myocardium, which may lead to microvascular ischaemia and adverse microvascular remodelling, causing CMD. Thus, anaemia may be a potentially correctible driver of CMD in ESRD.  This association needs to be confirmed in larger studies.

Abstract Figure 1

JAK-STAT inhibitor as a potential therapeutic opportunity in AML patients resistant to cytarabine and epigenetic therapy

The prognosis of AML is generally poor, with 5-year survival rate of 25%. There has been substantial progress in identification of new therapeutic targets, along with approval of at least three targeted therapies for AML in recent years. Nevertheless, treatment has largely remained unchanged over couple of decades, with ~40% patients not achieving remission. AML is a highly heterogenous disease and there is a need for a preclinical platform to understand the heterogeneity and tumor microenvironment that can guide therapy selection. In this study, we employed an ex vivo tumor explant model to study tumor microenvironment and to select a treatment course for AML patients. Our data reveal dysregulation of DNA methyltransferase (DNMT) and histone deacetylase (HDAC) in a subset of AML patients. Based on this observation, epigenetic modulators azacitidine and panobinostat alone and in combination, were evaluated as treatment regimens in cytarabine refractory tumors. More than 50% of the treated samples showed response to the combination therapy. In order to explore alternate treatment modalities for tumors refractory to these epigenetic modulators, TCGA data analysis was done which revealed increased expression and hypomethylation of IFNGR1/2, suggesting activation of JAK/STAT pathway in AML. This was further interrogated ex vivo, with p-STAT3 expression in patients' samples. Fedratinib, a JAK/STAT inhibitor was evaluated and 78% tumor efficacy response was achieved. Taken together, our data indicate that ex vivo platform derived from patient samples is capable in guiding optimal therapy selection for various classes of drugs including identification of novel targeted therapies.

Ischaemic mitral regurgitation: incidence, clinical and angiographic characteristics of 1000 patients with type 1 myocardial infarction undergoing percutaneous coronary intervention

Background

Previous studies of the incidence and severity of mitral regurgitation (MR) following acute myocardial infarction (MI) were limited by the study population (ST-elevation MI only), by diagnostic methods (lack of multiparametric quantification), or by the time-frame of study (late assessment post-MI). The true incidence of ischaemic MR (IMR) immediately following type 1 MI [non-ST-elevation (NSTEMI) and ST-elevation (STEMI)] patients in the modern era of universal early revascularisation remains unclear. Since even mild IMR confers a poor prognosis, factors which promote or protect against the development of MR require further evaluation.

Purpose

To determine the incidence, clinical and angiographic characteristics of patients with IMR following type 1 MI treated with PCI.

Methods

This was a single-centre study of 1000 consecutive, prospectively recruited patients admitted to the Queen Elizabeth Hospital Birmingham with type 1 MI who underwent PCI. Early inpatient transthoracic echocardiography (TTE) was performed by accredited echocardiographers using standard multiparametric quantification.

Results

MR was observed in 294/1000 patients (29.4%) post-MI, graded as mild (76%), moderate (21%) and severe (3%). Median time from symptom onset to PCI was 1 day (IQR 0–4) and to TTE 2 days (IQR 1–3).

Compared to patients without MR (MR-), those with MR (MR+) were older (73±12 years vs 66±13 years; p<0.001), male (75% vs 64%; p<0.001) and more likely to have a history of hypertension (HTN) (63% vs 55%; p=0.0117), heart failure (HF) (3.4% vs 1.1%; p=0.0140) and previous MI (28% vs 20%; p<0.005). MR+ patients more frequently presented with HF (8.5% vs 4.2%; p=0.0075), lower LV ejection fraction (LVEF) (50±14% vs 55±11%; p<0.001) and higher peak high sensitivity troponin T (765ng/L, IQR 170–3032 vs 400ng/L, IQR 51–1966; p<0.0001).

MR+ patients were more likely to have severe disease in the left circumflex (LCx) (50% vs 33%; p<0.0001) or right coronary artery (RCA) (51% vs 43%; p=0.0135). Incidence of severe disease in the left main stem and left anterior descending artery (LAD) did not significantly differ between the two groups.

Incidence of MR was equal (29%) amongst STEMI (126/431) and NSTEMI (168/569) patients. While the time to revascularisation did not affect the prevalence of MR following STEMI (linear regression analysis of door-to-balloon time in MR+ and MR- patients p=0.843), NSTEMI patients were more likely to develop MR if revascularisation was delayed (linear regression analysis of symptom onset to PCI time MR+ vs MR- p=0.061).

Conclusion

Almost 1/3 of patients with type 1 MI undergoing revascularisation have MR evident on pre-discharge TTE. Factors promoting MR include older age, male sex, HTN, HF, larger non-LAD territory infarct, and depressed LVEF. The incidence of MR following STEMIs and NSTEMIs is equal. Earlier revascularisation is unlikely to reduce MR in STEMI patients but may improve MR prevalence following NSTEMI.

Funding Acknowledgement

Type of funding source: None

Risk stratification on echocardiography and outcome in ischaemic mitral regurgitation

Background

Ischaemic mitral regurgitation (IMR) confers a poor prognosis. Transcatheter intervention may improve survival but benefit is likely to depend on severity of IMR relative to LV remodelling following myocardial infarction (MI). In theory, those with “discordant” IMR (significant regurgitant volume without severe LV dilatation or impairment), are expected to benefit most from mitral intervention. While subcategorization may help to inform treatment, there are no data on post-MI patients in this respect.

Purpose

To determine the incidence of discordant & concordant IMR categorised on echocardiography post-MI and impact on outcomes.

Methods

1000 consecutive patients admitted to our hospital with myocardial infarction who underwent coronary angioplasty were included. Early inpatient TTE was performed by accredited echocardiographers using standard multiparametric quantification.

Using TTE parameters, 4 subgroups were identified (figure) according to the degree of MR relative to LV remodelling. Thresholds were based on European guidelines (± 2SD from normal) and median value among survivors for vena contracta (VC):

– LVEF: 52% (♂), 54% (♀)

– Indexed LV end diastolic volume (LVEDVi): 74ml/m2 (♂), 61ml/m2 (♀)

– Effective regurgitant orifice area (EROA) ≥0.2cm2

– Regurgitant volume (RVol) ≥30ml

– VC ≥0.5cm

Results

MR was seen in 294/1000 patients (29.4%) with a severity of mild (76%), moderate (21%) and severe (3%). Concordant and discordant IMR were each seen in 16/294 (5%) of IMR patients post-MI.

