Spectral Graph Neural Network-Based Multi-Atlas Brain Network Fusion for Major Depressive Disorder Diagnosis

Major Depressive Disorder (MDD) imposes a substantial burden within the healthcare domain, impacting millions of individuals worldwide. Functional Magnetic Resonance Imaging (fMRI) has emerged as a promising tool for the objective diagnosis of MDD, enabling the investigation of functional connectivity patterns in the brain associated with this disorder. However, most existing methods focus on a single brain atlas, which limits their ability to capture the complex, multi-scale nature of functional brain networks. To address these limitations, we propose a novel multi-atlas fusion method that incorporates early and late fusion in a unified framework. Our method introduces the concept of the holistic Functional Connectivity Network (FCN), which captures both intra-atlas relationships within individual atlases and inter-regional relationships between atlases with different brain parcellation scales. This comprehensive representation enables the identification of potential disease-related patterns associated with MDD in the early stage of our framework. Moreover, by decoding the holistic FCN from various perspectives through multiple spectral Graph Convolutional Neural Networks and fusing their results with decision-level ensembles, we further improve the performance of MDD diagnosis. Our approach is easily implemented with minimal modifications to existing model structures and demonstrates a robust performance across different baseline models. Our method, evaluated on public resting-state fMRI datasets, surpasses the current multi-atlas fusion methods, enhancing the accuracy of MDD diagnosis. The proposed novel multi-atlas fusion framework provides a more reliable MDD diagnostic technique. Experimental results show our approach outperforms both single- and multi-atlas-based methods, demonstrating its effectiveness in advancing MDD diagnosis.

Graph-Based Conditional Generative Adversarial Networks for Major Depressive Disorder Diagnosis With Synthetic Functional Brain Network Generation

Major Depressive Disorder (MDD) is a pervasive disorder affecting millions of individuals, presenting a significant global health concern. Functional connectivity (FC) derived from resting-state functional Magnetic Resonance Imaging (rs-fMRI) serves as a crucial tool in revealing functional connectivity patterns associated with MDD, playing an essential role in precise diagnosis. However, the limited data availability of FC poses challenges for robust MDD diagnosis. To tackle this, some studies have employed Deep Neural Networks (DNN) architectures to construct Generative Adversarial Networks (GAN) for synthetic FC generation, but this tends to overlook the inherent topology characteristics of FC. To overcome this challenge, we propose a novel Graph Convolutional Networks (GCN)-based Conditional GAN with Class-Aware Discriminator (GC-GAN). GC-GAN utilizes GCN in both the generator and discriminator to capture intricate FC patterns among brain regions, and the class-aware discriminator ensures the diversity and quality of the generated synthetic FC. Additionally, we introduce a topology refinement technique to enhance MDD diagnosis performance by optimizing the topology using the augmented FC dataset. Our framework was evaluated on publicly available rs-fMRI datasets, and the results demonstrate that GC-GAN outperforms existing methods. This indicates the superior potential of GCN in capturing intricate topology characteristics and generating high-fidelity synthetic FC, thus contributing to a more robust MDD diagnosis.

Glutathione dynamics is a potential predictive and therapeutic trait for neoadjuvant chemotherapy response in bladder cancer

Radical cystectomy with preoperative cisplatin-based neoadjuvant chemotherapy (NAC) is the standard care for muscle-invasive bladder cancers (MIBCs). However, the complete response rate to this modality remains relatively low, and current clinicopathologic and molecular classifications are inadequate to predict NAC response in patients with MIBC. Here, we demonstrate that dysregulation of the glutathione (GSH) pathway is fundamental for MIBC NAC resistance. Comprehensive analysis of the multicohort transcriptomes reveals that GSH metabolism and immune-response genes are enriched in NAC-resistant and NAC-sensitive MIBCs, respectively. A machine-learning-based tumor/stroma classifier is applied for high-throughput digitalized immunohistochemistry analysis, finding that GSH dynamics proteins, including glutaminase-1, are associated with NAC resistance. GSH dynamics is activated in cisplatin-resistant MIBC cells, and combination treatment with a GSH dynamics modulator and cisplatin significantly suppresses tumor growth in an orthotopic xenograft animal model. Collectively, these findings demonstrate the predictive and therapeutic values of GSH dynamics in determining the NAC response in MIBCs.

Intercellular cross-talk through lineage-specific gap junction of cancer-associated fibroblasts related to stromal fibrosis and prognosis

Stromal fibrosis in cancer is usually associated with poor prognosis and chemotherapy resistance. It is thought to be caused by fibroblasts; however, the exact mechanism is not yet well understood. The study aimed to identify lineage-specific cancer-associated fibroblast (CAF) subgroup and their associations with extracellular matrix remodeling and clinical significances in various tumor types using single-cell and bulk RNA sequencing data. Through unsupervised clustering, six subclusters of CAFs were identified, including a cluster with exclusively high gap junction protein beta-2 (GJB2) expression. This cluster was named GJB2-positive CAF. It was found to be a unique subgroup of terminally differentiated CAFs associated with collagen gene expression and extracellular matrix remodeling. GJB2-positive CAFs showed higher communication frequency with vascular endothelial cells and cancer cells than GJB2-negative CAFs. Moreover, GJB2 was poorly expressed in normal tissues, indicating that its expression is dependent on interaction with other cells, including vascular endothelial cells and cancer cells. Finally, the study investigated the clinical significance of GJB2 signature score for GJB2-positive CAFs in cancer and found a correlation with poor prognosis. These results suggest that GJB2-positive CAF is a unique fibroblast subtype involved in extracellular matrix remodeling, with significant clinical implications in cancer.

Clinicogenomic characteristics and synthetic lethal implications of germline homologous recombination-deficient hepatocellular carcinoma

BACKGROUNDS AND AIMS

We performed an in-depth examination of pathogenic germline variants (PGVs) and somatic variants in DNA damage response (DDR) genes in hepatocellular carcinoma (HCC) to explore their clinical and genomic impacts.

APPROACH AND RESULTS

We used a merged whole-exome or RNA sequencing data set derived from in-house ( n = 230) and The Cancer Genome Atlas ( n = 362) databases of multiethnic HCC samples. We also evaluated synthetic lethal approaches targeting mutations in homologous recombination (HR) genes using HCC cells selected from five genomic databases of cancer cell lines. A total of 110 PGVs in DDR pathways in 96 patients were selected. Of the PGV carriers, 44 were HR-altered and found to be independently associated with poorer disease-free survival after hepatectomy. The most frequently altered HR gene in both germline and somatic tissues was POLQ , and this variant was detected in 22.7% (10/44) and 23.8% (5/21) of all the corresponding carriers, respectively. PGVs in HR were significantly associated with upregulation of proliferation and replication-related genes and familial risk of HCC. Samples harboring PGVs in HR with loss of heterozygosity were most strongly correlated with the genomic footprints of deficient HR, such as mutation burden and denovoSig2 (analogous to Catalogue of Somatic Mutations in Cancer [COSMIC] 3), and poor outcome. Pharmacologic experiments with HCC cells defective in BRCA2 or POLQ suggested that tumors with this phenotype are synthetic lethal with poly(ADP-ribose) polymerase inhibitors.

CONCLUSIONS

Our findings suggest that germline HR defects in HCC tend to confer a poor prognosis and result in distinctive genomic scarring. Tests of the clinical benefits of HR-directed treatments in the affected patients are needed.

Whole-genome sequencing reveals an association between small genomic deletions and an increased risk of developing Parkinson's disease

Single-nucleotide variants (SNVs) associated with Parkinson's disease (PD) have been investigated mainly through genome-wide association studies. However, other genomic alterations, including copy number variations, remain less explored. In this study, we conducted whole-genome sequencing of primary (310 PD patients and 100 healthy individuals) and independent (100 PD patients and 100 healthy individuals) cohorts from the Korean population to identify high-resolution small genomic deletions, gains, and SNVs. Global small genomic deletions and gains were found to be associated with an increased and decreased risk of PD development, respectively. Thirty significant locus deletions were identified in PD, with most being associated with an increased PD risk in both cohorts. Small genomic deletions in clustered loci located in the GPR27 region had high enhancer signals and showed the closest association with PD. GPR27 was found to be expressed specifically in brain tissue, and GPR27 copy number loss was associated with upregulated SNCA expression and downregulated dopamine neurotransmitter pathways. Clustering of small genomic deletions on chr20 in exon 1 of the GNAS isoform was detected. In addition, we found several PD-associated SNVs, including one in the enhancer region of the TCF7L2 intron, which exhibited a cis-acting regulatory mode and an association with the beta-catenin signaling pathway. These findings provide a global, whole-genome view of PD and suggest that small genomic deletions in regulatory domains contribute to the risk of PD development.

