CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods

BACKGROUND

The Critical Assessment of Genome Interpretation (CAGI) aims to advance the state-of-the-art for computational prediction of genetic variant impact, particularly where relevant to disease. The five complete editions of the CAGI community experiment comprised 50 challenges, in which participants made blind predictions of phenotypes from genetic data, and these were evaluated by independent assessors.

RESULTS

Performance was particularly strong for clinical pathogenic variants, including some difficult-to-diagnose cases, and extends to interpretation of cancer-related variants. Missense variant interpretation methods were able to estimate biochemical effects with increasing accuracy. Assessment of methods for regulatory variants and complex trait disease risk was less definitive and indicates performance potentially suitable for auxiliary use in the clinic.

CONCLUSIONS

Results show that while current methods are imperfect, they have major utility for research and clinical applications. Emerging methods and increasingly large, robust datasets for training and assessment promise further progress ahead.

Interface-guided phenotyping of coding variants in the transcription factor RUNX1 with SEUSS

Understanding the consequences of single amino acid substitutions in cancer driver genes remains an unmet need. Perturb-seq provides a tool to investigate the effects of individual mutations on cellular programs. Here we deploy SEUSS, a Perturb-seq like approach, to generate and assay mutations at physical interfaces of the RUNX1 Runt domain. We measured the impact of 115 mutations on RNA profiles in single myelogenous leukemia cells and used the profiles to categorize mutations into three functionally distinct groups: wild-type (WT)-like, loss-of-function (LOF)-like and hypomorphic. Notably, the largest concentration of functional mutations (non-WT-like) clustered at the DNA binding site and contained many of the more frequently observed mutations in human cancers. Hypomorphic variants shared characteristics with loss of function variants but had gene expression profiles indicative of response to neural growth factor and cytokine recruitment of neutrophils. Additionally, DNA accessibility changes upon perturbations were enriched for RUNX1 binding motifs, particularly near differentially expressed genes. Overall, our work demonstrates the potential of targeting protein interaction interfaces to better define the landscape of prospective phenotypes reachable by amino acid substitutions.

Predicting functional consequences of mutations using molecular interaction network features

Variant interpretation remains a central challenge for precision medicine. Missense variants are particularly difficult to understand as they change only a single amino acid in a protein sequence yet can have large and varied effects on protein activity. Numerous tools have been developed to identify missense variants with putative disease consequences from protein sequence and structure. However, biological function arises through higher order interactions among proteins and molecules within cells. We therefore sought to capture information about the potential of missense mutations to perturb protein interaction networks by integrating protein structure and interaction data. We developed 16 network-based annotations for missense mutations that provide orthogonal information to features classically used to prioritize variants. We then evaluated them in the context of a proven machine-learning framework for variant effect prediction across multiple benchmark datasets to demonstrate their potential to improve variant classification. Interestingly, network features resulted in larger performance gains for classifying somatic mutations than for germline variants, possibly due to different constraints on what mutations are tolerated at the cellular versus organismal level. Our results suggest that modeling variant potential to perturb context-specific interactome networks is a fruitful strategy to advance in silico variant effect prediction.

Susceptibility-Weighted Imaging of the Pediatric Brain after Repeat Doses of Gadolinium-Based Contrast Agent

BACKGROUND AND PURPOSE

Gadolinium complexes have paramagnetic properties; thus, we aimed to determine the susceptibility changes in the globus pallidus and dentate nucleus following administration of linear or macrocyclic gadolinium-based contrast agents in children.

MATERIALS AND METHODS

Thirty-three patients with linear gadolinium-based contrast agent gadopentetate dimeglumine administration, 33 age- and sex-matched patients with macrocyclic gadolinium-based contrast agent gadobutrol administration, and 33 age- and sex-matched control subjects without gadolinium exposure were enrolled in this retrospective study. The signal intensity on SWI and T1WI was determined in the dentate nucleus, middle cerebellar peduncle, globus pallidus, and pulvinar of the thalamus in an ROI-based analysis to calculate dentate nucleus-to-middle cerebellar peduncle and globus pallidus-to-thalamus ratios. A repeated measures ANOVA was performed to compare SWI_minimum, SWI_mean, and T1WI signal intensity ratios between gadolinium-based contrast agent groups and control subjects. Pearson correlation analysis was performed to determine any correlation between signal intensity ratios and variables.

RESULTS

Dentate nucleus-to-middle cerebellar peduncle and globus pallidus-to-thalamus ratios for both SWI_mean and SWI_minimum were lower for the linear gadolinium-based contrast agent group compared with macrocyclic gadolinium-based contrast agent and control groups (P < .05). No significant difference of the SWI_mean and SWI_minimum ratios were noted between the macrocyclic gadolinium-based contrast agent group and the control group (P > .05). Both dentate nucleus-to-middle cerebellar peduncle and globus pallidus-to-thalamus ratios on T1WI in the linear gadolinium-based contrast agent group were higher than in the control group and the macrocyclic gadolinium-based contrast agent group (P < .05). A negative correlation was identified between SWI_mean and SWI_minimum ratios and the number of linear gadolinium-based contrast agent administrations (dentate nucleus-to-middle cerebellar peduncle ratio: SWI_mean, r = -0.43, P = .005; SWI_minimum, r = -0.38, P = .011; globus pallidus-to-thalamus ratio: SWI_mean, r = -0.39, P = .009; SWI_minimum, r = -0.33, P = .017).