After a mean follow up of 3.2 years, IMR patients had a 3% rate of heart failure (HF) within 1 year and 19% mortality. Non-survivors had significantly worse IMR (PISA 0.65±0.25cm vs 0.54±0.19cm; p=0.033; VC 0.63±0.25cm vs 0.49±0.18cm; p=0.014), worse LV function (LVEF 44±17% vs 51±13%; p<0.001), larger LV (LVEDVi 67±23ml/m2 vs 60±22ml/m2; p=0.032) and larger indexed LA volume (LAVi) (44±22ml vs 35±15ml; p<0.001). Those with concordant IMR had the worst survival (50%) although almost 1 in 5 of those with discordant MR died within the follow up period (19%). Using multivariable Cox regression, significant predictors of mortality included LVEF (p<0.001; HR 0.96, 0.94–0.98) and LAVi (p<0.001; HR 1.02, 1.01–1.03) but not LVEDVi.

Conclusion

1) Significant predictors of mortality in IMR include LA dilatation and decline in LVEF, but not LV dilatation.

2) Although discordant severe IMR is uncommon following MI, mortality if left untreated remains high. Attention should be paid to early selection of this cohort for intervention.

Funding Acknowledgement

Type of funding source: None

Workplace based Potentially Malignant Oral Lesions Screening among Tobacco Consuming Migrant Construction Site Workers in Chennai, South India: A Pilot Study

Context:

Vulnerable population groups such as migrant workers are identified as emerging high-risk groups for oral cancer owing to the high prevalence of smokeless tobacco consumption. Premature deaths due to oral cancer can be prevented by screening the population with high tobacco consumption practices and detecting early reversible stages of oral mucosal cavity lesions and facilitating linkages for further care.

Aim:

To assess prevalence of potentially malignant oral mucosal cavity lesions among tobacco consuming migrant construction workers in sub-urban Chennai, India.

Settings and Designs:

A workplace based cross-sectional study design.

Materials and Methods:

A cross-sectional study was conducted at workplaces i.e., construction sites for screening potentially malignant oral mucosal cavity lesions among migrant workers across 23 construction sites of Chennai during September 2019 - February 2020. An onsite, group health education session was provided about the harms of tobacco use to the migrants.

Statistical Analysis Used:

Data entered in MS Excel was analysed using SPSS and multivariate analysis was performed.

Results:

Among 640 migrants included in the study, 411 (64.2%) were less than 30 years of age, 623 (97.4%) were from north-eastern states of India such as West Bengal, Bihar, Rajasthan, Uttar Pradesh, Jharkhand. A considerable size (272, 42.5%) could not read or write and 355 (55.4%) earn a monthly income of less than ten thousand rupees. Current tobacco users were 619 (96.7%), smokeless tobacco users (463, 72.34%), smokers (206, 32.2%) and dual users (52,8.12%). Inflammatory mucosal lesions in the oral cavity were 70.97% and more among smokeless tobacco users comparable to 22.58% among tobacco smokers and was significantly associated with up to 20 years of tobacco consumption.

Conclusions:

Prevalence of Potentially malignant oral lesions among smokeless tobacco using interstate migrant construction site workers is very high and need urgent interventions.

Self-care practices among type II diabetics in rural area of Kancheepuram district, Tamil Nadu

Introduction:

Type 2 diabetes mellitus is one of the most prevalent noncommunicable diseases in India. The acute and chronic complications of diabetes impact the physical, mental, and social well-being of the patients, thereby, placing a major burden on the health care system. Studies have shown that adequate self-care practices among the patients will facilitate good glycemic control and prevent complications.

Objectives:

To study the patterns of self-care practice among diabetic patients and the factors associated with them.

Methods:

This descriptive cross-sectional study was carried out among 250 diabetics in the rural field practice area of a Tertiary Medical College and Hospital in Chennai. The participants were interviewed on their diabetic status and various components of self-care practices adopted from The Summary of Diabetes Self-care Activities (SDSCA) Measure. Adherence to medication was assessed by using Morisky Medication Adherence Scale-4 (MMAS-4).

Results:

Our study observed that the overall prevalence of good self-care practices was very low (5.6%). Moderate self-care practices were prevalent in 42% of the study participants whereas the majority (52.4%) of the study population had poor self-care practices. In our study, the association between self-care activity with educational status and occupation was found to be statistically significant. Adherence was high for blood sugar testing (75.2%) and medication (70.4%) in the study population whereas adherence for foot care was poor (17.6%).

Conclusion:

Our study emphasized on the need for knowledge and awareness to be provided in rural areas regarding diabetes care management and self-care practices. Structured programs need to be planned to improve the attitude and practices of diabetic patients to promote better compliance towards diet, exercise, adherence to drugs, and appropriate foot care.

Perioperative intravenous contrast administration and the incidence of acute kidney injury after major gastrointestinal surgery: prospective, multicentre cohort study

BACKGROUND

This study aimed to determine the impact of preoperative exposure to intravenous contrast for CT and the risk of developing postoperative acute kidney injury (AKI) in patients undergoing major gastrointestinal surgery.

METHODS

This prospective, multicentre cohort study included adults undergoing gastrointestinal resection, stoma reversal or liver resection. Both elective and emergency procedures were included. Preoperative exposure to intravenous contrast was defined as exposure to contrast administered for the purposes of CT up to 7 days before surgery. The primary endpoint was the rate of AKI within 7 days. Propensity score-matched models were adjusted for patient, disease and operative variables. In a sensitivity analysis, a propensity score-matched model explored the association between preoperative exposure to contrast and AKI in the first 48 h after surgery.

RESULTS

A total of 5378 patients were included across 173 centres. Overall, 1249 patients (23·2 per cent) received intravenous contrast. The overall rate of AKI within 7 days of surgery was 13·4 per cent (718 of 5378). In the propensity score-matched model, preoperative exposure to contrast was not associated with AKI within 7 days (odds ratio (OR) 0·95, 95 per cent c.i. 0·73 to 1·21; P = 0·669). The sensitivity analysis showed no association between preoperative contrast administration and AKI within 48 h after operation (OR 1·09, 0·84 to 1·41; P = 0·498).

