Identification of the HNSC88 Molecular Signature for Predicting Subtypes of Head and Neck Cancer.

Head and neck squamous cell carcinoma (HNSC) exhibits genetic heterogeneity in etiologies, tumor sites, and biological processes, which significantly impact therapeutic strategies and prognosis. While the influence of human papillomavirus on clinical outcomes is established, the molecular subtypes determining additional treatment options for HNSC remain unclear and inconsistent. This study aims to identify distinct HNSC molecular subtypes to enhance diagnosis and prognosis accuracy. In this study, we collected three HNSC microarrays (n = 306) from the Gene Expression Omnibus (GEO), and HNSC RNA-Seq data (n = 566) from The Cancer Genome Atlas (TCGA) to identify differentially expressed genes (DEGs) and validate our results. Two scoring methods, representative score (RS) and perturbative score (PS), were developed for DEGs to summarize their possible activation functions and influence in tumorigenesis. Based on the RS and PS scoring, we selected candidate genes to cluster TCGA samples for the identification of molecular subtypes in HNSC. We have identified 289 up-regulated DEGs and selected 88 genes (called HNSC88) using the RS and PS scoring methods. Based on HNSC88 and TCGA samples, we determined three HNSC subtypes, including one HPV-associated subtype, and two HPV-negative subtypes. One of the HPV-negative subtypes showed a relationship to smoking behavior, while the other exhibited high expression in tumor immune response. The Kaplan-Meier method was used to compare overall survival among the three subtypes. The HPV-associated subtype showed a better prognosis compared to the other two HPV-negative subtypes (log rank, p = 0.0092 and 0.0001; hazard ratio, 1.36 and 1.39). Additionally, within the HPV-negative group, the smoking-related subgroup exhibited worse prognosis compared to the subgroup with high expression in immune response (log rank, p = 0.039; hazard ratio, 1.53). The HNSC88 not only enables the identification of HPV-associated subtypes, but also proposes two potential HPV-negative subtypes with distinct prognoses and molecular signatures. This study provides valuable strategies for summarizing the roles and influences of genes in tumorigenesis for identifying molecular signatures and subtypes of HNSC.

Discovery of moiety preference by Shapley value in protein kinase family using random forest models.

BACKGROUND: Human protein kinases play important roles in cancers, are highly co-regulated by kinase families rather than a single kinase, and complementarily regulate signaling pathways. Even though there are > 100,000 protein kinase inhibitors, only 67 kinase drugs are currently approved by the Food and Drug Administration (FDA). RESULTS: In this study, we used "merged moiety-based interpretable features (MMIFs)," which merged four moiety-based compound features, including Checkmol fingerprint, PubChem fingerprint, rings in drugs, and in-house moieties as the input features for building random forest (RF) models. By using > 200,000 bioactivity test data, we classified inhibitors as kinase family inhibitors or non-inhibitors in the machine learning. The results showed that our RF models achieved good accuracy (> 0.8) for the 10 kinase families. In addition, we found kinase common and specific moieties across families using the Shapley Additive exPlanations (SHAP) approach. We also verified our results using protein kinase complex structures containing important interactions of the hinges, DFGs, or P-loops in the ATP pocket of active sites. CONCLUSIONS: In summary, we not only constructed highly accurate prediction models for predicting inhibitors of kinase families but also discovered common and specific inhibitor moieties between different kinase families, providing new opportunities for designing protein kinase inhibitors.

CoMI: consensus mutual information for tissue-specific gene signatures.

BACKGROUND: The gene signatures have been considered as a promising early diagnosis and prognostic analysis to identify disease subtypes and to determine subsequent treatments. Tissue-specific gene signatures of a specific disease are an emergency requirement for precision medicine to improve the accuracy and reduce the side effects. Currently, many approaches have been proposed for identifying gene signatures for diagnosis and prognostic. However, they often lack of tissue-specific gene signatures. RESULTS: Here, we propose a new method, consensus mutual information (CoMI) for analyzing omics data and discovering gene signatures. CoMI can identify differentially expressed genes in multiple cancer omics data for reflecting both cancer-related and tissue-specific signatures, such as Cell growth and death in multiple cancers, Xenobiotics biodegradation and metabolism in LIHC, and Nervous system in GBM. Our method identified 50-gene signatures effectively distinguishing the GBM patients into high- and low-risk groups (log-rank p = 0.006) for diagnosis and prognosis. CONCLUSIONS: Our results demonstrate that CoMI can identify significant and consistent gene signatures with tissue-specific properties and can predict clinical outcomes for interested diseases. We believe that CoMI is useful for analyzing omics data and discovering gene signatures of diseases.

