Proteome-wide copy-number estimation from transcriptomics.

Protein copy numbers constrain systems-level properties of regulatory networks, but absolute proteomic data remain scarce compared to transcriptomics obtained by RNA sequencing. We addressed this persistent gap by relating mRNA to protein statistically using best-available data from quantitative proteomics-transcriptomics for 4366 genes in 369 cell lines. The approach starts with a central estimate of protein copy number and hierarchically appends mRNA-protein and mRNA-mRNA dependencies to define an optimal gene-specific model that links mRNAs to protein. For dozens of independent cell lines and primary prostate samples, these protein inferences from mRNA outmatch stringent null models, a count-based protein-abundance repository, and empirical protein-to-mRNA ratios. The optimal mRNA-to-protein relationships capture biological processes along with hundreds of known protein-protein interaction complexes, suggesting mechanistic relationships are embedded. We use the method to estimate viral-receptor abundances of CD55-CXADR from human heart transcriptomes and build 1489 systems-biology models of coxsackievirus B3 infection susceptibility. When applied to 796 RNA sequencing profiles of breast cancer from The Cancer Genome Atlas, inferred copy-number estimates collectively reclassify 26% of Luminal A and 29% of Luminal B tumors. Protein-based reassignments strongly involve a pharmacologic target for luminal breast cancer (CDK4) and an α-catenin that is often undetectable at the mRNA level (CTTNA2). Thus, by adopting a gene-centered perspective of mRNA-protein covariation across different biological contexts, we achieve accuracies comparable to the technical reproducibility limits of contemporary proteomics. The collection of gene-specific models is assembled as a web tool for users seeking mRNA-guided predictions of absolute protein abundance (http://janeslab.shinyapps.io/Pinferna).

Acute myeloid leukemia stratifies as two clinically relevant sphingolipidomic subtypes.

Acute myeloid leukemia (AML) is an aggressive disease with complex and heterogeneous biology. Although several genomic classifications have been proposed, there is a growing interest in going beyond genomics to stratify AML. In this study, we profile the sphingolipid family of bioactive molecules in 213 primary AML samples and 30 common human AML cell lines. Using an integrative approach, we identify two distinct sphingolipid subtypes in AML characterized by a reciprocal abundance of hexosylceramide (Hex) and sphingomyelin (SM) species. The two Hex-SM clusters organize diverse samples more robustly than known AML driver mutations and are coupled to latent transcriptional states. Using transcriptomic data, we develop a machine-learning classifier to infer the Hex-SM status of AML cases in TCGA and BeatAML clinical repositories. The analyses show that the sphingolipid subtype with deficient Hex and abundant SM is enriched for leukemic stemness transcriptional programs and comprises an unappreciated high-risk subgroup with poor clinical outcomes. Our sphingolipid-focused examination of AML identifies patients least likely to benefit from standard of care and raises the possibility that sphingolipidomic interventions could switch the subtype of AML patients who otherwise lack targetable alternatives.

Nucleocytoplasmic transport of active HER2 causes fractional escape from the DCIS-like state.

Activation of HER2/ErbB2 coincides with escape from ductal carcinoma in situ (DCIS) premalignancy and disrupts 3D organization of cultured breast-epithelial spheroids. The 3D phenotype is infrequent, however, and mechanisms for its incomplete penetrance have been elusive. Using inducible HER2/ErbB2-EGFR/ErbB1 heterodimers, we match phenotype penetrance to the frequency of co-occurring transcriptomic changes and uncover a reconfiguration in the karyopherin network regulating ErbB nucleocytoplasmic transport. Induction of the exportin CSE1L inhibits nuclear accumulation of ErbBs, whereas nuclear ErbBs silence the importin KPNA1 by inducing miR-205. When these negative feedbacks are incorporated into a validated systems model of nucleocytoplasmic transport, steady-state localization of ErbB cargo becomes ultrasensitive to initial CSE1L abundance. Erbb2-driven carcinomas with Cse1l deficiency outgrow less irregularly from mammary ducts, and NLS-attenuating mutants or variants of HER2 favor escape in 3D culture. We conclude here that adaptive nucleocytoplasmic relocalization of HER2 creates a systems-level molecular switch at the premalignant-to-malignant transition.