CONCLUSION

There was no association between preoperative intravenous contrast administered for CT up to 7 days before surgery and postoperative AKI. Risk of contrast-induced nephropathy should not be used as a reason to avoid contrast-enhanced CT.

MAP2K1 is a potential therapeutic target in erlotinib resistant head and neck squamous cell carcinoma

Epidermal growth factor receptor (EGFR) targeted therapies have shown limited efficacy in head and neck squamous cell carcinoma (HNSCC) patients despite its overexpression. Identifying molecular mechanisms associated with acquired resistance to EGFR-TKIs such as erlotinib remains an unmet need and a therapeutic challenge. In this study, we employed an integrated multi-omics approach to delineate mechanisms associated with acquired resistance to erlotinib by carrying out whole exome sequencing, quantitative proteomic and phosphoproteomic profiling. We observed amplification of several genes including AXL kinase and transcription factor YAP1 resulting in protein overexpression. We also observed expression of constitutively active mutant MAP2K1 (p.K57E) in erlotinib resistant SCC-R cells. An integrated analysis of genomic, proteomic and phosphoproteomic data revealed alterations in MAPK pathway and its downstream targets in SCC-R cells. We demonstrate that erlotinib-resistant cells are sensitive to MAPK pathway inhibition. This study revealed multiple genetic, proteomic and phosphoproteomic alterations associated with erlotinib resistant SCC-R cells. Our data indicates that therapeutic targeting of MAPK pathway is an effective strategy for treating erlotinib-resistant HNSCC tumors.

PIM1 kinase promotes gallbladder cancer cell proliferation via inhibition of proline-rich Akt substrate of 40 kDa (PRAS40)

Gallbladder cancer (GBC) is a rare malignancy, associated with poor disease prognosis with a 5-year survival of only 20%. This has been attributed to late presentation of the disease, lack of early diagnostic markers and limited efficacy of therapeutic interventions. Elucidation of molecular events in GBC can contribute to better management of the disease by aiding in the identification of therapeutic targets. To identify aberrantly activated signaling events in GBC, tandem mass tag-based quantitative phosphoproteomic analysis of five GBC cell lines was carried out. Proline-rich Akt substrate 40 kDa (PRAS40) was one of the proteins found to be hyperphosphorylated in all the invasive GBC cell lines. Tissue microarray-based immunohistochemical labeling of phospho-PRAS40 (T246) revealed moderate to strong staining in 77% of the primary gallbladder adenocarcinoma cases. Regulation of PRAS40 activity by inhibiting its upstream kinase PIM1 resulted in a significant decrease in cell proliferation, colony forming and invasive ability of GBC cells. Our results support the role of PRAS40 phosphorylation in GBC cell survival and aggressiveness. This study also elucidates phospho-PRAS40 as a clinical marker in GBC and the role of PIM1 as a therapeutic target in GBC.

Testican 1 (SPOCK1) and protein tyrosine phosphatase, receptor type S (PTPRS) show significant increase in saliva of tobacco users with oral cancer

Objectives:

To identify potential candidate proteins which are secretory in nature and present at a higher abundance in oral cancer patients with tobacco habits.

Methods:

Conditioned media of tobacco-treated and -untreated non-neoplastic oral keratinocytes were analyzed using iTRAQ-based mass spectrometry. Hypersecreted proteins; SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1 (SPOCK1); prosaposin (PSAP); and protein tyrosine phosphatase, receptor type S (PTPRS) were validated by enzyme-linked immunosorbent assay (ELISA) using saliva samples from oral cancer patients who are tobacco users.

Results:

Proteomic analysis of tobacco-treated and -untreated cells led to the identification of 2873 proteins. Among these, 378 proteins showed high abundance and 253 proteins showed low abundance (2-fold cutoff) in conditioned-media of tobacco-treated cells. ELISA-based validation showed significantly higher levels of SPOCK1, PSAP, and PTPRS in oral cancer patients with tobacco chewing habits compared to healthy controls. However, PSAP showed low specificity compared to SPOCK1 and PTPRS.

Conclusions:

This study indicates significantly increased levels of SPOCK1, PSAP, and PTPRS in saliva of oral cancer patients with tobacco habits. These protein biomarkers might be useful to identify tobacco users with high risk of developing oral cancers.

Dynamic Search Engine Platform for Cloud Service Level Agreements Using Semantic Annotation

This article describes how cloud applications are negotiated, deployed, monitored, evaluated and terminated through the service level agreements (SLA). The service definition & their objectives, performance measures, pricing, roles of the involved parties are stated as part of the SLA. Searching for SLA templates from the provider's place is considered as a cumbersome process for the consumer. Also, it is not guaranteed that retrieved SLAs always match with the consumer requirements. Hence, semantic search engine platforms for cloud SLA using a novel architecture are introduced here. SLA agreements are crawled from the web and annotation is performed in the agreement terms using SLA ontologies to fasten and improve the accuracy of the search process. In the proposed architecture, 3 ontologies are developed for SaaS, PaaS and IaaS as well as 140 SLA documents are gathered. Results revealed that the search efficacy is almost 90% in finding the desired SLA for the consumer to ease negotiation. Moreover, the performance is compared with similar search engine GoNTogle, and it was observed that proposed model produced good results.

Identification of potential biomarkers of head and neck squamous cell carcinoma using iTRAQ based quantitative proteomic approach

Head and neck squamous cell carcinoma (HNSCC) is one of the most common cancers in India. Despite improvements in treatment strategy, the survival rates of HNSCC patients remain poor. Thus, it is necessary to identify biomarkers that can be used for early detection of disease. In this study, we employed iTRAQ-based quantitative mass spectrometry analysis to identify dysregulated proteins from a panel of head and neck squamous cell carcinoma (HNSCC) cell lines. We identified 2468 proteins, of which 496 proteins were found to be dysregulated in at least two out of three HNSCC cell lines compared to immortalized normal oral keratinocytes. We detected increased expression of replication protein A1 (RPA1) and heat shock protein family H (Hsp110) member 1 (HSPH1), in HNSCC cell lines compared to control. The differentially expressed proteins were further validated using parallel reaction monitoring (PRM) and western blot analysis in HNSCC cell lines. Immunohistochemistry-based validation using HNSCC tissue microarrays revealed overexpression of RPA1 and HSPH1 in 15.7% and 32.2% of the tested cases, respectively. Our study illustrates quantitative proteomics as a robust approach for identification of potential HNSCC biomarkers. The proteomic data has been submitted to ProteomeXchange Consortium (http://www.proteomecentral.proteomexchange.org) via the PRIDE public data repository accessible using the data identifier - PXD009241.