Use of blood oxygen level-dependent magnetic resonance imaging to detect acute cellular rejection post-liver transplantation.

OBJECTIVES: Acute cellular rejection (ACR) is a major immune occurrence post-liver transplant that can cause abnormal liver function. Blood oxygen level-dependent (BOLD) magnetic resonance imaging (MRI) can be used to evaluate liver disease, but it has not been utilized in the diagnosis of ACR post-liver transplant. Therefore, the purpose of this study is to evaluate the diagnostic performance of BOLD MRI and to monitor treatment response in recipients with ACR. METHODS: This prospective study was approved by the local institutional review board. Fifty-five recipients with highly suspected ACR were enrolled in this study. Each patient underwent hepatic BOLD MRI, blood biochemistry, and biopsy before treatment. Of 55 patients, 19 recipients with ACR received a follow-up MRI after treatment. After obtaining the R2* maps, five regions-of-interest were placed on liver parenchyma to estimate the mean R2* values for statistical analysis. Receiver operating characteristic curve (ROC) analysis was performed to assess the diagnostic performance of R2* values in detecting patients with ACR. RESULTS: The histopathologic results showed that 27 recipients had ACR (14 mild, 11 moderate, and 2 severe) and their hepatic R2* values were significantly lower than those of patients without ACR. ROC analysis revealed that the sensitivity and specificity of the R2* values for detection of ACR were 82.1% and 89.9%, respectively. Moreover, the R2* values and liver function in patients with ACR significantly increased after immunosuppressive treatment. CONCLUSION: The non-invasive BOLD MRI technique may be useful for assessment of hepatic ACR and monitoring of treatment response after immunosuppressive therapy. KEY POINTS: • Patients with acute cellular rejection post-liver transplant exhibited significantly decreased R2* values in liver parenchyma. • R2* values and liver function were significantly increased after immunosuppressive therapy. • R2* values were constructive indicators in detecting acute cellular rejection due to their high sensitivity and specificity.

Quantification of Functional MR Predicts Early Response in Post-doxorubicin Drug-Eluting Beads Chemoembolization for Hepatocellular Carcinoma.

BACKGROUND: The purpose of this study was to assess the value of functional MRI (fMRI) of post-doxorubicin drug-eluting beads transcatheter arterial chemoembolization (DEB-TACE) for hepatocellular carcinoma (HCC) as an early imaging biomarker of response to therapy. METHODS: This prospective analysis included 21 consecutive patients undergoing fMRI before and after DEB-TACE at a single medical center from January 2013 to December 2014. Functional MRI, including relative changes in apparent diffusion coefficient (ADC) and choline levels measured at hydrogen-1 magnetic resonance spectroscopy (MRS) of treated lesions, was recorded at baseline before DEB-TACE, and at 1, 2, and 4 weeks after DEB-TACE therapy. Assessment of tumor response was based on dynamic contrast-enhanced computer tomography imaging response according to modified response evaluation criteria in solid tumors. RESULTS: At post-therapy, 76% (n = 16) of patients demonstrated objective tumor response, 10% (n = 2) had stable disease, and 3 (14%) had progressive disease. Stable disease and progressive disease were designated as non-response. At week 2, the mean change in ADC value of responsive tumors was 0.35 ± 0.24 mm2/s, which was greater than that of non-response tumors (mean 0.01 ± 0.13 × 10-3 mm2/s) (P = 0.006). Significant differences were found in mean choline/water ratio between responsive (7.8 ± 4.9 × 10-3) and non-responsive (17.2 ± 4.9 × 10-3) tumors (P = 0.005). Composite scores of choline/water ratio and relative change of ADC showed significantly better diagnostic accuracy in non-responsive tumors than responsive tumors (area under the curve = 1.0; P < 0.001). CONCLUSIONS: Combined DWI and MRS may be used as an early imaging biomarker of therapy response in HCC patients after chemoembolization therapy.

Predicting post-hepatectomy liver failure by combined volumetric, functional MR image and laboratory analysis.