CONCLUSIONS

SWI analysis of the pediatric brain demonstrated a statistically significant decrease in SWI_minimum and SWI_mean values for the dentate nucleus and globus pallidus after administration of linear gadolinium-based contrast agents but not macrocyclic gadolinium-based contrast agents.

In silico analysis suggests less effective MHC-II presentation of SARS-CoV-2 RBM peptides: Implication for neutralizing antibody responses

SARS-CoV-2 antibodies develop within two weeks of infection, but wane relatively rapidly post-infection, raising concerns about whether antibody responses will provide protection upon re-exposure. Here we revisit T-B cooperation as a prerequisite for effective and durable neutralizing antibody responses centered on a mutationally constrained RBM B cell epitope. T-B cooperation requires co-processing of B and T cell epitopes by the same B cell and is subject to MHC-II restriction. We evaluated MHC-II constraints relevant to the neutralizing antibody response to a mutationally-constrained B cell epitope in the receptor binding motif (RBM) of the spike protein. Examining common MHC-II alleles, we found that peptides surrounding this key B cell epitope are predicted to bind poorly, suggesting a lack MHC-II support in T-B cooperation, impacting generation of high-potency neutralizing antibodies in the general population. Additionally, we found that multiple microbial peptides had potential for RBM cross-reactivity, supporting previous exposures as a possible source of T cell memory.

Evaluation of anatomical landmark position differences for head computed tomography: A reliability study among technologists

INTRODUCTION

In computed tomography (CT) imaging protocols, lack of practice standards and variability in head positioning may all yield substantial inter-study image variance in the clinical setting which may limit the diagnostic and comparative value of subsequent scans. We aimed to evaluate repeatability of multiplanar reformatting of head CT based on the tuberculum sella (TS) to internal occipital protuberance (IOP) reference line and reduce variance.

METHODS

Reference lines that correspond to the TS-IOP plane on high-resolution CT scans were reviewed by technologists manually to calculate Yaw (z-rotation, rotation along the superoinferior direction), Pitch (x-rotation, rotation along the left-right direction), and Roll (y-rotation, rotation along the anteroposterior direction) angles in this pre-post design intervention study. The Yaw, Pitch, and Roll angles deviating from the reference TS-IOP in the head CT images before and after technologist training were measured with the technologists' actual graphical prescriptions, and their differences were calculated with t-tests. The intra-rater agreement was calculated using the intraclass correlation coefficient (ICC).

RESULTS

Mean pitch, yaw, and roll before technologist training was 6.7° ± 5.4°, 0.9° ± 1.5°, and 1.1° ± 1.2° and after training were 3.2° ± 2.6°, 0.6° ± 1.1°, and 0.6° ± 1.1°, respectively. Technologist training resulted in a significant decrease in pitch (p < 0.001) and roll (p = 0.001) inter-subject variability with respect to the TS-IOP line, however no significant difference for the yaw correction (p = 0.065) was noted. Intra-rater agreement regarding the reproducibility of TS-IOP reformation was excellent (ICC>0.950).

CONCLUSION

TS-IOP reference line corrected for direct roll, yaw, and pitch can be readily achieved by trained technologists.

IMPLICATIONS FOR PRACTICE

Adoption of the TS-IOP reference line should facilitate intra- and intermodality comparisons, leading to more reproducible and readily interpretable CT images.

MHC-II constrains the natural neutralizing antibody response to the SARS-CoV-2 spike RBM in humans

SARS-CoV-2 antibodies develop within two weeks of infection, but wane relatively rapidly post-infection, raising concerns about whether antibody responses will provide protection upon re-exposure. Here we revisit T-B cooperation as a prerequisite for effective and durable neutralizing antibody responses centered on a mutationally constrained RBM B cell epitope. T-B cooperation requires co-processing of B and T cell epitopes by the same B cell and is subject to MHC-II restriction. We evaluated MHC-II constraints relevant to the neutralizing antibody response to a mutationally-constrained B cell epitope in the receptor binding motif (RBM) of the spike protein. Examining common MHC-II alleles, we found that peptides surrounding this key B cell epitope are predicted to bind poorly, suggesting a lack MHC-II support in T-B cooperation, impacting generation of high-potency neutralizing antibodies in the general population. Additionally, we found that multiple microbial peptides had potential for RBM cross-reactivity, supporting previous exposures as a possible source of T cell memory.