A network map of IL-33 signaling pathway

Interleukin-33 (IL-33) is a member of the IL-1 family of cytokines that play a central role in the regulation of immune responses. Its release from epithelial and endothelial cells is mediated by pro-inflammatory cytokines, cell damage and by recognition of pathogen-associated molecular patterns (PAMPs). The activity of IL-33 is mediated by binding to the IL-33 receptor complex (IL-33R) and activation of NF-κB signaling via the classical MyD88/IRAK/TRAF6 module. IL-33 also induces the phosphorylation and activation of ERK1/2, JNK, p38 and PI3K/AKT signaling modules resulting in the production and release of pro-inflammatory cytokines. Aberrant signaling by IL-33 has been implicated in the pathogenesis of several acute and chronic inflammatory diseases, including asthma, atopic dermatitis, rheumatoid arthritis and ulcerative colitis among others. Considering the biomedical importance of IL-33, we developed a pathway resource of signaling events mediated by IL-33/IL-33R in this study. Using data mined from the published literature, we describe an integrated pathway reaction map of IL-33/IL-33R consisting of 681 proteins and 765 reactions. These include information pertaining to 19 physical interaction events, 740 enzyme catalysis events, 6 protein translocation events, 4 activation/inhibition events, 9 transcriptional regulators and 2492 gene regulation events. The pathway map is publicly available through NetPath ( http://www.netpath.org /), a resource of human signaling pathways developed previously by our group. This resource will provide a platform to the scientific community in facilitating identification of novel therapeutic targets for diseases associated with dysregulated IL-33 signaling. Database URL: http://www.netpath.org/pathways?path_id=NetPath_120 .

Long-Term Cigarette Smoke Exposure and Changes in MiRNA Expression and Proteome in Non-Small-Cell Lung Cancer

Chronic exposure to cigarette smoke markedly increases the risk for lung cancer. Regulation of gene expression at the post-transcriptional level by miRNAs influences a variety of cancer-related interactomes. Yet, relatively little is known on the effects of long-term cigarette smoke exposure on miRNA expression and gene regulation. NCI-H292 (H292) is a cell line sensitive to cigarette smoke with mucoepidermoid characteristics in culture. We report, in this study, original observations on long-term (12 months) cigarette smoke effects in the H292 cell line, using microarray-based miRNA expression profiling, and stable isotopic labeling with amino acids in cell culture-based quantitative proteomic analysis. We identified 112 upregulated and 147 downregulated miRNAs (by twofold) in cigarette smoke-treated H292 cells. The liquid chromatography-tandem mass spectrometry analysis identified 3,959 proteins, of which, 303 proteins were overexpressed and 112 proteins downregulated (by twofold). We observed 39 miRNA target pairs (proven targets) that were differentially expressed in response to chronic cigarette smoke exposure. Gene ontology analysis of the target proteins revealed enrichment of proteins in biological processes driving metabolism, cell communication, and nucleic acid metabolism. Pathway analysis revealed the enrichment of phagosome maturation, antigen presentation pathway, nuclear factor erythroid 2-related factor 2-mediated oxidative stress response, and cholesterol biosynthesis pathways in cigarette smoke-exposed cells. In conclusion, this report makes an important contribution to knowledge on molecular changes in a lung cell line in response to long term cigarette smoke exposure. The findings might inform future strategies for drug target, biomarker and diagnostics innovation in lung cancer, and clinical oncology. These observations also call for further research on the extent to which continuing or stopping cigarette smoking in patients diagnosed with lung cancer translates into molecular and clinical outcomes.

Chronic exposure to cigarette smoke leads to activation of p21 (RAC1)-activated kinase 6 (PAK6) in non-small cell lung cancer cells

Epidemiological data clearly establishes cigarette smoking as one of the major cause for lung cancer worldwide. Recently, targeted therapy has become one of the most preferred modes of treatment for cancer. Though certain targeted therapies such as anti-EGFR are in clinical practice, they have shown limited success in lung cancer patients who are smokers. This demands discovery of alternative drug targets through systematic investigation of cigarette smoke-induced signaling mechanisms. To study the signaling events activated in response to cigarette smoke, we carried out SILAC-based phosphoproteomic analysis of H358 lung cancer cells chronically exposed to cigarette smoke. We identified 1,812 phosphosites, of which 278 phosphosites were hyperphosphorylated (≥ 3-fold) in H358 cells chronically exposed to cigarette smoke. Our data revealed hyperphosphorylation of S560 within the conserved kinase domain of PAK6. Activation of PAK6 is associated with various processes in cancer including metastasis. Mechanistic studies revealed that inhibition of PAK6 led to reduction in cell proliferation, migration and invasion of the cigarette smoke treated cells. Further, siRNA mediated silencing of PAK6 resulted in decreased invasive abilities in a panel of non-small cell lung cancer (NSCLC) cells. Consistently, mice bearing tumor xenograft showed reduced tumor growth upon treatment with PF-3758309 (group II PAK inhibitor). Immunohistochemical analysis revealed overexpression of PAK6 in 66.6% (52/78) of NSCLC cases in tissue microarrays. Taken together, our study indicates that PAK6 is a promising novel therapeutic target for NSCLC, especially in smokers.