Sex difference in neurological outcome and post-cardiac arrest care in out-of-hospital cardiac arrest patients treated with targeted temperature management

Funding Acknowledgements

Type of funding sources: None.

Objectives

Conflicting results regarding sex-based differences in the outcomes of out-of-hospital cardiac arrest (OHCA) patients have been reported. Furthermore, no study has examined whether differences in in-hospital interventions and courses are driven by sex differences. This study evaluated the effect of sex on the in-hospital course of these patients as well as the survival rates and long-term neurological outcomes of comatose OHCA patients treated with targeted temperature management (TTM).

Methods

We retrospectively analyzed the Korean Hypothermia Network prospective registry composed of data collected from 22 hospitals in Korea between October 2015 and December 2018. To evaluate the effect of sex on patient outcomes, we created various multivariate logistic regression models including baseline characteristics, resuscitation, and in-hospital care variables with an interaction term (age × sex). We also performed a stratified analysis of different age groups (less than 50 years of age and older). Regarding the difference in in-hospital courses, we compared daily total and SOFA sub-scores between the sexes and analyzed whether the decision regarding early cardiac interventions and limitations in in-hospital care were associated with sex.

Results

Among 1339 patients included in the study, 952 were men and 387 were women. There were no differences in age or modified comorbidity index values between the gender groups. Women were more likely to experience cardiac arrest at home and unwitnessed arrests, whereas men were more likely to have shockable initial rhythm, cardiac cause arrest, and ST-segment elevation myocardial infarction (STEMI) on initial electrocardiography and undergo early coronary interventions. The rate of survival to discharge was similar, but men showed better 6-month neurological outcomes. After adjusting for confounders, the male sex was not associated with survival to discharge or good 6-month neurological outcomes. There was no association between sex and outcome in patients of reproductive age and no interaction between age and sex. Regarding the in-hospital course, the daily total and SOFA sub-scores were similar in both sexes. The adjusted effect of sex was not associated with the clinician’s decision to perform early cardiac interventions. The decision to discontinue life-sustaining treatment was determined by poor prognostic factors, not by sex.

Conclusions

The findings suggested that men had more favorable 6-month survivals and good neurological outcomes compared to women since they had more favorable resuscitation variables. However, after adjusting for confounders, there was no difference between the sexes. This result was consistent with the data in patients of reproductive age. The results regarding in-hospital course showed that daily patient severity scores, early cardiac interventions, resource consumption, and the rates of withdrawal/withholding of in-hospital care were similar in men and women.

Machine Learning for Intelligent-Reflecting-Surface-Based Wireless Communication towards 6G: A Review

An intelligent reflecting surface (IRS) is a programmable device that can be used to control electromagnetic waves propagation by changing the electric and magnetic properties of its surface. Therefore, IRS is considered a smart technology for the sixth generation (6G) of communication networks. In addition, machine learning (ML) techniques are now widely adopted in wireless communication as the computation power of devices has increased. As it is an emerging topic, we provide a comprehensive overview of the state-of-the-art on ML, especially on deep learning (DL)-based IRS-enhanced communication. We focus on their operating principles, channel estimation (CE), and the applications of machine learning to IRS-enhanced wireless networks. In addition, we systematically survey existing designs for IRS-enhanced wireless networks. Furthermore, we identify major issues and research opportunities associated with the integration of IRS and other emerging technologies for applications to next-generation wireless communication.

Efficient User-Serving Scheme in the User-Centric Cell-Free Massive MIMO System

A cell-free massive multiple input multiple output (MIMO) system is an attractive network model that is in the spotlight in 5G and future communication systems. Despite numerous advantages, the cell-free massive MIMO system has a problem in that it is difficult to operate in reality due to its vast amount of calculation. The user-centric cell-free massive MIMO model has a more feasible and scalable benefit than the cell-free massive MIMO model. However, this model has the disadvantage that as the number of users in the area increases, there are users who do not receive the service. In this paper, the proposed scheme creates connections for unserved users under a user-centric scheme without additional access point (AP) installation and disconnection for existing users. A downlink user-centric cell-free massive MIMO system model in which the APs are connected to the central processing unit (CPU) and the APs and users are geographically distributed is considered. First, the downlink spectral efficiency formula is derived and applied to the user-centric cell-free massive MIMO system. Then, the proposed scheme and power control algorithm are applied to the derived formula. The simulation results show that the unserved users within the area disappear by using the proposed scheme, while the bit error rate (BER) performance and sum rate improve compared to the existing scheme. In addition, it is shown that the proposed scheme works well even with a very large number of users in the area, and a significant service performance improvement for the worst 10% of users and the overall improvement of per-user throughput for the bottom 70% of users are ensured.

PET-Based Radiogenomics Supports mTOR Pathway Targeting for Hepatocellular Carcinoma

PURPOSE

This work aimed to explore in depth the genomic and molecular underpinnings of hepatocellular carcinoma (HCC) with increased 2[18F]fluoro-2-deoxy-d-glucose (FDG) uptake in PET and to identify therapeutic targets based on this imaging-genomic surrogate.

EXPERIMENTAL DESIGN

We used RNA sequencing and whole-exome sequencing data obtained from 117 patients with HCC who underwent hepatic resection with preoperative FDG-PET/CT imaging as a discovery cohort. The primary radiogenomic results were validated with transcriptomes from a second cohort of 81 patients with more advanced tumors. All patients were allocated to an FDG-avid or FDG-non-avid group according to the PET findings. We also screened potential drug candidates targeting FDG-avid HCCs in vitro and in vivo.

RESULTS

High FDG avidity conferred worse recurrence-free survival after HCC resection. Whole transcriptome analysis revealed upregulation of mTOR pathway signals in the FDG-avid tumors, together with higher abundance of associated mutations. These clinical and genomic findings were replicated in the validation set. A molecular signature of FDG-avid HCCs identified in the discovery set consistently predicted poor prognoses in the public-access datasets of two cohorts. Treatment with an mTOR inhibitor resulted in decreased FDG uptake followed by effective tumor control in both the hyperglycolytic HCC cell lines and xenograft mouse models.

CONCLUSIONS

Our PET-based radiogenomic analysis indicates that mTOR pathway genes are markedly activated and altered in HCCs with high FDG retention. This nuclear imaging biomarker may stimulate umbrella trials and tailored treatments in precision care of patients with HCC.

The benefits of the earlier use of sacubitril/valsartan in de novo heart failure with reduced ejection fraction patients

Aims

We evaluated the clinical outcomes and trajectory of cardiac reverse remodelling according to the timing of sacubitril/valsartan (Sac/Val) use in patients with heart failure (HF) with reduced ejection fraction (HFrEF).

Methods and results

Patients with de novo HFrEF who used Sac/Val between June 2017 and October 2019 were retrospectively enrolled. Patients were grouped into the earlier use group (initiation of Sac/Val < 3 months after the first HFrEF diagnosis) and the later use group (initiation of Sac/Val ≥ 3 months after the first HFrEF diagnosis). Primary outcome was a composite of HF hospitalization and cardiac death. Secondary outcomes were HF hospitalization, cardiac death, all‐cause death, significant ventricular arrhythmia (ventricular tachycardia or ventricular fibrillation), and echocardiographic evidence of cardiac reverse remodelling including left ventricular ejection fraction (LVEF) change during follow‐up. Among 115 enrolled patients, 67 were classified in the earlier use group, and 48 were classified in the later use group. Mean period of HFrEF diagnosis to Sac/Val use was 52.1 ± 14.3 days in the earlier use group, and 201.8 ± 127.3 days in the later use group. During the median follow‐up of 721 days, primary outcome occurred in 21 patients (18.3%). The earlier use group experienced significantly fewer primary outcome than the later use group (10.4% vs. 29.2%, P = 0.010). The Kaplan–Meier survival curve showed better event‐free survival in the earlier use group than in the later use group (log rank = 0.017). There were no significant differences in cardiac death, all‐cause death, and ventricular arrhythmia between two groups (1.5% vs. 2.1%, P = 0.811; 1.5% vs. 4.2%, P = 0.375; 3.0% vs. 0%, P = 0.227, respectively). Despite a significantly lower baseline LVEF in the earlier use group (21.3 ± 6.4% vs. 24.8 ± 7.9%, P = 0.012), an early prominent increase of LVEF was noted before 6 months (35.2 ± 11.9% vs. 27.8 ± 8.8%, P = 0.007). A delayed improvement of LVEF in the later use group resulted in similar LVEF at last follow‐up in both groups (40.7 ± 13.4% vs. 39.4 ± 10.9%, P = 0.686). Although the trajectory of left ventricular remodelling showed similar pattern in two groups, left atrial (LA) reverse remodelling was less prominent in the later use group during the follow‐up period (final LA volume index: 43.6 ± 14.3 mL/m² vs. 55.2 ± 17.1 mL/m², P = 0.011).