Phenotypically supervised single-cell sequencing parses within-cell-type heterogeneity

To better understand cellular communication driving diverse behaviors, we need to uncover the molecular mechanisms of within-cell-type functional heterogeneity. While single-cell RNA sequencing (scRNAseq) has advanced our understanding of cell heterogeneity, linking individual cell phenotypes to transcriptomic data remains challenging. Here, we used a phenotypic cell sorting technique to ask whether phenotypically supervised scRNAseq analysis (pheno-scRNAseq) can provide more insight into heterogeneous cell behaviors than unsupervised scRNAseq. Using a simple 3D in vitro breast cancer (BRCA) model, we conducted pheno-scRNAseq on invasive and non-invasive cells and compared the results to phenotype-agnostic scRNAseq analysis. Pheno-scRNAseq identified unique and more selective differentially expressed genes than unsupervised scRNAseq analysis. Functional studies validated the utility of pheno-scRNAseq in understanding within-cell-type functional heterogeneity and revealed that migration phenotypes were coordinated with specific metabolic, proliferation, stress, and immune phenotypes. This approach lends new insight into the molecular systems underlying BRCA cell phenotypic heterogeneity.

Abstract 4403: Predicting therapeutic sensitivities from molecular interaction network rewiring of RUNX1-RUNX1T1 fusion

Cancer driver events are thought to converge on a subset of molecular systems that regulate the hallmark behaviors of cancer cells. However, the complexity of biological systems makes it difficult to evaluate the impact of individual mutations at the level of such cellular processes and behaviors. In order to overcome this, we propose to study the effects of cancer mutations by modeling them as perturbations to molecular network architectures, allowing network-based prediction of drug sensitivities.

We first built the infrastructure to study protein-protein interaction network rewiring by variants by mapping different classes of variants onto edges of the PPI network using protein structure information. Mutations that cause a larger disruption to the underlying network architecture can create more vulnerabilities that can be used as drug targets. Therefore, in this project we decided to focus on fusion events which can interfere with many interactions of their parent proteins. In order to assess the disruption that can be caused by fusion events, we collected 2,699 cancer fusion proteins and demonstrated the centrality of their parents within a high confidence human PPI network of 12,047 proteins. This indicates that the parent proteins of fusion genes tend to interact with more protein partners and are more likely to display network topological properties suggesting a role in information transduction in molecular interaction networks.

As leukemias are often impacted by chromosomal aberrations that can result in fusion and tend to harbor fewer somatic mutations than solid tumors, they provide a good setting to develop a network-based model to study fusion events in the context of drug responses. Therefore, we chose to study the RUNX1-RUNX1T1 translocation, t(8;21)(q22;q22), in AML which is thought to be a pre-leukemic event that can result in tumors after receiving additional mutations. This translocation replaces the transactivation domain of RUNX1 with most of the RUNX1T1 protein which changes its function as an essential transcriptional activator of hematopoiesis.

In order to study the transcriptional effects of RUNX1-RUNX1T1 fusion on the underlying interactome network architecture, U937T cells induced with RUNX1-RUNX1T1 fusion were grown in triplicate and RNA was harvested prior to induction and at certain times post-induction. Wild type U937T cells with no perturbation serve as negative control. RNA sequencing was performed, followed by alignment of the reads to the reference genome. A differential gene expression analysis showed that 1,582 genes are differentially expressed in fusion induced cells versus wild type at FDR&lt;0.05, among which 47 of them encode proteins in RUNX1-RUNX1T1 subnetwork. Gene set enrichment analysis using these genes revealed that 30 gene sets are significantly enriched at nominal p-value&lt;0.01.

Citation Format: Kivilcim Ozturk, Hannah Carter. Predicting therapeutic sensitivities from molecular interaction network rewiring of RUNX1-RUNX1T1 fusion [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4403.

Pediatric Acute Toxic Leukoencephalopathy: Prediction of the Clinical Outcome by FLAIR and DWI for Various Etiologies

BACKGROUND AND PURPOSE

Pediatric acute toxic leukoencephalopathy is a clinicoradiologic entity comprising various etiologies. This study aimed to identify the MR imaging appearance of pediatric acute toxic leukoencephalopathy from various etiologies and determine whether the etiology correlates with clinical outcome.

MATERIALS AND METHODS

We retrospectively reviewed the electronic records of patients with pediatric acute toxic leukoencephalopathy younger than 19 years of age who had MR imaging within <2 weeks of presentation, including DWI and FLAIR sequences. Two neuroradiologists scored the DWI and FLAIR severity and measured the percentage ADC reduction within the visibly affected regions and normal-appearing WM. The percentage ADC reduction and DWI and FLAIR severity were correlated with clinical outcome using the Spearman correlation.

RESULTS

Of 22 children, 3 were excluded due to a nontoxic cause or incomplete examination. Regarding the included 19 children (mean age, 13 years), the etiologies of pediatric acute toxic leukoencephalopathy were the following: methotrexate (n = 6), bone marrow transplantation (n = 4), fludarabine (n = 3), cytarabine (n = 1), carboplatin (n = 1), vincristine (n = 1), cyclosporine (n = 1), uremia (n = 1), and bevacizumab (n = 1). Three subgroups were analyzed (chemotherapy, n = 12; immunosuppression, n = 5; others, n = 2). There was a strong correlation of FLAIR (r  = 0.773, P < .001) and DWI (r = 0.851, P < .001) severity with clinical outcome, and patients treated with fludarabine had the worst outcomes. High percentage ADC reduction values were associated with adverse outcomes, and lower percentage ADC reduction values were associated with favorable outcomes (r = 0.570, P = .011).