Targeting focal adhesion kinase overcomes erlotinib resistance in smoke induced lung cancer by altering phosphorylation of epidermal growth factor receptor

EGFR-based targeted therapies have shown limited success in smokers. Identification of alternate signaling mechanism(s) leading to TKI resistance in smokers is critically important. We observed increased resistance to erlotinib in H358 NSCLC (non-small cell lung carcinoma) cells chronically exposed to cigarette smoke (H358-S) compared to parental cells. SILAC-based mass-spectrometry approach was used to study altered signaling in H358-S cell line. Importantly, among the top phosphosites in H358-S cells we observed hyperphosphorylation of EGFR (Y1197) and non-receptor tyrosine kinase FAK (Y576/577). Supporting these observations, a transcriptomic-based pathway activation analysis of TCGA NSCLC datasets revealed that FAK and EGFR internalization pathways were significantly upregulated in smoking patients, compared to the never-smokers and were associated with elevated PI3K signaling and lower level of caspase cascade and E-cadherin pathways activation. We show that inhibition of FAK led to decreased cellular proliferation and invasive ability of the smoke-exposed cells, and restored their dependency on EGFR signaling. Our data suggests that activation of focal adhesion pathway significantly contributes to erlotinib resistance, and that FAK is a potential therapeutic target for management of erlotinib resistance in smoke-induced NSCLC.

miRNA and Proteomic Dysregulation in Non-Small Cell Lung Cancer in Response to Cigarette Smoke

BACKGROUND

Dysregulation of miRNAs is associated with the development of non-small cell lung cancer (NSCLC). It is imperative to study the dysregulation of miRNAs by cigarette smoke which will affect their targets, either leading to the overexpression of oncoproteins or downregulation of tumor suppressor proteins.

OBJECTIVE AND METHODS

In this study, we carried out miRNA sequencing and SILAC-based proteomic analysis of H358 cells chronically exposed to cigarette smoke condensate. Using bioinformatics analysis, we mapped the dysregulated miRNAs to differentially expressed target proteins identified in our data. Gene ontology-based enrichment and pathway analysis was performed using the deregulated targets to study the role of cigarette smoke-mediated miRNA dysregulation in NSCLC cell line.

RESULTS

miRNA sequencing resulted in the identification of 208 miRNAs, of which 6 miRNAs were found to be significantly dysregulated (2 fold, Log Base 2; p-value ≤ 0.05) in H358-Smoke cells. Proteomic analysis of the smoke exposed cells compared to the untreated parental cells resulted in the quantification of 2,610 proteins, of which 690 proteins were found to be differentially expressed (fold change ≥ 2). Gene ontology based analysis of target proteins revealed enrichment of proteins driving metabolism and a decrease in expression of proteins associated with immune response in the cells exposed to cigarette smoke. Pathway study using Ingenuity Pathway Analysis (IPA) revealed activation of NRF2-mediated oxidative stress response and actin-cytoskeleton signaling, and repression of protein kinase A signaling in H358-Smoke cells. We also identified 5 novel miRNAs in H358-Smoke cells using unassigned reads of small RNA-Seq dataset.

CONCLUSION

In summary, this study indicates that chronic exposure to cigarette smoke leads to widespread dysregulation of miRNAs and their targets, resulting in signaling aberrations in NSCLC cell line. The miRNAs and their targets identified in the study need to be further investigated to explore their role as potential therapeutic targets and/or molecular markers in NSCLC especially in smokers.

Impact of obstructive sleep apnea on neurological recovery after ischemic stroke: A prospective study

OBJECTIVES

The presence of obstructive sleep apnea (OSA) has been found to adversely affect the neurological recovery after acute ischemic stroke (AIS) in previous observational studies. However, in most of these studies, diagnosis of OSA was based on oximetry data alone, raising concern in the accuracy of diagnosis as well as estimation of severity. Purpose of our study was to determine the prevalence and severity of OSA (based on polysomnography and American Association of Sleep Medicine [AASM] criteria) in patients with AIS and to compare the post-stroke neurological and functional outcome, in those with and without OSA.

MATERIALS AND METHODS

A prospective single-centre study was conducted over a period of eighteen months from January 2013. The demographic and clinical data were collected, and the etiology of stroke was classified according to TOAST classification. Subsequently, all selected patients (N=99) underwent premorbid sleep status assessment by Epworth Sleepiness Scale followed by polysomnography using Resmed ApneaLink polysomnograph. Data were analyzed to find out the prevalence and severity of OSA as well as its impact on neurological recovery as assessed by National Institutes of Health Stroke Scale (NIHSS) and modified Rankin scale (mRS) at different time points, starting from admission.

RESULTS

There was a high prevalence of OSA (~60%) with a quarter of them having severe OSA. The OSA group had a significantly higher mean NIHSS score at discharge (P=.002) and significantly higher mRS score (irrespective of severity of OSA) at all points of evaluation.

CONCLUSION

Ischemic stroke patients with OSA tend to have poor neurological and functional recovery, across all segments of stroke and OSA severity.

Chronic Cigarette Smoke Mediated Global Changes in Lung Mucoepidermoid Cells: A Phosphoproteomic Analysis

Proteomics analysis of chronic cigarette smoke exposure is a rapidly emerging postgenomics research field. While smoking is a major cause of lung cancer, functional studies using proteomics approaches could enrich our mechanistic understanding of the elusive lung cancer global molecular signaling and cigarette smoke relationship. We report in this study on a stable isotope labeling by amino acids in cell culture-based quantitative phosphoproteomic analysis of a human lung mucoepidermoid carcinoma cell line, H292 cells, chronically exposed to cigarette smoke. Using high resolution Orbitrap Velos mass spectrometer, we identified the hyperphosphorylation of 493 sites, which corresponds to 341 proteins and 195 hypophosphorylated sites, mapping to 142 proteins upon smoke exposure (2.0-fold change). We report differential phosphorylation of multiple kinases, including PAK6, EPHA4, LYN, mitogen-activated protein kinase, and phosphatases, including TMEM55B, PTPN14, TIGAR, among others, in response to chronic cigarette smoke exposure. Bioinformatics analysis revealed that the molecules differentially phosphorylated upon chronic exposure of cigarette smoke are associated with PI3K/AKT/mTOR and CDC42-PAK signaling pathways. These signaling networks are involved in multiple cellular processes, including cell polarity, cytoskeletal remodeling, cellular migration, protein synthesis, autophagy, and apoptosis. The present study contributes to emerging proteomics insights on cigarette smoke mediated global signaling in lung cells, which in turn may aid in development of precision medicine therapeutics and postgenomics biomarkers.