Conclusions

Earlier use of Sac/Val was related with better clinical outcome and earlier left ventricular reverse remodelling. Remodelling of LA was less prominent in the later use group implying delayed response in diastolic function.

Comprehensive characterization of viral integrations and genomic aberrations in HBV-infected intrahepatic cholangiocarcinomas

BACKGROUND AND AIMS

Despite the epidemiological association between intrahepatic cholangiocarcinoma (iCCA) and HBV infection, little is known about the relevant oncogenic effects. We sought to identify the landscape and mechanism of HBV integration, along with the genomic architecture of HBV-infected iCCA (HBV-iCCA) tumors.

APPROACH AND RESULTS

We profiled a cohort of 108 HBV-iCCAs using whole-genome sequencing, deep sequencing, and RNA sequencing, together with preconstructed data sets of HBV-infected HCC (HBV-HCC; n = 167) and combined hepatocellular cholangiocarcinoma (HBV-cHCC/CCA; n = 59), and conventional (n = 154) and fluke-related iCCAs (n = 16). Platforms based on primary iCCA cell lines to evaluate the functional effects of chimeric transcripts were also used. We found that HBV had inserted at multiple sites in the iCCA genomes in 45 (41.7%) of the tumors. Recurrent viral integration breakpoints were found at nine different sites. The most common insertional hotspot (7 tumors) was in the TERT (telomerase reverse transcriptase) promoter, where insertions and mutations (11 tumors) were mutually exclusive, and were accompanied by promoter hyperactivity. Recurrent HBV integration events (5 tumors) were also detected in FAT2 (FAT atypical cadherin 2), and were associated with enrichment of epithelial-mesenchymal transition-related genes. A distinctive intergenic insertion (chr9p21.3), between DMRTA1 (DMRT like family A1) and LINC01239 (long intergenic non-protein coding RNA 1239), had oncogenic effects through activation of the mammalian target of rapamycin (mTOR)/4EBP/S6K pathway. Regarding the mutational profiles of primary liver cancers, the overall landscape of HBV-iCCA was closer to that of nonviral conventional iCCA, than to HBV-HCC and HBV-cHCC/CCA.

CONCLUSIONS

Our findings provide insight into the behavior of iCCAs driven by various pathogenic mechanisms involving HBV integration events and associated genomic aberrations. This knowledge should be of use in managing HBV carriers.

Community-Based Multi-Site Randomized Controlled Trial of Behavioral Activation for Patients with Depressive Disorders

Behavioral activation (BA) is a beneficial and relatively cost-effective treatment option for depression. This study utilized a pragmatic randomized controlled research design to investigate whether BA, as compared with treatment as usual (TAU), led to superior treatment effects, when delivered in community mental health settings by retrained community mental health professionals. Patients with depressive disorders (n = 64) were randomly assigned to a 10-session BA (n = 31) or TAU (n = 33) group. The depressive symptoms and behavioral engagement were assessed at the baseline, post-treatment, and a six-month follow-up. Results showed that, as compared to the TAU group, the BA group had: (1) a reduction in depression severity, as evidenced by large effect sizes and greater response rates, and (2) an increase in behavioral engagement. However, the post-treatment gains were not maintained at the six-month follow-up. The implications and limitations of the study are also discussed (KCT0004098, June 27, 2019, retrospectively registered).

Estimation of the journal distance of Genomics & Informatics from other bioinformatics-driven journals, 2003-2018

This study explored the trends of Genomics & Informatics during the period of 2003-2018 in comparison with 11 other scholarly journals: BMC Bioinformatics, Algorithms for Molecular Biology: AMB, BMC Systems Biology, Journal of Computational Biology, Briefings in Bioinformatics, BMC Genomics, Nucleic Acids Research, American Journal of Human Genetics, Oncogenesis, Disease Markers, and Microarrays. In total, 22,423 research articles were reviewed. Content analysis was the main method employed in the current research. The results were interpreted using descriptive analysis, a clustering analysis, word embedding, and deep learning techniques. Trends are discussed for the 12 journals, both individually and collectively. This is an extension of our previous study (PMCID: PMC6808643).

Clinicopathological and molecular characterization of chromophobe hepatocellular carcinoma

BACKGROUND AND AIMS

Chromophobe hepatocellular carcinoma (HCC) is a newly included subtype of HCC in the 5th edition of the WHO classification with distinctive histological features (chromophobic cytoplasm with anaplastic nuclei and pseudocyst formation) and is strongly associated with the alternative lengthening of telomeres (ALT) phenotype. However, the clinicopathologic characterization and molecular features of chromophobe HCC are unknown.

METHODS

To comprehensively characterize chromophobe HCC, whole exome sequencing, copy number variation, and transcriptomic analyses were performed in 224 surgically resected HCC cases. Additionally, telomere-specific fluorescence in situ hybridization was used to assess ALT. These genomic profiles and ALT status were compared with clinicopathological features among subtypes of HCC, particularly chromophobe HCC and conventional HCC.

RESULTS

Chromophobe HCC was observed in 10.3% (23/224) cases and, compared to conventional HCC, was more frequent in females (P = .023). The overall and recurrence-free survival outcomes were similar between patients with chromophobe HCC and conventional HCC. However, chromophobe HCC displayed significantly more upregulated genes involving cell cycle progression and DNA repair. Additionally, ALT was significantly enriched in chromophobe HCC (87%; 20/23) compared to conventional HCC (2.2%, 4/178; P < .001). Somatic mutations in ALT-associated genes, including ATRX, SMARCAL1, FANCG, FANCM, SP100, TSPYL5, and RAD52 were more frequent in chromophobe HCC (30.4%, 7/23 cases) compared to conventional HCC (11.8%, 21/178 cases; P = .024).

CONCLUSIONS

Chromophobe HCC is a unique subtype of HCC with a prevalence of ~10%. Compared to conventional HCC, chromophobe HCC is associated with female predominance and ALT, although overall and recurrence-free outcomes are similar to conventional HCC.

Immuno-genomic classification of colorectal cancer organoids reveals cancer cells with intrinsic immunogenic properties associated with patient survival

Background

The intrinsic immuno-ge7nomic characteristics of colorectal cancer cells that affect tumor biology and shape the tumor immune microenvironment (TIM) are unclear.

Methods

We developed a patient-derived colorectal cancer organoid (CCO) model and performed pairwise analysis of 87 CCOs and their matched primary tumors. The TIM type of the primary tumor was classified as immuno-active, immuno-exhausted, or immuno-desert.

Results

The gene expression profiles, signaling pathways, major oncogenic mutations, and histology of the CCOs recapitulated those of the primary tumors, but not the TIM of primary tumors. Two distinct intrinsic molecular subgroups of highly proliferative and mesenchymal phenotypes with clinical significance were identified in CCOs with various cancer signaling pathways. CCOs showed variable expression of cancer-specific immune-related genes such as those encoding HLA-I and HLA-II, and molecules involved in immune checkpoint activation/inhibition. Among these genes, the expression of HLA-II in CCOs was associated with favorable patient survival. K-means clustering analysis based on HLA-II expression in CCOs revealed a subgroup of patients, in whom cancer cells exhibited Intrinsically Immunogenic Properties (Ca-IIP), and were characterized by high expression of signatures associated with HLA-I, HLA-II, antigen presentation, and immune stimulation. Patients with the Ca-IIP phenotype had an excellent prognosis, irrespective of age, disease stage, intrinsic molecular type, or TIM status. Ca-IIP was negatively correlated with intrinsic E2F/MYC signaling. Analysis of the correlation between CCO immuno-genotype and TIM phenotype revealed that the TIM phenotype was associated with microsatellite instability, Wnt/β-catenin signaling, APC/KRAS mutations, and the unfolded protein response pathway linked to the FBXW7 mutation in cancer cells. However, Ca-IIP was not associated with the TIM phenotype.