CONCLUSIONS

The DWI and FLAIR severity scores appear highly prognostic, whereas percentage ADC reduction is moderately prognostic for clinical outcomes in pediatric acute toxic leukoencephalopathy. Immunosuppressive pediatric acute toxic leukoencephalopathy tends toward favorable outcomes, and fludarabine tends toward worse outcomes.

Counterpoint: Conventional Fluoroscopy-Guided Selective Cervical Nerve Root Block-A Safe, Effective, and Efficient Modality in the Hands of an Experienced Proceduralist

BACKGROUND AND PURPOSE

The conventional fluoroscopy-guided (CF) selective cervical nerve root block (SCNRB) is being used commonly as a treatment for cervical radicular pain as well as a diagnostic tool. This study aimed to identify any major complications and determine the safety and clinical utility of CF-SCNRB performed in a university hospital and associated outpatient clinics.

MATERIALS AND METHODS

Two-hundred fifty-four conventional fluoroscopy-guided selective cervical nerve root blocks were retrospectively identified from 2011 to 2018 using a radiology report search tool. Each procedure was performed by an experienced neuroradiologist performing spinal injections on a full-time basis in clinical practice. A 10-point pain scale was used for pre- and postprocedural pain-level assessment. Successful conventional, fluoroscopy-guided, selective cervical nerve root block was defined as a patient-reported pain scale reduction of at least 50% and/or alleviation of numbness or paresthesia at ≥2 weeks postinjection. All clinically important immediate and delayed complications were also recorded.

RESULTS

Two-hundred fifty-four conventional fluoroscopy-guided selective cervical nerve root blocks were performed via an anterolateral approach with an average fluoroscopy time of 24.3 seconds for all cases. There were no aborted procedures and no major or permanent complications. There were 14 minor complications; 12 of these were periprocedural and resolved by the 2-week follow-up visit. One-hundred eighty-five patients (75.2%) reported pain improvement of >50% from baseline at 15 minutes postinjection. Overall, 172 patients (67.7%) reported >50% pain scale reduction or alleviation from paresthesia at least 2 weeks postinjection.

CONCLUSIONS

Conventional fluoroscopy-guided selective cervical nerve root block is an efficacious, efficient, and safe outpatient procedure when performed by a skilled and experienced proceduralist.

Prevalence of the extensor digitorum, extensor digiti minimi and extensor indicis tendons and their variations

We aimed to investigate tendon variations of the extensor digitorum (ED), extensor digiti minimi (EDM), and extensor indicis proprius (EIP) muscles. Our study was performed on 43 fetal cadavers (86 extremities), aged between 17 and 40 weeks of gestation. The number of ED tendons varied from three to six, proximal to the extensor retinaculum (ER), and from three to eight, distal to the ER. The ED most often had four tendons, both proximally and distally from the ER. The ED tendons of the fourth finger were observed to be most frequently duplicated. The most common juncturae tendinum (JT) was type 1 in the second intermetacarpal space (IMCS), type 2 in the third IMCS, and type 3r in the fourth IMCS according to von Schroeder classification. The number of EIP and EDM tendons varied from one to two and from one to five, respectively. The EIP double tendons inserted both into the ulnar and palmar sides of the extensor digitorum of the second finger, which had not been reported in the literature. In our study, 7% of hands had variant muscles. In 4.7% of hands, the extensor indicis et medii communis was observed, while the extensor medii proprius and the extensor digitorum brevis manus were observed in 1.2% and 1.2% of hands, respectively. Knowing the prevalence of the ED, EDM and EIP tendons and their variations in the fetal period should help to treat partial loss of hand function or injury after birth and to correct congenital hand deformities.

Performance of computational methods for the evaluation of pericentriolar material 1 missense variants in CAGI-5

The CAGI-5 pericentriolar material 1 (PCM1) challenge aimed to predict the effect of 38 transgenic human missense mutations in the PCM1 protein implicated in schizophrenia. Participants were provided with 16 benign variants (negative controls), 10 hypomorphic, and 12 loss of function variants. Six groups participated and were asked to predict the probability of effect and standard deviation associated to each mutation. Here, we present the challenge assessment. Prediction performance was evaluated using different measures to conclude in a final ranking which highlights the strengths and weaknesses of each group. The results show a great variety of predictions where some methods performed significantly better than others. Benign variants played an important role as negative controls, highlighting predictors biased to identify disease phenotypes. The best predictor, Bromberg lab, used a neural-network-based method able to discriminate between neutral and non-neutral single nucleotide polymorphisms. The CAGI-5 PCM1 challenge allowed us to evaluate the state of the art techniques for interpreting the effect of novel variants for a difficult target protein.