Efficacy of Eutectic Mixture of Local Anesthetic Cream and Vibrator Device in Pain Reduction during Peripheral Venous Cannulation in a Tertiary Care Center of Central Nepal.

Background Venous cannulation is a commonly performed procedure which often leads to patient anxiety. Application of a vibrator device and or prior use of topical anesthetics are proven methods to decrease associated pain. Objective To compare the clinical efficacy of prior use of Eutectic Mixture of Local Anesthetic (EMLA) cream and vibrator device in pain reduction during peripheral venous cannulation. Method A true experimental study was conducted in November 2019 among 78 patients aged 20-60 years receiving peripheral cannulation at operation theatre. They were included using consecutive sampling and sorted to interventional and noninterventional group using simple random sampling lottery method. Participants in the non-interventional group received peripheral cannulation using routine technique whereas participants in the interventional group received topical Eutectic Mixture of Local Anesthetic cream or vibrator device prior to cannulation. Perceived post cannulation pain intensity was measured using numerical pain rating scale. Kruskal-Wallis test was used for data comparison. Result The mean age of the participants was 40.57 ± 12.5 years. The median pain score of Eutectic Mixture of Local Anesthetic cream, vibrator and no intervention was 3, 3 and 6 respectively. The reduction in median pain intensity was significantly greater with topical anesthetic cream and vibrator device when compared to the noninterventional group (p < 0.05). Conclusion Prior interventions with Eutectic Mixture of Local Anesthetic or vibrator device are useful in reducing pain intensity during peripheral venous cannulation. Routine use of these in day to day practice could be a part of standard nursing care practice.

An Integrative Gene Expression and Mathematical Flux Balance Analysis Identifies Targetable Redox Vulnerabilities in Melanoma Cells.

Melanomas harboring BRAF mutations can be treated with BRAF inhibitors (BRAFi), but responses are varied and tumor recurrence is inevitable. Here we used an integrative approach of experimentation and mathematical flux balance analyses in BRAF-mutated melanoma cells to discover that elevated antioxidant capacity is linked to BRAFi sensitivity in melanoma cells. High levels of antioxidant metabolites in cells with reduced BRAFi sensitivity confirmed this conclusion. By extending our analyses to other melanoma subtypes in The Cancer Genome Atlas, we predict that elevated redox capacity is a general feature of melanomas, not previously observed. We propose that redox vulnerabilities could be exploited for therapeutic benefits and identify unsuspected combination targets to enhance the effects of BRAFi in any melanoma, regardless of mutational status. SIGNIFICANCE: An integrative bioinformatics, flux balance analysis, and experimental approach identify targetable redox vulnerabilities and show the potential for modulation of cancer antioxidant defense to augment the benefits of existing therapies in melanoma.

Drug-Tolerant Idling Melanoma Cells Exhibit Theory-Predicted Metabolic Low-Low Phenotype.

Cancer cells adjust their metabolic profiles to evade treatment. Metabolic adaptation is complex and hence better understood by an integrated theoretical-experimental approach. Using a minimal kinetic model, we predicted a previously undescribed Low/Low (L/L) phenotype, characterized by low oxidative phosphorylation (OXPHOS) and low glycolysis. Here, we report that L/L metabolism is observed in BRAF-mutated melanoma cells that enter a drug-tolerant "idling state" upon long-term MAPK inhibition (MAPKi). Consistently, using publicly available RNA-sequencing data of both cell lines and patient samples, we show that melanoma cells decrease their glycolysis and/or OXPHOS activity upon MAPKi and converge toward the L/L phenotype. L/L metabolism is unfavorable for tumor growth, yet supports successful cell division at ~50% rate. Thus, L/L drug-tolerant idling cells are a reservoir for accumulating mutations responsible for relapse, and it should be considered as a target subpopulation for improving MAPKi outcomes in melanoma treatment.