Conclusions

We identified a Ca-IIP phenotype from a large set of CCOs. Our findings may provide an unprecedented opportunity to develop new strategies for optimal patient stratification in this era of immunotherapy.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13046-021-02034-1.

Prognostic Molecular Indices of Resectable Hepatocellular Carcinoma: Implications of S100P for Early Recurrence

BACKGROUND

Although hepatocellular carcinomas (HCCs) often recur in patients undergoing hepatectomy, there are no reliable biomarkers of this undesirable event. Recent RNA-based efforts have developed valuable genetic indices prognostic of cancer outcomes. We aimed to identify molecular predictors of early recurrence after resection of HCC, and reveal the genomolecular structure of the resected tumors.

METHOD

Based on the transcriptomic and genomic datasets of 206 HCC samples surgically resected in the Asan Medical Center (AMC), we performed a differential gene expression analysis to identify quantitative markers associated with early recurrence and used the unsupervised clustering method to classify genomolecular subtypes.

RESULTS

Differential gene expression profiling revealed that S100P was the highest-ranked overexpressed gene in HCCs that recurred within 2 years of surgery. This trend was reproduced in immunohistochemical studies of the original cohort and an independent AMC cohort. S100P expression also independently predicted HCC-specific mortality post-resection (adjusted hazard ratio 1.09, 95% confidence interval 1.01-1.19; p = 0.042). Validation in a Chinese cohort and in in vitro experiments confirmed the prognostic value of S100P in HCC. We further identified five discrete molecular subtypes of HCC; a subtype with stem cell features ('AMC-C4') was associated with the worst prognosis, both in our series and another two Asian datasets, and S100P was most strongly upregulated in that subtype.

CONCLUSION

We identified a promising prognostic biomolecule, S100P, associated with early recurrence after HCC resection, and established the genomolecular architecture of tumors affecting clinical outcomes, particularly in Asian patients. These new insights into molecular mediators should contribute to effective care for affected patients.

Characterization of early postzygotic somatic mutations through multi-organ analysis

Mosaicisms caused by postzygotic mutational events are of increasing interest because of their potential association with various human diseases. Postzygotic somatic mutations have not been well characterized however in terms of their developmental lineage in humans. We conducted whole-genome sequencing (WGS) and targeted deep sequencing in 15 organs across three developmental lineages from a single male fetus with polycystic kidney disease (PKD) of 21 weeks gestational age. This fetus had no detectable neurological abnormalities at autopsy but germline mutations in the PKHD1 gene were identified that may have been associated with the PKD. Eight early embryonic mosaic variants with no alteration of protein function were detected. These variants were thought to have occurred at the two or four cell stages after fertilization with a mutational pattern involving frequent C>T and T>C transitions. In our current analyses, no tendency toward organ-specific mutation occurrences was found as the eight variants were detected in all 15 organs. However different allele fractions of these variants were found in different organs, suggesting a tissue-specific asymmetric growth of cells that reflected the developmental germ layer of each organ. This indicated that somatic mutation occurrences, even in early embryogenesis, can affect specific organ development or disease. Our current analyses demonstrate that multi-organ analysis is helpful for understanding genomic mosaicism. Our results also provide insights into the biological role of mosaicism in embryonic development and disease.

Organizing an in-class hackathon to correct PDF-to-text conversion errors of Genomics & Informatics 1.0

This paper describes a community effort to improve earlier versions of the full-text corpus of Genomics & Informatics by semi-automatically detecting and correcting PDF-to-text conversion errors and optical character recognition errors during the first hackathon of Genomics & Informatics Annotation Hackathon (GIAH) event. Extracting text from multi-column biomedical documents such as Genomics & Informatics is known to be notoriously difficult. The hackathon was piloted as part of a coding competition of the ELTEC College of Engineering at Ewha Womans University in order to enable researchers and students to create or annotate their own versions of the Genomics & Informatics corpus, to gain and create knowledge about corpus linguistics, and simultaneously to acquire tangible and transferable skills. The proposed projects during the hackathon harness an internal database containing different versions of the corpus and annotations.

Comprehensive characteristics of somatic mutations in the normal tissues of patients with cancer and existence of somatic mutant clones linked to cancer development

BACKGROUND

Somatic mutations are a major driver of cancer development and many have now been identified in various cancer types, but the comprehensive somatic mutation status of the normal tissues matched to tumours has not been revealed.

METHOD

We analysed the somatic mutations of whole exome sequencing data in 392 patient tumour and normal tissue pairs based on the corresponding blood samples across 10 tumour types.

RESULTS

Many of the mutations involved in oncogenic pathways such as PI3K, NOTCH and TP53, were identified in the normal tissues. The ageing-related mutational signature was the most prominent contributing signature found and the mutations in the normal tissues were frequently in genes involved in late replication time (p<0.0001). Variants were rarely overlapping across tissue types but shared variants between normal and matched tumour tissue were present. These shared variants were frequently pathogenic when compared with non-shared variants (p=0.001) and showed a higher variant-allele-fraction (p<0.0001). Normal tissue-specific mutated genes were frequently non-cancer-associated (p=0.009). PIK3CA mutations were identified in 6 normal tissues and were harboured by all of the matched cancer tissues. Multiple types of PIK3CA mutations were found in normal breast and matched cancer tissues. The PIK3CA mutations exclusively present in normal tissue may indicate clonal expansions unrelated to the tumour. In addition, PIK3CA mutation was appeared that they arose before the occurrence of the allelic imbalance.

CONCLUSION

Our current results suggest that somatic mutant clones exist in normal tissues and that their clonal expansion could be linked to cancer development.

Predictors of permanent stoma creation in patients with mid or low rectal cancer: results of a multicentre cohort study with preoperative evaluation of anal function

AIM

Preoperative factors predictive of permanent stoma creation were investigated in a long-term follow-up of patients with mid or low rectal cancer.

METHOD

We included patients who underwent radical resection for mid or low rectal cancer with available data for preoperative anal function measured by manometry and Faecal Incontinence Severity Index questionnaire between January 2005 and December 2015 in three tertiary referral hospitals. A permanent stoma was defined as a stoma present until the patient's last follow-up visit or death. Preoperative factors that predicted permanent stoma creation were analysed.

RESULTS

Over a median follow-up of 57.4 months (range 12-143 months), a permanent stoma was created in 144/577 (25.0%) patients, including 89 (15.4%) who underwent abdominoperineal resection, one (0.2%) who underwent Hartmann's operation without reversal, 15 (2.6%) with a diverting ileostomy at the time of initial sphincter-preserving surgery without undergoing stoma reversal, and 39 (6.8%) who underwent permanent ileostomy formation after sphincter-preserving surgery. Patients with permanent stoma creation had a shorter tumour distance from the anal verge (P < 0.001), larger tumour size (P = 0.020) and higher preoperative Faecal Incontinence Severity Index score (P = 0.020). On multivariable analysis, tumour distance from the anal verge predicted permanent stoma formation (relative risk 0.53 per centimetre increase; 95% confidence interval 0.46-0.60; P < 0.001) but preoperative anal function did not.

CONCLUSION

Tumour distance from the anal verge was the only preoperative determinant of permanent stoma creation in rectal cancer patients. These data may help mid and low rectal cancer patients understand the need for permanent stoma.

Spontaneous mutations in the single TTN gene represent high tumor mutation burden

Tumor mutation burden (TMB) is an emerging biomarker, whose calculation requires targeted sequencing of many genes. We investigated if the measurement of mutation counts within a single gene is representative of TMB. Whole-exome sequencing (WES) data from the pan-cancer cohort (n = 10,224) of TCGA, and targeted sequencing (tNGS) and TTN gene sequencing from 24 colorectal cancer samples (AMC cohort) were analyzed. TTN was identified as the most frequently mutated gene within the pan-cancer cohort, and its mutation number best correlated with TMB assessed by WES (rho = 0.917, p < 2.2e-16). Colorectal cancer was one of good candidates for the application of this diagnostic model of TTN-TMB, and the correlation coefficients were 0.936 and 0.92 for TMB by WES and TMB by tNGS, respectively. Higher than expected TTN mutation frequencies observed in other FLAGS (FrequentLy mutAted GeneS) are associated with late replication time. Diagnostic accuracy for high TMB group did not differ between TTN-TMB and TMB assessed by tNGS. Classification modeling by machine learning using TTN-TMB for MSI-H diagnosis was constructed, and the diagnostic accuracy was 0.873 by area under the curve in external validation. TTN mutation was enriched in samples possessing high immunostimulatory signatures. We suggest that the mutation load within TTN represents high TMB status.