Elevated neoantigen levels in tumors with somatic mutations in the HLA-A, HLA-B, HLA-C and B2M genes

Background

The major histocompatibility complex class I (MHC-I) molecule is a protein complex that displays intracellular peptides to T cells, allowing the immune system to recognize and destroy infected or cancerous cells. MHC-I is composed of a highly polymorphic HLA-encoded alpha chain that binds the peptide and a Beta-2-microglobulin (B2M) protein that acts as a stabilizing scaffold. HLA mutations have been implicated as a mechanism of immune evasion during tumorigenesis, and B2M is considered a tumor suppressor gene. However, the implications of somatic HLA and B2M mutations have not been fully explored in the context of antigen presentation via the MHC-I molecule during tumor development. To understand the effect that B2M and HLA MHC-I molecule mutations have on mutagenesis, we analyzed the accumulation of mutations in patients from The Cancer Genome Atlas according to their MHC-I molecule mutation status.

Results

Somatic B2M and HLA mutations in microsatellite stable tumors were associated with higher overall mutation burden and a larger fraction of HLA-binding neoantigens when compared to B2M and HLA wild type tumors. B2M and HLA mutations were highly enriched in patients with microsatellite instability. B2M mutations tended to occur relatively early during patients’ respective tumor development, whereas HLA mutations were either early or late events. In addition, B2M and HLA mutated patients had higher levels of immune infiltration by natural killer and CD8+ T cells and higher levels of cytotoxicity.

Conclusions

Our findings add to a growing body of evidence that somatic B2M and HLA mutations are a mechanism of immune evasion by demonstrating that such mutations are associated with a higher load of neoantigens that should be presented via MHC-I.

Electronic supplementary material

The online version of this article (10.1186/s12920-019-0544-1) contains supplementary material, which is available to authorized users.

Differentiation of hepatocellular carcinoma from non-hepatocellular malignant tumours of liver by chemical-shift MRI at 3 T

AIM

To evaluate the diagnostic performance of chemical shift magnetic resonance imaging (MRI) in distinguishing hepatocellular carcinomas (HCCs) from non-hepatocellular malignant tumours (non-HCCs) of the liver.

MATERIALS AND METHODS

Patients with a diagnosis of malignant liver tumours examined at 3 T MRI were included in this retrospective study. Forty-seven HCCs and 75 non-HCCs that were studied with chemical-shift MRI between January 2012 and October 2016 were retrieved from the radiology database. Two blinded observers measured the signal intensities of the tumours, adjacent normal-looking liver parenchyma, and spleen on chemical-shift MRI. The fat quantification for HCCs, non-HCCs, and adjacent normal-looking liver parenchyma were calculated by using the spleen as a reference standard. The subtraction scores were calculated by subtracting fat percentages in liver parenchyma from those in tumours. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the fat percentage subtraction scores in distinguishing HCCs from non-HCCs were calculated.

RESULTS

According to the optimal cut-off value acquired from both readers, a subtraction score >-0.26 was considered to be a HCC. Fat signal percentage subtraction scores were ≥-0.26 in 45 of 47 HCCs and were <-0.26 in 69 of 75 non-HCCs. The sensitivity, specificity, PPV, and NPV of fat signal percentage subtraction score to differentiate HCCs from non-HCCs were found to be 95.7%, 89.3%, 84.9%, and 97.1%, respectively.

CONCLUSION

Intracytoplasmic lipid in HCCs demonstrated by quantitative chemical-shift MRI may be a potentially powerful imaging biomarker to distinguish HCCs from the other malignant liver tumours.

Strategies for Network GWAS Evaluated Using Classroom Crowd Science

Biological networks can substantially boost power to identify disease genes in genome-wide association studies. To explore different network GWAS methods, we challenged students of a UC San Diego graduate level bioinformatics course, Network Biology and Biomedicine, to explore and improve such algorithms during a four-week-long classroom competition. Here, we report the many creative solutions and share our experiences in conducting classroom crowd science as both a research and pedagogical tool.

Identifying Driver Interfaces Enriched for Somatic Missense Mutations in Tumors

Human cancers often harbor large numbers of somatic mutations. However, only a small proportion of these mutations are expected to contribute to tumor growth and progression. Therefore, determining causal driver mutations and the genes they target is becoming an important challenge in cancer genomics. Here we describe an approach for mapping somatic mutations onto 3D structures of human proteins in complex to identify "driver interfaces." Our strategy relies on identifying protein-interaction interfaces that are unexpectedly biased toward nonsynonymous mutations, which suggests that these interfaces are subject to positive selection during tumorigenesis, implicating the interacting proteins as candidate drivers.