Longevity effect of a polysaccharide from Chlorophytum borivilianum on Caenorhabditis elegans and Saccharomyces cerevisiae

The traditional Indian medicine, Ayurveda, provides insights and practical solutions towards a healthy life style. Rasayana is a branch of Ayurveda known for preserving and promoting health, enhancing the quality of life and delaying the aging process. In the traditional knowledge, the Rasayana herb, Chlorophytum borivilianum (C. borivilanum) is regarded as a general health promoting tonic that delays aging and increases lifespan, cognitive function and physical strength. Aging is a complex and multifactorial physiological phenomenon that manifests itself over a wide range of biological systems, tissues, and functions. Longevity is an obvious marker of physiological aging. Simple model systems such as the single-cell budding yeast Saccharomyces cerevisiae (S. cerevisiae) and the nematode, Caenorhabditis elegans (C. elegans) are widely used to study the aging process and longevity. Here, we show that a polysaccharide fraction obtained from C. borivilianum increases the lifespan of S. cerevisiae and C. elegans, using an automated screening platform (Chronoscreen^TM). Chemical analysis of this extract revealed a low molecular weight polysaccharide of 1000 Da, predominantly comprising Glu1→6Glu linkage. This polysaccharide showed significant dose-dependent extension of the median lifespan of S. cerevisiae by up to 41% and of the median lifespan of C. elegans by up to 10%. Taking cue from these results and the traditionally described benefits of Rasayanas on skin rejuvenation, we tested in vitro the polysaccharide for potential skin benefits. In a keratinocyte culture, we observed that this polysaccharide increased cell proliferation significantly, and induced synthesis of hyaluronic acid (HA), a well-known extracellular matrix component. Furthermore, when added to culture medium of human reconstructed epidermis, we observed an enhanced production of epidermal markers, e.g. CD44 and HA that are otherwise diminished in aged skin. Together, these results suggest that in addition to life-span extension of S. cerevisiae and C. elegans, a polysaccharide from the Rasayana herb, C. borivilianum may have beneficial effects on skin aging parameters.

Corrigendum: A dual specificity kinase, DYRK1A, as a potential therapeutic target for head and neck squamous cell carcinoma

This corrects the article DOI: 10.1038/srep36132.

Comparison of two different doses dexmedetomidine as an adjuvant to bupivacaine in sub-arachnoid block for abdominal hysterectomies. A randomized double blinded study

Background: Abdominal hysterectomy is often a long duration procedure and warrants intense pain relief in the post-operative period. Dexmedetomidine when added to bupivacaine in subarachnoid block prolongs the duration of surgical anaesthesia, decreases blood loss and prolongs duration of post-operative pain relief. Aims and Objective: To compare two different doses dexmedetomidine as an adjuvant to bupivacaine in sub-arachnoid block in abdominal hysterectomy surgeries. Materials and Methods: 60 patients of age group 30-60 years posted for elective abdominal hysterectomies under American Society of Anaesthesiologists (ASA) physical classification I or II were randomly allocated into 2 groups of 30 each. Group A received 5 micrograms (μg) of dexmedetomidine along with 3.5 ml of 0.5% bupivacaine in sub-arachnoid block. Group B received 10 μg of dexmedetomidine along with 3.5 ml of 0.5% bupivacaine in sub-arachnoid block. Changes in blood pressure, heart rate, respiratory rate, oxygen saturation, ephedrine consumption, blood loss, duration of sensory block, duration of motor block, duration of analgesia were compared between two groups. Results: There was no significant difference in change in heart rate, respiratory rate, oxygen saturation, duration of sensory block, duration of motor block between two groups. Patients in group B had significant decrease in blood pressure, blood loss and significant increase in ephedrine consumption compared to Group A. The duration of analgesia was also prolonged in group B compared to Group A. Conclusion: Dexmedetomidine in dose of 10 μg is a better adjuvant to bupivacaine for abdominal hysterectomy surgeries.Asian Journal of Medical Sciences Vol.8(2) 2017 59-63

Urethral Stenting for Obstructive Uropathy Utilizing Digital Radiography for Guidance: Feasibility and Clinical Outcome in 26 Dogs

Background

Urethral stent placement is an interventional treatment option to alleviate urethral outflow obstruction. It has been described utilizing fluoroscopy, but fluoroscopy is not as readily available in private practice as digital radiography.

Objectives

To describe the use of digital radiography for urethral stent placement in dogs with obstructive uropathy.

Animals

Twenty‐six client‐owned dogs presented for dysuria associated with benign and malignant causes of obstructive uropathy that underwent urethral stent placement.

Methods

Retrospective study.

Results

Causes of obstructive uropathy included transitional cell carcinoma, prostatic carcinoma, hemangiosarcoma, obstructive proliferative urethritis, compressive vaginal leiomyosarcoma, and detrusor‐sphincter dyssynergia. Survival time range was 1–48 months (median, 5 months). All dogs were discharged from the hospital with urine outflow restored. Intraprocedural complications included guide wire penetration of the urethral wall in 1 dog and improper stent placement in a second dog. Both complications were successfully managed at the time of the procedure with no follow‐up problems noted in either patient.

Conclusion and Clinical Importance

Urethral stent placement can be successfully performed utilizing digital radiography. The complications experienced can be avoided by more cautious progression with each step through the procedure and serial radiography. The application of digital radiography may allow treatment of urethral obstruction to become more readily available.

Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes

Complementing genome sequence with deep transcriptome and proteome data could enable more accurate assembly and annotation of newly sequenced genomes. Here, we provide a proof-of-concept of an integrated approach for analysis of the genome and proteome of Anopheles stephensi, which is one of the most important vectors of the malaria parasite. To achieve broad coverage of genes, we carried out transcriptome sequencing and deep proteome profiling of multiple anatomically distinct sites. Based on transcriptomic data alone, we identified and corrected 535 events of incomplete genome assembly involving 1196 scaffolds and 868 protein-coding gene models. This proteogenomic approach enabled us to add 365 genes that were missed during genome annotation and identify 917 gene correction events through discovery of 151 novel exons, 297 protein extensions, 231 exon extensions, 192 novel protein start sites, 19 novel translational frames, 28 events of joining of exons, and 76 events of joining of adjacent genes as a single gene. Incorporation of proteomic evidence allowed us to change the designation of more than 87 predicted “noncoding RNAs” to conventional mRNAs coded by protein-coding genes. Importantly, extension of the newly corrected genome assemblies and gene models to 15 other newly assembled Anopheline genomes led to the discovery of a large number of apparent discrepancies in assembly and annotation of these genomes. Our data provide a framework for how future genome sequencing efforts should incorporate transcriptomic and proteomic analysis in combination with simultaneous manual curation to achieve near complete assembly and accurate annotation of genomes.