Dynamics of drug response informs rational combination regimens.

Metabolic plasticity in cancer has been linked to the development of drug-tolerant populations. In this issue of Science Signaling, Goldman et al integrate metabolic plasticity with phenotypic state transitions to examine how this reprogramming can be therapeutically exploited.

Quantifying Drug Combination Synergy along Potency and Efficacy Axes.

Two goals motivate treating diseases with drug combinations: reduce off-target toxicity by minimizing doses (synergistic potency) and improve outcomes by escalating effect (synergistic efficacy). Established drug synergy frameworks obscure such distinction, failing to harness the potential of modern chemical libraries. We therefore developed multi-dimensional synergy of combinations (MuSyC), a formalism based on a generalized, multi-dimensional Hill equation, which decouples synergistic potency and efficacy. In mutant-EGFR-driven lung cancer, MuSyC reveals that combining a mutant-EGFR inhibitor with inhibitors of other kinases may result only in synergistic potency, whereas synergistic efficacy can be achieved by co-targeting mutant-EGFR and epigenetic regulation or microtubule polymerization. In mutant-BRAF melanoma, MuSyC determines whether a molecular correlate of BRAFi insensitivity alters a BRAF inhibitor's potency, efficacy, or both. These findings showcase MuSyC's potential to transform the enterprise of drug-combination screens by precisely guiding translation of combinations toward dose reduction, improved efficacy, or both.

A Nonquiescent "Idling" Population State in Drug-Treated, BRAF-Mutated Melanoma.

Targeted therapy is an effective standard of care in BRAF-mutated malignant melanoma. However, the duration of tumor remission varies unpredictably among patients, and relapse is almost inevitable. Here, we examine the responses of several BRAF-mutated melanoma cell lines (including isogenic subclones) to BRAF inhibitors. We observe complex response dynamics across cell lines, with short-term responses (<100 h) varying from cell line to cell line. In the long term, however, we observe equilibration of all drug-treated populations into a nonquiescent state characterized by a balanced rate of death and division, which we term the "idling" state, and to our knowledge, this state has not been previously reported. Using mathematical modeling, we propose that the observed population-level dynamics are the result of cells transitioning between basins of attraction within a drug-modified phenotypic landscape. Each basin is associated with a drug-induced proliferation rate, a recently introduced metric of an antiproliferative drug effect. The idling population state represents a new dynamic equilibrium in which cells are distributed across the landscape such that the population achieves zero net growth. By fitting our model to experimental drug-response data, we infer the phenotypic landscapes of all considered melanoma cell lines and provide a unifying view of how BRAF-mutated melanomas respond to BRAF inhibition. We hypothesize that the residual disease observed in patients after targeted therapy is composed of a significant number of idling cells. Thus, defining molecular determinants of the phenotypic landscape that idling populations occupy may lead to "targeted landscaping" therapies based on rational modification of the landscape to favor basins with greater drug susceptibility.

Acute Upper Gastrointestinal Bleeding in a Tertiary Care Centre of Nepal.

INTRODUCTION: AUGIB is characterized by hematemesis or melena or both. Peptic ulcers and variceal bleed account for majority of cases. Use of proton pump inhibitors in current era is associated with a gradual reduction in burden of peptic ulcer disease. We conducted this study to look into the cause of AUGIB in our community. METHODS: We studied 100 patients in one year period who presented to us with hematemesis or melena. The study was conducted in department of Gastroenterology, Bir hospital, Kathmandu. We identified the culprit lesions by upper gastrointestinal endoscopy. RESULTS: The average age of patients with AUGIB was 51.6 years with 59 (59%) males. Duodenal ulcers are most common 29 (29%), followed by varices 23 (23%) and gastric ulcers 14 (14%). More than one lesion was identified in 38 (38%) patients. Patients with variceal bleed were more likely to present with hematemesis alone as compared to those with ulcer bleed (P=0.005). Variceal bleed patients presented earlier to the hospital (P=0.005), had lower MAP at presentation (P=0.0002), had lower hemoglobin level (P=0.0001) and higher serum creatinine level at presentation (P=0.001). Patients with variceal bleed were more likely to have consumed alcohol 20 (86.9%) and patients with ulcer bleed were more likely to be smokers 29 (67.4%) or consume tobacco 14 (32.5%) (P=0.006). CONCLUSIONS: Ulcer related bleeding is still the most common cause of AUGIB. Many patients with AUGIB have more than one lesions identified during upper gastrointestinal endoscopy.