Integrating molecular networks with genetic variant interpretation for precision medicine

More reliable and cheaper sequencing technologies have revealed the vast mutational landscapes characteristic of many phenotypes. The analysis of such genetic variants has led to successful identification of altered proteins underlying many Mendelian disorders. Nevertheless the simple one‐variant one‐phenotype model valid for many monogenic diseases does not capture the complexity of polygenic traits and disorders. Although experimental and computational approaches have improved detection of functionally deleterious variants and important interactions between gene products, the development of comprehensive models relating genotype and phenotypes remains a challenge in the field of genomic medicine. In this context, a new view of the pathologic state as significant perturbation of the network of interactions between biomolecules is crucial for the identification of biochemical pathways associated with complex phenotypes. Seminal studies in systems biology combined the analysis of genetic variation with protein–protein interaction networks to demonstrate that even as biological systems evolve to be robust to genetic variation, their topologies create disease vulnerabilities. More recent analyses model the impact of genetic variants as changes to the “wiring” of the interactome to better capture heterogeneity in genotype–phenotype relationships. These studies lay the foundation for using networks to predict variant effects at scale using machine‐learning or algorithmic approaches. A wealth of databases and resources for the annotation of genotype–phenotype relationships have been developed to support developments in this area. This overview describes how study of the molecular interactome has generated insights linking the organization of biological systems to disease mechanism, and how this information can enable precision medicine.

This article is categorized under:

Translational, Genomic, and Systems Medicine > Translational Medicine

Biological Mechanisms > Cell Signaling

Models of Systems Properties and Processes > Mechanistic Models

Analytical and Computational Methods > Computational Methods

The Emerging Potential for Network Analysis to Inform Precision Cancer Medicine

Precision cancer medicine promises to tailor clinical decisions to patients using genomic information. Indeed, successes of drugs targeting genetic alterations in tumors, such as imatinib that targets BCR-ABL in chronic myelogenous leukemia, have demonstrated the power of this approach. However, biological systems are complex, and patients may differ not only by the specific genetic alterations in their tumor, but also by more subtle interactions among such alterations. Systems biology and more specifically, network analysis, provides a framework for advancing precision medicine beyond clinical actionability of individual mutations. Here we discuss applications of network analysis to study tumor biology, early methods for N-of-1 tumor genome analysis, and the path for such tools to the clinic.

Systemic lupus erythematosus with C1q deficiency: treatment with fresh frozen plasma

Treatment and outcome of systemic lupus erythematosus (SLE) in C1q deficient patients are rarely reported. The aim of this report is to share our experience about the course of management of three cases diagnosed as SLE with C1q deficiency, in light of present literature. Initial and dominant complaints of three cases from two different families were cutaneous manifestations. One patient was also diagnosed with arthritis and thrombocytopenia. Antinuclear antibody was positive in all cases, whereas anti-dsDNA was negative with normal levels of complement C3, C4 and decreased CH50 activity. C1QA gene of two patients had homozygous nonsense mutation (c.622 > T/p.Gln208Ter). Previously, all of them had been treated with steroids, hydroxychloroquine and methotrexate or azathioprine. It was learned that they had responded only to high dosage prednisolone and their symptoms flared up during dosage reduction even under methotrexate or azathioprine. All symptoms of all three cases improved by daily fresh frozen plasma (FFP) infusions, and once cutaneous lesions subsided, the infusions were reduced to a frequency that would prevent the flare up of the symptoms. Literature search revealed seven reports on fresh frozen plasma treatment in SLE with C1q deficient patients. In this report, it is concluded that severe cutaneous lesions, as seen in these C1q deficient SLE patients, cannot be controlled with conventional immunosuppressive treatment. Instead, regular fresh frozen plasma infusions are proposed as a more reasonable method of treatment.

A comparison of two endoscopic posterior cordotomy techniques: Laser cordotomy vs diathermy-assisted cordotomy

OBJECTIVES

To compare respiratory function, swallowing and voice quality of bilateral abductor vocal fold paralysis (BAVFP) patients undergoing laser and diathermy-assisted posterior cordotomy.

DESIGN

Prospective study.

SETTING

Tertiary academic hospital.

PARTICIPANTS

Thirty patients were included in the study (groups 1 and 2, 15 patients each). Mean age was 53 ± 14.27 years with a range of 31-78 years (12 [40%] males, 18 [60%] females).

MAIN OUTCOME MEASURES

Sufficient airway, complications, FEV1, FEV1/FVC, peak expiratory flow rate (PEF), voice quality VAS, fundamental frequency, jitter, shimmer, NHR, amplitude perturbation quotient (APQ) and pitch perturbation quotient (PPQ) scores.

RESULTS

A sufficient laryngeal airway was achieved in all patients. Six patients (20%) developed postoperative granulation tissue (2 in group 1 and 4 in group 2). There was a statistically significant improvement in FEV1, FEV1/FVC and PEF measurements at the postoperative sixth month compared to preoperative measurements in both of the groups (P < .05). Preoperative median voice quality VAS scores in groups 1 and 2 were 8 (IQR = 1) and 8 (IQR = 3), respectively. Postoperative sixth-month voice quality VAS scores in groups 1 and 2 were 6 (IQR = 1) and 6 (IQR = 0), respectively. Postoperative VAS scores were significantly lower in both groups (P < .05). The postoperative changes in fundamental frequency, NHR, jitter, shimmer, APQ and PPQ were not statistically significant in both of the groups (P > .05).

CONCLUSIONS

Laser and diathermy-assisted posterior cordotomy are both minimally invasive, effective techniques with a long-term sufficient laryngeal airway. Despite lower quality of voice VAS scores, objective acoustic outcomes were not significantly lower in both of the groups.