3334Updated meta-analysis of biodegradable polymer drug-eluting stent versus second-generation durable polymer drug-eluting stent implantations

Background

Data regarding clinical outcomes of biodegradable polymer drug-eluting stent (BP-DES) versus second-generation durable polymer drug-eluting stent (DP-DES) in patients undergoing percutaneous coronary intervention (PCI) are inconclusive.

Purpose

We aimed to perform a meta-analysis to investigate the clinical outcomes of BP-DES compared with second-generation DP-DES in patients who have undergone PCI.

Methods

We searched PubMed, MEDLINE, EMBASE, and Cochrane databases through January 2019 for randomized controlled trials comparing BP-DES with second-generation DP-DES in patients treated with PCI. All-cause death, cardiac death, myocardial infarction (MI), target vessel revascularization (TVR), target lesion revascularization (TLR), definite/probable stent thrombosis (ST) were compared between the groups. Additionally, a landmark analysis with the landmark set at 1 year and a subgroup analysis according to stent characteristics were performed.

Results

Data from 23 trials including 28802 randomized patients were analyzed. At a median follow up of 3.1 years, no significant differences were found in terms of all-cause death (odds ratio [OR] 1.05, 95% confidence interval [CI] 0.95–1.16), cardiac death (OR 1.01, 95% CI 0.87–1.17), MI (OR 0.92, 95% CI 0.82–1.03), TVR (OR 0.97, 95% CI 0.86–1.11), TLR (OR 0.97, 95% CI 0.85–1.11), and definite/probable ST (OR 0.86, 95% CI 0.70–1.07) between the groups. Landmark analysis showed that there were similar risks in all-cause death (OR 1.04, 95% CI 0.93–1.17), cardiac death (OR 1.11, 95% CI 0.92–1.36), MI (OR 0.94, 95% CI 0.79–1.13), TVR (OR 0.95, 95% CI 0.73–1.23), TLR (OR 1.00, 95% CI 0.80–1.24), and definite/probable ST (OR 0.92, 95% CI 0.67–1.28) between the groups. The similar tendency of any study endpoints between the groups was consistent in the subgroup, including stent platform (stainless steel vs. alloy), the drug coating distribution (abluminal vs. circumferential), the polymer degradation period (<6 months vs. >6 months), or the drug release duration (<6 months vs. >6 months) of BP-DES, or the DAPT duration (≥6 months vs. ≥12 months). However, the uses of BP-DES with sirolimus-eluting (OR 0.84, 95% CI 0.72–0.98) or ultrathin strut (defined as <70μm; OR 0.81, 95% CI 0.68–0.97) were predictive for lower risk of MI.

Clinical outcomes

Conclusions

In our updated meta-analysis, BP-DES implantation was associated with comparable clinical outcomes compared with second-generation DP-DES implantation. However, PCI with ultrathin biodegradable polymer sirolimus-eluting stent could reduce the risk of MI.

P2799Long-term outcomes after percutaneous coronary intervention with biodegradable polymer drug-eluting stent versus second-generation durable polymer drug-eluting stent: evidence from a meta-analysis

Background

The true benefit of biodegradable polymer drug-eluting stent (BP-DES) over second-generation durable polymer drug-eluting stent (DP-DES) expected to be represented during late period of follow-up after percutaneous coronary intervention (PCI), but prior meta-analysis only evaluated short-term outcomes.

Purpose

We aimed to compare the long-term clinical outcomes after PCI with BP-DES versus second-generation DP-DES by a meta-analysis of randomized controlled trials.

Methods

Randomized controlled trials comparing BP-DES with second-generation DP-DES implantations were searched through PubMed, MEDLINE, EMBASE, and Cochrane databases. All-cause death, cardiac death, myocardial infarction (MI), target vessel revascularization (TVR), target lesion revascularization (TLR), and definite/probable stent thrombosis (ST) were compared between the groups. In addition, a landmark analysis with the landmark set at 1-year and a subgroup analysis based on stent characteristics were performed.

Results

Fifteen trials that included a total of 21311 randomized patients with at least 2 years follow-up were analyzed. At a median follow-up of 4.2 years, no significant differences in the risks of all-cause death (odds ratio [OR] 1.03, 95% confidence interval [CI] 0.94–1.14), cardiac death (OR 1.03, 95% CI 0.88–1.20), MI (OR 0.90, 95% CI 0.79–1.01), TVR (OR 0.96, 95% CI 0.82–1.12), TLR (OR 0.97, 95% CI 0.85–1.11), and definite/probable ST (OR 0.84, 95% CI 0.67–1.05) were found between the groups. In the 1-year landmark analysis, the rates of all-cause death (OR 1.04, 95% CI 0.93–1.17), cardiac death (OR 1.11, 95% CI 0.92–1.36), MI (OR 0.94, 95% CI 0.79–1.13), TVR (OR 0.95, 95% CI 0.73–1.23), TLR (OR 1.00, 95% CI 0.80–1.24), and definite/probable ST (OR 0.94, 95% CI 0.67–1.31) were similar between the groups. There were comparable rates of any study endpoints between the groups regardless of stent platform (stainless steel vs. alloy), the polymer degradation period (<6 months vs. >6 months) or the drug release duration (<6 months vs. >6 months) of BP-DES, or the DAPT duration (≥6 months vs. ≥12 months). However, the use of BP-DES with sirolimus eluting (OR 0.82, 95% CI 0.70–0.97), circumferential drug distribution (OR 0.79, 95% CI 0.65–0.96), thin strut (defined as <100μm; OR 0.83, 95% CI 0.70–0.97), or ultrathin strut (defined as <70μm; OR 0.78, 95% CI 0.64–0.94) were associated with lower rates of MI than did second-generation DP-DES. Moreover, BP-DES with circumferential drug distribution (OR 0.82, 95% CI 0.69–0.98) was predictive for reduced rates of TVR.

Clinical outcomes

Conclusions

In this meta-analysis, long-term clinical outcomes were equivalent between BP-DES and second-generation DP-DES implantations. However, among BP-DESs, the improved risks of MI in those with sirolimus eluting, circumferential drug distribution, thin strut, or ultrathin strut and decreased rates of TVR in those with circumferential drug distribution were noted.

Immunogenomic landscape of hepatocellular carcinoma with immune cell stroma and EBV-positive tumor-infiltrating lymphocytes

BACKGROUND & AIMS

The immunogenomic characteristics of hepatocellular carcinomas (HCCs) with immune cell stroma (HCC-IS), defined histologically, have not been clarified. We investigated the clinical and molecular features of HCC-IS and the prognostic impact of Epstein-Barr virus (EBV) infection.

METHODS

We evaluated 219 patients with conventional HCC (C-HCC) and 47 with HCC-IS using in situ hybridization for EBV, immunohistochemistry, multiplex immunofluorescence staining, and whole exome and transcriptome sequencing. Human leukocyte antigen types were also extracted from the sequencing data. Genomic and prognostic parameters were compared between HCC-IS and C-HCC.

RESULTS

CD8 T cell infiltration was more frequent in HCC-IS than C-HCC (mean fraction/sample, 22.6% vs. 8.9%, false discovery rate q <0.001), as was EBV positivity in CD20-positive tumor-infiltrating lymphocytes (TILs) (74.5% vs. 4.6%, p <0.001). CTNNB1 mutations were not identified in any HCC-IS, while they were present in 24.1% of C-HCC (p = 0.016). Inhibitory and stimulatory immune modulators were expressed at similar levels in HCC-IS and EBV-positive C-HCC. Global hypermethylation, and expression of PD-1 and PD-L1 in TILs, and PD-L1 in tumors, were also associated with HCC-IS (p <0.001), whereas human leukocyte antigen type did not differ according to HCC type or EBV positivity. HCC-IS was an independent factor for favorable recurrence-free survival (adjusted hazard ratio [aHR] 0.23; p = 0.002). However, a subgroup of tumors with a high density of EBV-positive TILs had poorer recurrence-free (aHR 25.48; p <0.001) and overall (aHR 9.6; p = 0.003) survival, and significant enrichment of CD8 T cell exhaustion signatures (q = 0.0296).

CONCLUSIONS

HCC-IS is a distinct HCC subtype associated with a good prognosis and frequent EBV-positive TILs. However, paradoxically, a high density of EBV-positive TILs in tumors is associated with inferior prognostic outcomes. Patients with HCC-IS could be candidates for immunotherapy.