Colorectal Cancer in Different Age Groups in a Tertiary Hospital in Nepal.

INTRODUCTION: Some studies have suggested that colorectal cancer at a younger age had distinct biological characteristics: different clinical presentations, more advanced stage at time of diagnosis and poorly differentiated carcinoma. The aim of the study is to analyze clinical and histopathological differences between younger (≤40 years of age) and older (>40 years of age) colorectal cancer patients. METHODS: A cross-sectional analysis was conducted amongst the colorectal cancer patients who visited Bir Hospital between July 2015 and April 2017. All colonoscopically diagnosed and histopathologically proven cases of colon cancer were included. Chi-square test and independent t - test was performed to analyze the difference between clinical presentations and histopathological findings among two groups of patients and P value of <0.05 was considered as significant. RESULTS: Thirty younger patients and thirty older patients were enrolled without any differences in gender proportion. There were no statistical differences between clinical presentation and histological grade and type in younger and older patients. The younger patients had more complaints of altered bowel habit (P <0.001) while older patients mostly presented with per rectal bleeding (P< 0.008). CONCLUSIONS: In this study, colorectal cancer at younger ages showed similar characteristics to those of older patients except altered bowel habit was more common in younger patients while per rectal bleeding was more common in older patients. Although colorectal cancer incidence increases with age, younger patients with altered bowel habits, weight loss, anemia and anorexia should also be given due medical attention and undergo evaluation promptly.

Efficacy of Prophylactic use of Ciprofloxacin and Metronidazole in Mild and Moderately Severe Acute Pancreatitis.

INTRODUCTION: There are new concepts and developments in the diagnosis and management of acute pancreatitis. Current evidence suggests that there is no role of prophylactic antibiotics use in acute pancreatitis. However, it is still a common practice to administer prophylactic antibiotics in a country like Nepal. So, we have conducted a study in mild and moderately severe acute pancreatitis to study the efficacy of prophylactic antibiotics. METHODS: A case control study was conducted among 76 patients comparing efficacy of prophylactic antibiotics versus no antibiotics in patients with mild and moderately severe acute pancreatitis. RESULTS: The two most common etiology of acute pancreatitis in AG and NAG were alcohol 21 (55.2%) vs. 24 (63.1%) and biliary 10 (26.3%) vs. 4 (10.5%) respectively. Pancreatic necrosis was seen in five (13.1 %) in AG and four (10.5%) in NAG. Four (10.5%) developed extra pancreatic complications in AG and five (13.1%) in NAG. There was one (2.6%) death in AG and no death in NAG. Abdominal pain improvement seen in AG vs. NAG was 3.2 days vs. 2.4 days (P=0.002). The hospital stay was 7.7±2.23 days in AG and 7.5±1.85 days in NAG (P=0.65). CONCLUSIONS: The routine use of prophylactic antibiotics for mild and moderately severe acute pancreatitis is not associated with improvement in meaningful clinical outcomes.

Nerve Conduction and Heart Rate variability in Patients with Hypothyroidism at a Tertiary Care Centre in Eastern Nepal.