Efficiency of rifampicin in emergency treatment of severe hyperbilirubinemia : report of two cases and review of literature

We showed in this study that rifampicin therapy is more effective than plasmapheresis and steroid treatment in diseases associated with severe hyperbilirubinemia. In our opinion, rifampicin treatment may suitable especially for patients with persistent hyperbilirubinemia, and it would be appropriate to use rifampicin as a challenge therapy to patients with severe hyperbilirubinemia, but liver function tests in these patients must be monitored closely.

Effects of rapamycin treatment on pancreatic fibrosis, cellular apoptosis and oxidative stress in experimental chronic pancreatitis model

PURPOSE

Rapamycin reduces hepatic fibrosis by inhibiting hepatic stellate cell activation. The present study investigated whether rapamycin treatment could modify the degree of fibrosis, cellular apoptosis and oxidative stress (OS) in an experimental model of CP.

METHODS

Fifty-five male, Sprague-Dawley rats weighing 200-400g were randomized into four groups. CP was induced by intraductal trinitrobenzene sulfonic acid (TNBS) infusion in group A (n = 15) and group B (n = 15). Group C (n = 15) received intraductal TNBS and was killed for histologic confirmation at four weeks. Group D (n = 10) received intraductal saline instead of TNBS. Group A and group D received oral rapamycin (2 mg/kg/d) for two weeks after CP was induced while group B received oral tap water instead of rapamycin. Blood and pancreatic tissue specimens were collected and oxidative stress parameters, fibrosis and cellular apoptosis were determined.

RESULTS

Tissue and blood malondialdehyde (MDA) levels were significantly lower in rapamycin treated group compared to controls (p < 0.001). Superoxide dismutase (SOD) and glutathion peroxidase (GSH-Px) activities were also significantly higher in the active treatment group (p < 0.001 for both). Tissue and blood MDA, SOD, GSH-Px measurements was similar in rapamycin group and pancreatic cannulation group (p > 0.05). Histopathologic fibrosis scores were similar in rapamycin and control groups. Apoptotic cell counts tended to be lower in rapamycin treated animals.

CONCLUSIONS

Administration of rapamycin alleviated OS and, in part, prevented apoptotic cell death in experimental CP, but did not reduce fibrosis.

Low frequency of a decreased ankle brachial index and associated conditions in the practice of internal medicine in a Turkish population sample

AIM

Peripheral arterial disease (PAD) is a less known condition in the practice of internal medicine, mostly due to lack of specific symptoms and low rates of physician awareness. However, cardiovascular disease (CVD) incidence is not significantly different among patients with symptomatic or asymptomatic disease. Ankle brachial index (ABI) measurement is an easy and cost-effective tool for the diagnosis of PAD. In the present study, frequency of low ABI and associated factors were investigated in the setting of internal medicine practice.

METHODS

Patients over 70 years of age and patients between 50 and 69 years with CVD or at least one atherothrombosis risk factor were included in the study. ABI was determined with handheld Doppler. Measurements were determined for both lower extremities. Lower of the right or left ABIs was taken as the final value. Low ABI was defined as ≤0.9.

RESULTS

A total of 303 subjects between 50 and 83 years of age were enrolled (female/male: 186/117). Mean ABI was 1.14±0.15. A low ABI was detected in 15 cases (4.95%). Prevalence was 7% in females and 1.7% in males (P=0.039). Low ABI value was not associated with any of the demographic parameters, presence of major risk factors or basic laboratory values. A high ABI was found by 5.6%.

CONCLUSION

In the present study, frequency of PAD as determined by ABI was found lower than those reported previously in most European countries. Nonetheless, our results showed that PAD affects at least 1 in 20 outpatients in the practice of internal medicine.

Accuracy of intrasheath injection techniques for de Quervain's disease: a cadaveric study

The purpose of this study was to assess the accuracy of injections of dye into the first extensor compartment of the wrist using three different techniques in 150 wrists in 75 fresh cadavers. To compare injections, 50 wrists from 25 cadavers were used for each technique. After the injections, the first extensor compartment was dissected and the dispersion of dye around the abductor pollicis longus and extensor pollicis brevis tendons was investigated. In 72 % of all the wrists, acrylic dye was dispersed into one compartment containing both the abductor pollicis longus and extensor pollicis brevis tendons, but in 28% of the wrists there was a separate compartment for extensor pollicis brevis and dye entered only one of the compartments (14% for each compartment). For accurate injections, we think the injections should be made separately over the two tendons, to allow for the possibility of a septum within the compartment.

Comparative evaluation of in vitro parameters of tamoxifen citrate loaded poly(lactide-co-glycolide), poly(epsilon-caprolactone) and chitosan nanoparticles

Tamoxifen (TAM), the clinical choice for the antiestrogen treatment of advanced or metastatic breast cancer, was formulated in nanoparticulate carrier systems in the form of poly(lactide-co-glycolide) (PLGA), poly-epsilon-caprolactone (PCL) and chitosan (CS) nanoparticles. The PLGA and PCL nanoparticles were prepared by a nanoprecipitation technique whereas the CS nanoparticles were prepared by the ionic gelation method. Mean particle sizes were under 260 nm for PLGA and PCL nanoparticles and around 400 nm for CS nanoparticles. Polydispersity indices were less than 0.4 for all formulations. Zeta potential values were positive for TAM loaded nanoparticles because of the positive charge of the drug. Drug loading values were significantly higher for PCL nanoparticles when compared to PLGA and CS nanoparticles. All nanoparticle formulations exhibited controlled release properties. These results indicate that TAM loaded PLGA, PCL and CS nanoparticles may provide promising carrier systems for tumor targeting.