LAY SUMMARY

Hepatocellular carcinomas with histologic evidence of abundant immune cell infiltration are characterized by frequent activation of Epstein-Barr virus in tumor-infiltrating lymphocytes and less aggressive clinical behavior. However, a high density of Epstein-Barr virus-positive tumor-infiltrating lymphocytes is associated with inferior prognostic outcomes, possibly as a result of immune escape due to significant CD8 T cell exhaustion.

Detection of chromosome structural variation by targeted next-generation sequencing and a deep learning application

Molecular testing is increasingly important in cancer diagnosis. Targeted next generation sequencing (NGS) is widely accepted method but structural variation (SV) detection by targeted NGS remains challenging. In the brain tumor, identification of molecular alterations, including 1p/19q co-deletion, is essential for accurate glial tumor classification. Hence, we used targeted NGS to detect 1p/19q co-deletion using a newly developed deep learning (DL) model in 61 tumors, including 19 oligodendroglial tumors. An ensemble 1-dimentional convolution neural network was developed and used to detect the 1p/19q co-deletion. External validation was performed using 427 low-grade glial tumors from The Cancer Genome Atlas (TCGA). Manual review of the copy number plot from the targeted NGS identified the 1p/19q co-deletion in all 19 oligodendroglial tumors. Our DL model also perfectly detected the 1p/19q co-deletion (area under the curve, AUC = 1) in the testing set, and yielded reproducible results (AUC = 0.9652) in the validation set (n = 427), although the validation data were generated on a completely different platform (SNP Array 6.0 platform). In conclusion, targeted NGS using a cancer gene panel is a promising approach for classifying glial tumors, and DL can be successfully integrated for the SV detection in NGS data.

Does the Bed Frame Deflection Occur along with Mattress Deflection during In-Hospital Cardiopulmonary Resuscitation? an Experiment Using Mechanical Devices

Objectives

When we perform chest compression on a patient on a bed, the mattress and bed frame can be depressed together with the patient's chest. This study was conducted to assess whether bed frame deflection occurred during chest compressions.

Methods

We designed a firm bed (“bed like the ground,” BLG) to assess the bed frame deflection in the Stryker Trauma Stretcher (STS) and the ER stretcher cart (ER-SC). The STS included a soft mattress and the ER-SC a hard mattress. We performed 50 continuous chest compressions on the Resusci Anne Skill Reporter with CPRmeter in each experiment. The experiments were done in four settings. Test 1 included the BLG; test 2 included a mattress and backboard on each bed; test 3 included the mattress of each bed and a backboard on the BLG; and test 4 included the mattress of each bed on the BLG. We calculated the mattress and bed frame deflections using the gaps of compression depths between the values measured by Resusci Anne and CPRmeter.

Results

The mattress deflections of the STS and ER-SC mattress were determined to be 11.2 and 0.67 mm, respectively. The bed frame deflection for the STS and ER-SC were 0.95 and 5.17 mm, respectively.

Conclusion

The study confirms that bed frame deflection will occur when we perform chest compressions on the manikin lying on a bed. Additionally, the bed frame deflections differ depending on the type of bed. (Hong Kong j.emerg.med. 2016;23:35-41)

Accuracy of Plain Abdominal Radiography in the Differentiation between Small Bowel Obstruction and Small Bowel Ileus in Acute Abdomen Presenting to Emergency Department

Introduction

Our purpose was to evaluate whether plain abdominal radiography (PAR) could accurately differentiate between small bowel obstruction (SBO) and small bowel ileus (SBI) in an emergency setting. We also evaluated the value of known classic signs on the PAR for differentiating between SBO and SBI.

Methods

This retrospective study included 216 emergency room patients who had small bowel distension (maximal small bowel diameter ≥2.5 cm) on the PAR and who underwent successive abdominal computed tomography. One radiologist and one emergency physician retrospectively reviewed PAR in consensus, unaware of the patients' clinical data; they divided the patients into an SBO group and an SBI group according to the radiographic findings. Presence or numeric values of 10 radiographic signs were also recorded. Final diagnoses of SBO and SBI were established by a combined analysis of medical charts, surgical records, radiographic findings on abdominal computed tomography, and small bowel studies. The differential diagnoses based on PAR and the final diagnoses were compared, and the sensitivity and specificity of PAR were calculated. We also evaluated the differences among 10 radiographic signs between the final SBO and SBI groups.

Results

Sensitivity and specificity of PAR for SBO were 82.0% and 92.4%, respectively. Among the 10 radiographic signs, all except maximal colon diameter were statistically significant predictors on the final diagnosis.

Conclusions

PAR is an accurate and effective initial imaging modality for differentiating between SBO and SBI in an emergency setting, and most of the classic radiographic signs have a diagnostic value.

Temporal patterns of patient-reported trismus and associated mouth-opening distances in radiotherapy for head and neck cancer: A prospective cohort study

OBJECTIVES

To identify temporal patterns of patient-reported trismus during the first year post-radiotherapy, and to study their associations with maximal interincisal opening distances (MIOs).

DESIGN

Single institution case series.

SETTING

University hospital ENT clinic.

PARTICIPANTS

One hundred and ninety-six subjects who received radiotherapy (RT) for head and neck cancer (HNC) with or without chemotherapy in 2007-2012 to a total dose of 64.6/68 Gy in 38/34 fractions, respectively. All subjects were prospectively assessed for mouth-opening ability (Gothenburg Trismus Questionnaire (GTQ), European Organization for Research and Treatment of Cancer quality of life Questionnaire (EORTC QLQ-H&N35), and MIO) pre-RT and at 3, 6 and 12 months after RT.

MAIN OUTCOME MEASURES

Correlations between temporally robust GTQ symptoms and MIO as given by Pearson's correlation coefficients (P_r ); temporally robust GTQ-symptom domains as given by factor analysis; rates of trismus with respect to baseline by risk ratios (RRs).

RESULTS

Four temporally robust domains were identified: Eating (3-7 symptoms), Jaw (3-7), Pain (2-5) and Quality of Life (QoL, 2-5), and included 2-3 persistent symptoms across all post-RT assessments. The median RR for a moderate/severe (>2/>3) cut-off was the highest for Jaw (3.7/3.6) and QoL (3.2/2.9). The median P_r between temporally robust symptoms and MIO post-radiotherapy was 0.25-0.35/0.34-0.43/0.24-0.31/0.34-0.50 for Eating/Jaw/Pain/QoL, respectively.

CONCLUSIONS

Mouth-opening distances in patients with HNC post-RT can be understood in terms of associated patient-reported outcomes on trismus-related difficulties. Our data suggest that a reduction in MIO can be expected as patients communicate their mouth-opening status to interfere with private/social life, a clinical warning signal for emerging or worsening trismus as patients are being followed after RT.

Long-term outcomes of locally or radically resected T1 colorectal cancer

AIM

Little is known about the long-term outcome of T1 colorectal cancer (CRC) following curative resection. The present study addressed the long-term outcome of locally or radically resected T1 CRCs.

METHOD

A total of 430 patients with T1 CRC who underwent local or radical resection were considered. Unfavourable histological factors were defined as positive resection margin, deep submucosal invasion, vascular invasion, Grade 3 and budding. The patients were classified as low-risk (unfavourable histological factor negative, n = 65) or high-risk (unfavourable histological factor positive, n = 365).

RESULTS

Over a median follow-up of 78.4 months, disease recurred in 16 (3.7%) patients in the high-risk group, and no recurrence in the low-risk group. Resection type and vascular invasion were significantly associated with recurrence. In the vascular invasion (+) high-risk group, both 5-year disease-free survival rate and 5-year overall survival rate were significantly associated with resection type (radical 94.6%, local 43.8%, P < 0.001, and radical 99.1%, local 66.7%, P < 0.001). In the vascular invasion (-) high-risk group, 5-year disease-free survival rate was also significantly associated with resection type (radical 98.9%, local 84.7%, P = 0.001). However, 5-year overall survival rate was not associated with resection type (radical 98.9%, local 95.2%, P = 0.816).

CONCLUSION

Local resection may be effective and oncologically safe in low-risk T1 CRC. Although additional surgery should be recommended for the locally resected high-risk T1 CRC cases, intensive surveillance without additional surgery and timely salvage operation may offer another treatment option, if vascular invasion is negative.