INTRODUCTION: Thyroid hormone effects on many organs including central and peripheral nervous systems. However, these hormones do not affect all systems/organs to a similar extent. Thus, we conducted this study to explore the effect of thyroid hormones on somatic nervous system assessed by Nerve conduction study and cardiac autonomic activity assessed by heart rate variability. METHODS: The study included newly diagnosed hypothyroid patients and healthy controls. In all subjects NCS were performed in median, ulnar, tibial and sural nerves using Nihonkohden machine Cardiac autonomic control was assessed using Short-term Heart Rate Variability and parameters were analyzed by Time Domain and Frequency Domain methods. RESULTS: Both the groups were comparable in term of age, Body Mass Index, Pulse Rate, Systolic Blood Pressure and Diastolic Blood Pressure. Sensory parameters of NCS showed significant decrease in left median nerve SNAP amplitude (38.24±10.23 Vs 31.59±14.06, P=0.048) and nerve conduction velocity of bilateral median nerve in hypothyroid patients. In motor parameters of NCS, onset latencies of bilateral median nerves and right ulnar nerve were significantly increased in hypothyroid patients. All Time Domain measures of HRV and Frequency Domain measures; LF Power, HF Power and Total Power were significantly decreased (P<0.05) in hypothyroid patients. These HRV parameters are indicators of parasympathetic activity. CONCLUSIONS: In newly diagnosed hypothyroid patients, especially median nerve functions (both sensory and motor) and parasympathetic activity were decreased. It reflects that in hypothyroidism both autonomic nervous system and other somatic nerves are not affected in a similar extent.

An unbiased metric of antiproliferative drug effect in vitro.

In vitro cell proliferation assays are widely used in pharmacology, molecular biology, and drug discovery. Using theoretical modeling and experimentation, we show that current metrics of antiproliferative small molecule effect suffer from time-dependent bias, leading to inaccurate assessments of parameters such as drug potency and efficacy. We propose the drug-induced proliferation (DIP) rate, the slope of the line on a plot of cell population doublings versus time, as an alternative, time-independent metric.

Perception on Informed Consent Regarding Nursing Care Practices in a Tertiary Care Center.

Background Consent for care procedures is mandatory after receipt of adequate information. It maintains patient's rights and autonomy to make thoughtful decisions. Poor communication often leads to poor health quality. Objective To assess hospitalized patients' perception on informed consent regarding nursing care practices in a tertiary care center. Method This is a descriptive cross-sectional study among 113 admitted patients conducted in February 2012 at Dhulikhel Hospital, Nepal. Patients of various wards were selected using purposive non-probability sampling with at least 3 days of hospitalization. Close ended structured questionnaire was used to assess patients' perception on three different areas of informed consent (information giving, opportunity to make decision and taking prior consent). Result Among the participants 71.6% perceived positively regarding informed consent towards nursing care practices with a mean score of 3.32 ± 1.28. Patients' perception on various areas of informed consent viz. information giving, opportunities to make specific decision and taking prior consent were all positive with mean values of 3.43±1.12, 2.88±1.23, 3.65±1.49 respectively. Comparison of mean perception of informed consent with various variables revealed insignificant correlation (p-value >0.05) for age, educational level and previous hospitalization while it was significant (p-value < 0.05) for communication skills of nurses. Conclusion Majority of patients have positive perception on informed consent towards nursing care practices. Communication skills of nurses affect the perception of patients' regardless of age, education level and past experiences.

Effect of Teachers Training Workshop Outcomes on Real Classroom Situations of Undergraduate Medical Students.