A dual specificity kinase, DYRK1A, as a potential therapeutic target for head and neck squamous cell carcinoma

Despite advances in clinical management, 5-year survival rate in patients with late-stage head and neck squamous cell carcinoma (HNSCC) has not improved significantly over the past decade. Targeted therapies have emerged as one of the most promising approaches to treat several malignancies. Though tyrosine phosphorylation accounts for a minority of total phosphorylation, it is critical for activation of signaling pathways and plays a significant role in driving cancers. To identify activated tyrosine kinase signaling pathways in HNSCC, we compared the phosphotyrosine profiles of a panel of HNSCC cell lines to a normal oral keratinocyte cell line. Dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A (DYRK1A) was one of the kinases hyperphosphorylated at Tyr-321 in all HNSCC cell lines. Inhibition of DYRK1A resulted in an increased apoptosis and decrease in invasion and colony formation ability of HNSCC cell lines. Further, administration of the small molecular inhibitor against DYRK1A in mice bearing HNSCC xenograft tumors induced regression of tumor growth. Immunohistochemical labeling of DYRK1A in primary tumor tissues using tissue microarrays revealed strong to moderate staining of DYRK1A in 97.5% (39/40) of HNSCC tissues analyzed. Taken together our results suggest that DYRK1A could be a novel therapeutic target in HNSCC.

Dysregulation of splicing proteins in head and neck squamous cell carcinoma

Signaling plays an important role in regulating all cellular pathways. Altered signaling is one of the hallmarks of cancers. Phosphoproteomics enables interrogation of kinase mediated signaling pathways in biological systems. In cancers, this approach can be utilized to identify aberrantly activated pathways that potentially drive proliferation and tumorigenesis. To identify signaling alterations in head and neck squamous cell carcinoma (HNSCC), we carried out proteomic and phosphoproteomic analysis of HNSCC cell lines using a combination of tandem mass tag (TMT) labeling approach and titanium dioxide-based enrichment. We identified 4,920 phosphosites corresponding to 2,212 proteins in six HNSCC cell lines compared to a normal oral cell line. Our data indicated significant enrichment of proteins associated with splicing. We observed hyperphosphorylation of SRSF protein kinase 2 (SRPK2) and its downstream substrates in HNSCC cell lines. SRPK2 is a splicing kinase, known to phosphorylate serine/arginine (SR) rich domain proteins and regulate splicing process in eukaryotes. Although genome-wide studies have reported the contribution of alternative splicing events of several genes in the progression of cancer, the involvement of splicing kinases in HNSCC is not known. In this study, we studied the role of SRPK2 in HNSCC. Inhibition of SRPK2 resulted in significant decrease in colony forming and invasive ability in a panel of HNSCC cell lines. Our results indicate that phosphorylation of SRPK2 plays a crucial role in the regulation of splicing process in HNSCC and that splicing kinases can be developed as a new class of therapeutic target in HNSCC.

A Potential Biomarker in Amyotrophic Lateral Sclerosis: Can Assessment of Brain Iron Deposition with SWI and Corticospinal Tract Degeneration with DTI Help?

BACKGROUND AND PURPOSE

Iron-mediated oxidative stress plays a pivotal role in the pathogenesis of amyotrophic lateral sclerosis. This study aimed to assess iron deposition qualitatively and quantitatively by using SWI and microstructural changes in the corticospinal tract by using DTI in patients with amyotrophic lateral sclerosis.

MATERIALS AND METHODS

Seventeen patients with amyotrophic lateral sclerosis and 15 age- and sex-matched controls underwent brain MR imaging with SWI and DTI. SWI was analyzed for both signal-intensity scoring and quantitative estimation of iron deposition in the anterior and posterior banks of the motor and sensory cortices and deep gray nuclei. The diffusion measurements along the corticospinal tract at the level of pons and medulla were obtained by ROI analysis.

RESULTS

Patients with amyotrophic lateral sclerosis showed reduced signal-intensity grades in the posterior bank of the motor cortex bilaterally. Quantitative analysis confirmed significantly higher iron content in the posterior bank of the motor cortex in patients with amyotrophic lateral sclerosis. In contrast, no significant differences were noted for the anterior bank of the motor cortex, anterior and posterior banks of the sensory cortex, and deep nuclei. Receiver operating characteristic comparison showed a cutoff of 35μg Fe/g of tissue with an area under the curve of 0.78 (P = .008) for the posterior bank of the motor cortex in discriminating patients with amyotrophic lateral sclerosis from controls. Fractional anisotropy was lower in the pyramidal tracts of patients with amyotrophic lateral sclerosis at the pons and medulla on either side, along with higher directionally averaged mean diffusivity values. The combination of SWI and DTI revealed an area under the curve of 0.784 for differentiating patients with amyotrophic lateral sclerosis from controls.

CONCLUSIONS

Measurements of motor cortex iron deposition and diffusion tensor parameters of the corticospinal tract may be useful biomarkers for the diagnosis of clinically suspected amyotrophic lateral sclerosis.

Chronic exposure to chewing tobacco selects for overexpression of stearoyl-CoA desaturase in normal oral keratinocytes

Chewing tobacco is a common practice in certain socio-economic sections of southern Asia, particularly in the Indian subcontinent and has been well associated with head and neck squamous cell carcinoma. The molecular mechanisms of chewing tobacco which leads to malignancy remains unclear. In large majority of studies, short-term exposure to tobacco has been evaluated. From a biological perspective, however, long-term (chronic) exposure to tobacco mimics the pathogenesis of oral cancer more closely. We developed a cell line model to investigate the chronic effects of chewing tobacco. Chronic exposure to tobacco resulted in higher cellular proliferation and invasive ability of the normal oral keratinocytes (OKF6/TERT1). We carried out quantitative proteomic analysis of OKF6/TERT1 cells chronically treated with chewing tobacco compared to the untreated cells. We identified a total of 3,636 proteins among which expression of 408 proteins were found to be significantly altered. Among the overexpressed proteins, stearoyl-CoA desaturase (SCD) was found to be 2.6-fold overexpressed in the tobacco treated cells. Silencing/inhibition of SCD using its specific siRNA or inhibitor led to a decrease in cellular proliferation, invasion and colony forming ability of not only the tobacco treated cells but also in a panel of head and neck cancer cell lines. These findings suggest that chronic exposure to chewing tobacco induced carcinogenesis in non-malignant oral epithelial cells and SCD plays an essential role in this process. The current study provides evidence that SCD can act as a potential therapeutic target in head and neck squamous cell carcinoma, especially in patients who are users of tobacco.