Temporal changes in physiological parameters of systemic inflammatory response syndrome during the three days prior to a diagnosis of sepsis: a case-control study

AIMS AND OBJECTIVES

This study was conducted to determine temporal patterns of early changes in physiological parameters of systemic inflammatory response syndrome over three days prior to a diagnosis of sepsis.

BACKGROUND

Early detection and timely management of systemic inflammatory response syndrome are often not implemented due to a failure to recognise or diagnose systemic inflammatory response syndrome.

DESIGN

A retrospective case-control study design was adopted.

METHODS

All 81 study subjects in an intensive care unit were included: 33 case subjects who received a definitive diagnosis of sepsis and 48 control patients who were not diagnosed with systemic inflammatory response syndrome or sepsis. Vital signs (temperatures, heart rates, blood pressures and respiratory rates) and white blood cell count, urine output, serum creatinine concentration, platelet count and serum glucose level data were collected for one, two and three days prior to sepsis diagnosis.

RESULTS

Homogeneity test revealed greater proportions of the aged and subjects with diabetes mellitus, hypertension and wound in the case group. Analysis also showed significant intergroup differences in systemic inflammatory response syndrome criteria score, heart rates, platelet counts and blood glucose levels, but no intergroup differences in body temperatures, blood pressures, respiratory rates, urine outputs or serum creatinine levels. A larger proportion of case subjects were fitted with a central venous or Foley catheter.

CONCLUSIONS

The presence of a wound, hypertension or diabetes mellitus, and the use of an invasive medical device may increase the risk of systemic inflammatory response syndrome. Of the physiological parameters examined, heart rate, platelet counts, and blood glucose levels might serve as significant early signs of systemic inflammatory response syndrome.

RELEVANCE TO CLINICAL PRACTICE

Caution should be observed whenever diabetic or hypertension patients develop sudden and persistent hyperglycaemia or tachycardia, and nurses should also be aware of the potential for systemic inflammatory response syndrome in patients with a central venous or indwelling urinary catheter.

Lymph node size is not a reliable criterion for predicting nodal metastasis in rectal neuroendocrine tumours

AIM

The study was designed to assess the correlation between lymph node (LN) size and LN metastasis in patients with rectal neuroendocrine tumours (NETs).

METHOD

Forty patients who underwent curative resection with lymphadenectomy for a rectal NET between January 2007 and December 2012 were included. The short and long diameters of entire nodes were microscopically measured using a slide gauge.

RESULTS

In all, 1052 LNs were collected from the 40 patients, with 49 (4.7%) showing evidence of metastasis. Metastasis-positive LNs had significantly greater long and short diameters (P < 0.001) than metastasis-negative LNs. Of the 49 metastatic LNs, 29 (59.2%) were ≤ 5 mm in largest diameter. In five patients, the largest metastatic LN was only 2-3 mm in diameter. In clinically node-negative (cN0) patients, 18 (51.4%) patients had metastatic LNs (pN1).

CONCLUSION

The size of LNs containing metastasis varied widely, with some being very small. LN size alone is therefore not a sufficient predictor of tumour metastasis in rectal NETs. Radical surgery with lymphadenectomy should be considered for patients with rectal NETs with high risk factors for LN metastasis, even those without LN enlargement.

Cytokine-release kinetics of platelet-rich plasma according to various activation protocols

Objectives

This study was conducted to evaluate the cytokine-release kinetics of platelet-rich plasma (PRP) according to different activation protocols.

Methods

Two manual preparation procedures (single-spin (SS) at 900 g for five minutes; double-spin (DS) at 900 g for five minutes and then 1500 g for 15 minutes) were performed for each of 14 healthy subjects. Both preparations were tested for platelet activation by one of three activation protocols: no activation, activation with calcium (Ca) only, or calcium with a low dose (50 IU per 1 ml PRP) of thrombin. Each preparation was divided into four aliquots and incubated for one hour, 24 hours, 72 hours, and seven days. The cytokine-release kinetics were evaluated by assessing PDGF, TGF, VEGF, FGF, IL-1, and MMP-9 concentrations with bead-based sandwich immunoassay.

Results

The concentration of cytokine released from PRP varied over time and was influenced by various activation protocols. Ca-only activation had a significant effect on the DS PRPs (where the VEGF, FGF, and IL-1 concentrations were sustained) while Ca/thrombin activation had effects on both SS and DS PRPs (where the PDGF and VEGF concentrations were sustained and the TGF and FGF concentrations were short). The IL-1 content showed a significant increase with Ca-only or Ca/thrombin activation while these activations did not increase the MMP-9 concentration.

Conclusion

The SS and DS methods differed in their effect on cytokine release, and this effect varied among the cytokines analysed. In addition, low dose of thrombin/calcium activation increased the overall cytokine release of the PRP preparations over seven days, relative to that with a calcium-only supplement or non-activation.

Cite this article: Professor J. H. Oh. Cytokine-release kinetics of platelet-rich plasma according to various activation protocols. Bone Joint Res 2016;5:37–45. DOI: 10.1302/2046-3758.52.2000540

The measurement of bone mineral density of bilateral proximal humeri using DXA in patients with unilateral rotator cuff tear

We propose that the measurement of the bone mineral density (BMD) of the proximal humerus be standardized using the dual energy X-ray absorptiometry (DXA) in patients supposed to undergo rotator cuff repair surgery as well as those with the fracture of the proximal humerus as the BMD of the proximal humerus is decreased in these patients.

INTRODUCTION

We propose that the measurement of the BMD of the proximal humerus be standardized using the DXA in patients who are supposed to undergo rotator cuff repair surgery as well as those with the fracture of the proximal humerus.

METHODS

We conducted the prospective study in 213 patients with unilateral rotator cuff tear but without contralateral shoulder pain or disease. In these patients, we preoperatively measured the BMD of the bilateral proximal humeri with a repeat measurement in 20 patients. We predefined three regions of interest (ROIs) in the proximal humerus with the consideration of the rotator cuff repair surgery as well as proximal humeral fractures.

RESULTS

The measurement of the BMD of the proximal humerus using the DXA showed excellent reliability (intraclass correlation coefficient > .90). BMD values of all three ROIs in the affected shoulder were significantly lower than those in asymptomatic shoulder (all p < 0.05). In female patients, the BMD values of ROIs in bilateral shoulder were significantly lower than those in male patients (all p < 0.001). In multiple regressions, however, there were no significant correlations between other clinical characteristics, except for the gender, and the BMD of GT in the affected shoulder.

CONCLUSIONS

It is imperative that the bone quality of the proximal humerus be accurately evaluated prior to surgery in patients who are supposed to undergo rotator cuff repair using suture anchors as well as in those with proximal humeral fractures. This is because the BMD of the proximal humerus is decreased in these patients.

Effects of Rashba and Dresselhaus spin-orbit interactions on the ground state of two-dimensional localized spins

Starting with the indirect exchange model influenced by the Rashba and the Dresselhaus spin-orbit interactions, we derive the Dzyaloshinskii-Moriya interaction of localized spins. The strength of the Dzyaloshinskii-Moriya interaction is compared with that of the Heisenberg exchange term as a function of atomic distance. Using the calculated interaction strengths, we discuss the formation of various atomic ground states as a function of temperature and external magnetic field. By plotting the magnetic field-temperature phase diagram, we present approximate phase boundaries between the spiral, Skyrmion and ferromagnetic states of the two-dimensional weak ferromagnetic system.

Dopaminergic manipulations and its effects on neurogenesis and motor function in a transgenic mouse model of Huntington's disease

Huntington's disease (HD) is an inherited neurodegenerative disorder that is classically defined by a triad of movement and cognitive and psychiatric abnormalities with a well-established pathology that affects the dopaminergic systems of the brain. This has classically been described in terms of an early loss of dopamine D2 receptors (D2R), although interestingly the treatments most effectively used to treat patients with HD block these same receptors. We therefore sought to examine the dopaminergic system in HD not only in terms of striatal function but also at extrastriatal sites especially the hippocampus, given that transgenic (Tg) mice also exhibit deficits in hippocampal-dependent cognitive tests and a reduction in adult hippocampal neurogenesis. We showed that there was an early reduction of D2R in both the striatum and dentate gyrus (DG) of the hippocampus in the R6/1 transgenic HD mouse ahead of any overt motor signs and before striatal neuronal loss. Despite downregulation of D2Rs in these sites, further reduction of the dopaminergic input to these sites by either medial forebrain bundle lesions or receptor blockade using sulpiride was able to improve both deficits in motor performance and adult hippocampal neurogenesis. In contrast, a reduction in dopaminergic innervation of the neurogenic niches resulted in impaired neurogenesis in healthy WT mice. This study therefore provides evidence that D2R blockade improves hippocampal and striatal deficits in HD mice although the underlying mechanism for this is unclear, and suggests that agents working within this network may have greater effects than previously thought.