BACKGROUND: Faculty development by conducting regular training, workshops and research related to medical education has been a key feature to upgrade quality of medical education. OBJECTIVE: The aim of this study was to explore responses of the health science teachers, students and peers after the workshop after providing training on student assessment tools and teaching-learning methods. METHOD: Two teacher-training workshops were conducted to the faculty members of B.P. Koirala Institute of Health Sciences from the departments of basic, clinical and allied sciences in Oct. 2010 and Jan. 2011. Qualitative questionnaire based study was conducted, and the questions were validated before the study by expert peer review process. The effect of the training workshop in real classroom outcomes was assessed incorporating student's feedback, evaluation by peers and the self-evaluation by the teacher trainees. RESULT: Pre-test and post-test scores of the participating teachers, before and after the workshop were 62.53 and 71.17 respectively. Among the participants 90.3% teachers expressed enhanced in their role as a teacher for medical undergraduates after the workshop. CONCLUSION: In present study, the faculty members showed accrued interest to participate in teacher's training workshops. The peer evaluation of teacher's performance in their real classroom situations were rated higher than evaluation by the students. Therefore, such training workshops will have a greater impact on the ability of teachers in effective teaching in real classroom situations.

Knowledge and Practice of Health Care Workers regarding Needle Stick Injuries in a Tertiary Care Center of Nepal.

Background Needle stick injuries are common health hazards among health care workers. Considering the increasing prevalence of body fluid borne infectious diseases; knowledge regarding the common errors and universal precautions are vital for the prevention of such accidents. Objective This study aimed to assess for knowledge and practice approaches among health care workers regarding needle stick injuries. Method This is a cross sectional survey was conducted using an anonymous, self-reporting 25-item structured questionnaire at a tertiary care center of central Nepal. A total of 165 health care personnel of working experience of more than 6 months were included in the study. Questionnaire included aspects of prevalence and knowledge on needle stick injury, hepatitis B immunization status and post exposure prophylaxis for HIV. Result Prevalence of needle stick injury was found to be 703 per 1000 health care worker (70.3%) during their working tenure and majority of the injury happened among nurses (p<0.05) besides other professions. Seventy nine (47.9%) participants experienced the injury more than one time in their career and the mean number of injury was 2.06±1.16. The practice of needle recapping is still prevalent and 80% participants often use single handed technique. Vaccination against hepatitis B virus was not completed by 31% health workers. Inadequate knowledge about post exposure prophylaxis for HIV was reported by 46% participants. Conclusion High prevalence of needle stick injury with a high rate of ignorance was noted. These issues need to be addressed, through appropriate education and interventional strategies.

Clinical and electroencephalographic profile of children.

BACKGROUND: Reports on pediatric electroencephalogram of Nepalese patients are rare. OBJECTIVE: We aimed to study the relationship between provisional clinical and electrophysiological diagnoses of pediatric patients with documentation of demographic profiles, and type and frequency of the disorders/diseases. METHODS: Electroencephalographic reports of 634 children from 2006 to 2009 were analyzed at neurophysiology laboratory, department of Basic and Clinical Physiology, B. P. Koirala Institute of Health Sciences, Dharan, Nepal, retrospectively. Chi-Square test was applied after detail descriptive statistics. RESULTS: Male and female were 72.2 % (n=458/634) and 27.76 % (n=176/634) respectively. Most frequent EEG abnormality was seizure disorder (n=370, 59.39%), then febrile seizure (n= 94, 15.08%) and birth asphyxia with hypoxic-induced encephalopathy (n=68, 10.91%). Electroencephalogram showed significant epileptiform discharges in seizure disorder (p=0.001, OR= 2.26, 95 % CI= 1.61 to 3.18) and in cerebral palsy (p=0.049, OR=6.88, 95 % CI=0.89 to 145.95), specifically in 6 to 12 (p=0.001, OR=2.94, 95 % CI=1.43 to 6.06) and one to five (p=0.019) years, respectively. Electroencephalogram detected significantly less epileptiform discharges (p=0.001, OR=0.25, 95 % CI= 0.15 to 0.42) in febrile seizure specifically in 1 to 5 years (p=0.003, OR=0.16, 95 % CI= 0.04 to 0.63). CONCLUSION: Predominant Electroencephalographic abnormality was seizure disorder, followed by febrile seizure and birth asphyxia with hypoxic-induced encephalopathy respectively. Electroencephalographic abnormality was highly associated with seizure disorder and cerebral palsy but was not associated with febrile seizure.