The influence of technological parameters on the physicochemical properties of blank PLGA nanoparticles

In this work, PLGA nanoparticles were prepared by an emulsification-diffusion technique. The main objective was to optimize the preparation of formulations by evaluating the influence of the technological parameters on the physicochemical properties of PLGA nanoparticles. The effects of variations in polymer and emulsifier concentrations, and homogenization duration, rate and type on the particle size distribution, surface charge and morphology of nanoparticles were assessed. The smallest nanoparticles (177.53 +/- 2.78 nm) were obtained with a 2% PLGA (w/v) concentration in the organic phase and 3% PVA (w/v) in the aqueous phase and were prepared by an emulsification-diffusion method via ultrasonic homogenization at a power of 80 W applied for 30 s. It was observed that nanoparticles prepared by Ultra Turrax were more spherical but larger. In addition, increasing the PVA concentration in the aqueous phase, increasing the PLGA concentration in the organic phase and increasing the homogenization rate decreased the zeta potential values of PLGA nanoparticles.

The use of adjunctive topical mitomycin in endoscopic congenital choanal atresia repair

OBJECTIVE

To evaluate the efficacy of topical mitomycin in providing the patency of the neochoanae in children undergoing transnasal endoscopic congenital choanal atresia (CA) repair.

METHODS

A retrospective analysis of surgical results in CA patients who were treated in Selcuk University, Meram Medical Faculty, Department of Otolaryngology between November 2002 and November 2009 was performed. All patients underwent transnasal endoscopic approach using nasal telescopes and traditional sinus instrumentation together with a microdebrider. Mitomycin was used according to the senior surgeon's preference, and certainly not in a randomized fashion. After completion of surgery, mitomycin 0.4 mg/ml was applied to the neochoanae for 3 min. Postoperative stenting was performed in all patients.

RESULTS

CA was unilateral in 8 subjects (mean age 71.8+/-41.7 months; range 18 months-144 months) and bilateral in 12 subjects (mean age 4.6+/-1.3 days; range 3-7 days). Among the subjects, 75% was female in both groups. Fourteen subjects under endoscopic repair without mitomycin, whereas mitomycin was used in 6 patients (4 bilateral, 2 unilateral). Stents were left at least 3 weeks postoperatively (mean 31+/-10 days; range 21-45 days). The patients were followed-up at least 6 months (range 6-72 months). No symptomatic restenosis requiring further dilatations was seen in patients treated with preoperative mitomycin, whereas restenosis was detected in 6 subjects (42.9%) treated without mitomycin postoperatively within 6 months period (Fisher's Exact Test 2-sided, p=0.12). These subjects underwent revision endoscopic repair with mitomycin and had no need for further dilatations with acceptable control of symptoms during a follow-up period ranging between 14 and 78 months.

CONCLUSION

Mitomycin improves the surgical treatment outcome of CA and reduces the rate of restenosis significantly without any complications. However, further prospective randomized studies are needed to fully investigate the benefits of mitomycin therapy in CA surgery.

Effectiveness of corticosteroids in otitis media with effusion: an experimental study

Objective:

The aim of the present study was to investigate the dose-related effectiveness of corticosteroids in the management of otitis media with effusion, by using the objective assessment techniques of tympanometry and cytokine measurement.

Materials and methods:

The eustachian tubes of 42 male rats were obstructed. Thirty-six subjects with effusion were randomly divided into three equal groups: controls; 0.5 mg/kg/day corticosteroid; and 1 mg/kg/day corticosteroid. Concentrations of interleukin-1β and tumour necrosis factor α in the middle-ear effusions were analysed using enzyme-linked immunosorbent assay.

Results:

An effusion occurred on the 14th post-operative day and was present on the 30th post-operative day in the control group. Otomicroscopic examination and tympanometric measurement showed an improvement in the intervention groups. There was a significant difference between both intervention groups and the control group for both interleukin-1β and tumour necrosis factor α concentrations (p < 0.01). However, there was no significant difference between the 0.5 mg/kg and the 1 mg/kg corticosteroid groups (p > 0.05).

Conclusion:

The study confirmed a short term beneficial effect of systemic steroids on resolution of otitis media with effusion in a rat model. Our results support the theory that corticosteroids significantly decrease concentrations of both interleukin-1β and tumour necrosis factor α. In our model, the 0.5 mg/kg corticosteroid dose was as effective as the 1 mg/kg corticosteroid dose. Further studies should be carried out to determine the optimal dose and duration of corticosteroids in the treatment of otitis media with effusion.