Pretreatment of magnesium sulphate improves intubating conditions of rapid sequence tracheal intubation using alfentanil, propofol, and rocuronium - a randomized trial

Background

We investigated the effects of a magnesium sulfate pretreatment on intubating conditions and cardiovascular responses during rapid sequence tracheal intubation (RSI) in this double-blind randomized study.

Methods

Adult patients (n = 154) were randomly allocated to a rocuronium-0.6, rocuronium-0.9, or magnesium group. The magnesium group was pretreated with 50 mg/kg MgSO₄, and the other two groups received the same volume of isotonic saline. Anesthesia was induced with alfentanil, propofol, and either 0.6 mg/kg (rocuronium-0.6 and magnesium groups) or 0.9 mg/kg (rocuronium-0.9 group) rocuronium. An anesthesiologist, blinded to the group assignments, performed RSI and assessed the intubating conditions. Systolic arterial pressure (SAP) and heart rate (HR) were recorded before the magnesium sulfate or normal saline was administered, before anesthesia induction, before intubation, and every minute after intubation for 5 min.

Results

Airway features were similar among the three groups. The intubating conditions were improved significantly in the magnesium group (P < 0.001) compared with the other two groups. Significant increases in SAP at 1 min after intubation were observed in the rocuronium-0.6 and -0.9 groups when compared with the magnesium group (P < 0.05). HR was comparable among the three groups (P > 0.05). No hypertensive episode occurred during the immediate post-intubation period in the magnesium group (P = 0.001), and tachycardia occurred most frequently in the rocuronium-0.6 group (P < 0.05).

Conclusions

MgSO₄ administered prior to RSI using alfentanil, propofol, and rocuronium may improve intubating conditions and prevent post-intubation hypertension.

4-O-methylhonokiol, a PPARγ agonist, inhibits prostate tumour growth: p21-mediated suppression of NF-κB activity

BACKGROUND AND PURPOSE

The effects of 4-O-methylhonokiol (MH), a constituent of Magnolia officinalis, were investigated on human prostate cancer cells and its mechanism of action elucidated.

EXPERIMENTAL APPROACH

The anti-cancer effects of MH were examined in prostate cancer and normal cells. The effects were validated in vivo using a mouse xenograft model.

KEY RESULTS

MH increased the expression of PPARγ in prostate PC-3 and LNCap cells. The pull-down assay and molecular docking study indicated that MH directly binds to PPARγ. MH also increased transcriptional activity of PPARγ but decreased NF-κB activity. MH inhibited the growth of human prostate cancer cells, an effect attenuated by the PPARγ antagonist GW9662. MH induced apoptotic cell death and this was related to G(0) -G(1) phase cell cycle arrest. MH increased the expression of the cell cycle regulator p21, and apoptotic proteins, whereas it decreased phosphorylation of Rb and anti-apoptotic proteins. Transfection of PC3 cells with p21 siRNA or a p21 mutant plasmid on the cyclin D1/ cycline-dependent kinase 4 binding site abolished the effects of MH on cell growth, cell viability and related protein expression. In the animal studies, MH inhibited tumour growth, NF-κB activity and expression of anti-apoptotic proteins, whereas it increased the transcriptional activity and expression of PPARγ, and the expression of apoptotic proteins and p21 in tumour tissues.

CONCLUSIONS AND IMPLICATION

MH inhibits growth of human prostate cancer cells through activation of PPARγ, suppression of NF-κB and arrest of the cell cycle. Thus, MH might be a useful tool for treatment of prostate cancer.

Antitumor activity of IL-32β through the activation of lymphocytes, and the inactivation of NF-κB and STAT3 signals

Cytokine and activation of lymphocytes are critical for tumor growth. We investigated whether interleukin (IL)-32β overexpression changes other cytokine levels and activates cytotoxic lymphocyte, and thus modify tumor growth. Herein, IL-32β inhibited B16 melanoma growth in IL-32β-overexpressing transgenic mice (IL-32β mice), and downregulated the expressions of anti-apoptotic proteins (bcl-2, IAP, and XIAP) and cell growth regulatory proteins (Ki-67 antigen (Ki-67) and proliferating cell nuclear antigen (PCNA)), but upregulated the expressions of pro-apoptotic proteins (bax, cleaved caspase-3, and cleaved caspase-9). IL-32β also inhibited colon and prostate tumor growth in athymic nude mice inoculated with IL-32β-transfected SW620 colon or PC3 prostate cancer cells. The forced expression of IL-32β also inhibited cell growth in cultured colon and prostate cancer cells, and these inhibitory effects were abolished by IL-32 small interfering RNA (siRNA). IL-10 levels were elevated, but IL-1β, IL-6, and tumor necrosis factor-alpha (TNF-α) levels were reduced in the tumor tissues and spleens of IL-32β mice, and athymic nude mice. The number of cytotoxic T (CD8(+)) and natural killer (NK) cells in tumor tissues, spleen, and blood was significantly elevated in IL-32β mice and athymic nude mice inoculated with IL-32β-transfected cancer cells. Constituted activated NF-κB and STAT3 levels were reduced in the tumor tissues of IL-32β mice and athymic nude mice, as well as in IL-32β-transfected cultured cancer cells. These findings suggest that IL-32β inhibits tumor growth by increasing cytotoxic lymphocyte numbers, and by inactivating the NF-κB and STAT3 pathways through changing of cytokine levels in tumor tissues.

Clinicopathological characteristics of T1 colorectal cancer without background adenoma

AIM

Background adenoma (BGA) is defined as benign adenomatous tissue contiguous to resected carcinomas, and the absence of BGA in a tumour is considered a histological criterion of de novo cancers. The present study aimed to identify the clinicopathological characteristics of T1 colorectal cancer (CRC) without BGA.

METHOD

A retrospective review was carried out of prospectively collected data from two centres: the National Cancer Center, Korea; and Chonnam National University Hwasun Hospital, Korea. A total of 590 patients with T1 CRC, treated by endoscopic or surgical resection between January 2001 and August 2011, were enrolled. Details regarding gender, age, tumour location, endoscopic gross type, tumour size, depth of submucosal (SM) invasion, angiolymphatic invasion, tumour grade, budding and lymph node (LN) metastasis were evaluated with regard to the presence or absence of BGA.

RESULTS

BGA was absent in 197 (33.4%) patients. Tumour size <20 mm, flat or depressed type, deep SM depth and tumour budding were associated with the absence of BGA in univariate and multivariate analyses (P < 0.05). In surgically resected patients, LN metastases were significantly associated with the absence of BGA (P = 0.022).

CONCLUSION

T1 CRC without BGA presented several characteristics of small size (<20 mm), flat or depressed type, deep SM depth (SM 2/3), LN metastasis and tumour budding. These results indicate that de novo cancers may have a more invasive potential.

The outcomes of navigation-assisted bone tumour surgery: minimum three-year follow-up

We evaluated the oncological and functional outcome of 18 patients, whose malignant bone tumours were excised with the assistance of navigation, and who were followed up for more than three years. There were 11 men and seven women, with a mean age of 31.8 years (10 to 57). There were ten operations on the pelvic ring and eight joint-preserving limb salvage procedures. The resection margins were free of tumour in all specimens. The tumours, which were stage IIB in all patients, included osteosarcoma, high-grade chondrosarcoma, Ewing's sarcoma, malignant fibrous histiocytoma of bone, and adamantinoma. The overall three-year survival rate of the 18 patients was 88.9% (95% confidence interval (CI) 75.4 to 100). The three-year survival rate of the patients with pelvic malignancy was 80.0% (95% CI 55.3 to 100), and of the patients with metaphyseal malignancy was 100%. The event-free survival was 66.7% (95% CI 44.9 to 88.5). Local recurrence occurred in two patients, both of whom had a pelvic malignancy. The mean Musculoskeletal Tumor Society functional score was 26.9 points at a mean follow-up of 48.2 months (22 to 79). We suggest that navigation can be helpful during surgery for musculoskeletal tumours; it can maximise the accuracy of resection and minimise the unnecessary sacrifice of normal tissue by providing precise intra-operative three-dimensional radiological information.