Silencing of high-mobility group box 2 (HMGB2) modulates cisplatin and 5-fluorouracil sensitivity in head and neck squamous cell carcinoma

Dysregulation of protein expression is associated with most diseases including cancer. MS-based proteomic analysis is widely employed as a tool to study protein dysregulation in cancers. Proteins that are differentially expressed in head and neck squamous cell carcinoma (HNSCC) cell lines compared to the normal oral cell line could serve as biomarkers for patient stratification. To understand the proteomic complexity in HNSCC, we carried out iTRAQ-based MS analysis on a panel of HNSCC cell lines in addition to a normal oral keratinocyte cell line. LC-MS/MS analysis of total proteome of the HNSCC cell lines led to the identification of 3263 proteins, of which 185 proteins were overexpressed and 190 proteins were downregulated more than twofold in at least two of the three HNSCC cell lines studied. Among the overexpressed proteins, 23 proteins were related to DNA replication and repair. These included high-mobility group box 2 (HMGB2) protein, which was overexpressed in all three HNSCC lines studied. Overexpression of HMGB2 has been reported in various cancers, yet its role in HNSCC remains unclear. Immunohistochemical labeling of HMGB2 in a panel of HNSCC tumors using tissue microarrays revealed overexpression in 77% (54 of 70) of tumors. The HMGB proteins are known to bind to DNA structure resulting from cisplatin-DNA adducts and affect the chemosensitivity of cells. We observed that siRNA-mediated silencing of HMGB2 increased the sensitivity of the HNSCC cell lines to cisplatin and 5-FU. We hypothesize that targeting HMGB2 could enhance the efficacy of existing chemotherapeutic regimens for treatment of HNSCC. All MS data have been deposited in the ProteomeXchange with identifier PXD000737 (http://proteomecentral.proteomexchange.org/dataset/PXD000737).

Pancreatic Cancer Database: an integrative resource for pancreatic cancer

Pancreatic cancer is the fourth leading cause of cancer-related death in the world. The etiology of pancreatic cancer is heterogeneous with a wide range of alterations that have already been reported at the level of the genome, transcriptome, and proteome. The past decade has witnessed a large number of experimental studies using high-throughput technology platforms to identify genes whose expression at the transcript or protein levels is altered in pancreatic cancer. Based on expression studies, a number of molecules have also been proposed as potential biomarkers for diagnosis and prognosis of this deadly cancer. Currently, there are no repositories which provide an integrative view of multiple Omics data sets from published research on pancreatic cancer. Here, we describe the development of a web-based resource, Pancreatic Cancer Database (http://www.pancreaticcancerdatabase.org), as a unified platform for pancreatic cancer research. PCD contains manually curated information pertaining to quantitative alterations in miRNA, mRNA, and proteins obtained from small-scale as well as high-throughput studies of pancreatic cancer tissues and cell lines. We believe that PCD will serve as an integrative platform for scientific community involved in pancreatic cancer research.

Proteogenomic analysis of pathogenic yeast Cryptococcus neoformans using high resolution mass spectrometry

Background

Cryptococcus neoformans, a basidiomycetous fungus of universal occurrence, is a significant opportunistic human pathogen causing meningitis. Owing to an increase in the number of immunosuppressed individuals along with emergence of drug-resistant strains, C. neoformans is gaining importance as a pathogen. Although, whole genome sequencing of three varieties of C. neoformans has been completed recently, no global proteomic studies have yet been reported.

Results

We performed a comprehensive proteomic analysis of C. neoformans var. grubii (Serotype A), which is the most virulent variety, in order to provide protein-level evidence for computationally predicted gene models and to refine the existing annotations. We confirmed the protein-coding potential of 3,674 genes from a total of 6,980 predicted protein-coding genes. We also identified 4 novel genes and corrected 104 predicted gene models. In addition, our studies led to the correction of translational start site, splice junctions and reading frame used for translation in a number of proteins. Finally, we validated a subset of our novel findings by RT-PCR and sequencing.

Conclusions

Proteogenomic investigation described here facilitated the validation and refinement of computationally derived gene models in the intron-rich genome of C. neoformans, an important fungal pathogen in humans.

Plasma Proteome Database as a resource for proteomics research: 2014 update

Plasma Proteome Database (PPD; http://www.plasmaproteomedatabase.org/) was initially described in the year 2005 as a part of Human Proteome Organization's (HUPO's) pilot initiative on Human Plasma Proteome Project. Since then, improvements in proteomic technologies and increased throughput have led to identification of a large number of novel plasma proteins. To keep up with this increase in data, we have significantly enriched the proteomic information in PPD. This database currently contains information on 10,546 proteins detected in serum/plasma of which 3784 have been reported in two or more studies. The latest version of the database also incorporates mass spectrometry-derived data including experimentally verified proteotypic peptides used for multiple reaction monitoring assays. Other novel features include published plasma/serum concentrations for 1278 proteins along with a separate category of plasma-derived extracellular vesicle proteins. As plasma proteins have become a major thrust in the field of biomarkers, we have enabled a batch-based query designated Plasma Proteome Explorer, which will permit the users in screening a list of proteins or peptides against known plasma proteins to assess novelty of their data set. We believe that PPD will facilitate both clinical and basic research by serving as a comprehensive reference of plasma proteins in humans and accelerate biomarker discovery and translation efforts.

NetSlim: high-confidence curated signaling maps

We previously developed NetPath as a resource for comprehensive manually curated signal transduction pathways. The pathways in NetPath contain a large number of molecules and reactions which can sometimes be difficult to visualize or interpret given their complexity. To overcome this potential limitation, we have developed a set of more stringent curation and inclusion criteria for pathway reactions to generate high-confidence signaling maps. NetSlim is a new resource that contains this ‘core’ subset of reactions for each pathway for easy visualization and manipulation. The pathways in NetSlim are freely available at http://www.netpath.org/netslim.

Database URL:www.netpath.org/netslim