BACKGROUND & AIMS: To assess the efficacy of functional MR image with volumetric, liver function test and indocyanine green clearance (ICG) in identifying the patients who are at risk of post-hepatectomy liver failure (PHLF). METHODS: We retrospectively included 115 patients undergoing gadoxetic acid-enhanced MR imaging before hepatectomy at one medical centre from January 2013 to December 2015. Contrast enhancement ratio (CER) between transitional and hepatobiliary phases (3 and 30 minutes post-contrast) was calculated. Total liver volume (TLV) and spleen volume (Sp) were measured. Post-operatively, the histological Ishak fibrosis score was collected. Potential risk factors for liver failure were analysed, and the performance was examined by receiver operating characteristic curve. RESULTS: Post-hepatectomy liver failure (PHLF) occurred in 16 patients (13.9%). TLV/SLV, ADC value, CERHBP/TP and total liver contrast enhancement ratio (tCER) were associated with PHLF (P < .05). Between PHLF and non-PHLF groups, remnant liver volume (RLV), RLV/SLV, Sp/RLV, remnant liver contrast enhancement ratio (rCER) and Ishak fibrosis score showed statistical difference. rCER showed superiority in diagnostic performance (AUC = 0.78) with the optimal cut-off value of 1.23. CONCLUSIONS: Gadoxetic acid-enhanced MR imaging with volumetric is a reliable method for evaluating functional liver volume and determining the risk of PHLF.

Usefulness of Diffusion-Weighted Imaging in Evaluating Acute Cellular Rejection and Monitoring Treatment Response in Liver Transplant Recipients.

Acute cellular rejection (ACR) is a significant immune issue among recipients following liver transplantation. Although diffusion-weighted magnetic resonance imaging (DWI) is widely used for diagnosing liver disease, it has not yet been utilized for monitoring ACR in patients after liver transplantation. Therefore, the aim of this study was to evaluate the efficacy of DWI in monitoring treatment response among recipients with ACR. This study enrolled 25 recipients with highly suspected ACR rejection, and all subjects underwent both biochemistry and DWI scans before and after treatment. A pathological biopsy was performed 4 to 24 h after the first MRI examination to confirm ACR and degree of rejection. All patients were followed up and underwent a repeated MRI scan when their liver function returned to the normal range. After data acquisition, the DWI data were post-processed to obtain the apparent diffusion coefficient (ADC) map on a voxel-by-voxel basis. Five regions of interest were identified on the liver parenchyma to measure the mean ADC values from each patient. Finally, the mean ADC values and biochemical markers were statistically compared between ACR and non-ACR groups. A receiver operating characteristic (ROC) curve was constructed to evaluate the performance of the ADC and biochemical data in detecting ACR, and correlation analysis was used to understand the relationship between the ADC values, biochemical markers, and the degree of rejection. The histopathologic results revealed that 20 recipients had ACR, including 10 mild, 9 moderate, and 1 severe rejection. The results demonstrated that the ACR patients had significantly lower hepatic ADC values than those in patients without ACR. After treatment, the hepatic ADC values in ACR patients significantly increased to levels similar to those in non-ACR patients with treatment. The ROC analysis showed that the sensitivity and specificity for detecting ACR were 80% and 95%, respectively. Furthermore, the correlation analysis revealed that the mean ADC value and alanine aminotransferase level had strong and moderate negative correlation with the degree of rejection, respectively (r = -0.72 and -0.47). The ADC values were useful for detecting hepatic ACR and monitoring treatment response after immunosuppressive therapy.

Psoas muscle area as a predictor of low muscle mass in Asian patients with compensated advanced chronic liver disease.

PURPOSE: The relationship between the psoas muscle index (PMI) and the appendicular skeletal muscle index (ASMI) in patients with compensated advanced chronic liver disease (cACLD) is not yet understood. Our goal is to determine which level of the lumbar spine best represents the appendicular skeletal muscle. METHODS AND MATERIALS: This retrospective study involved patients with cACLD between January 2020 and December 2021. We documented the patients' body weight, height, gait speed, handgrip strength, appendicular skeletal muscle measured by DXA, and psoas muscle area segmented on computed tomography or magnetic resonance imaging. Low muscle mass, as defined by the Asian working group for sarcopenia, is less than 7.0 kg/m2 in males and less than 5.4 kg/m2 in females. We analyzed the correlation between PMI and ASMI. RESULTS: A total of 134 patients were enrolled in the study, with 74 being male and 60 being female. The mean age was 63.9 ± 7.7 years old. Significant associations (p < 0.001) were found between PMI of all levels and ASMI. In the analysis of Pearson's correlation coefficients, it was noted that the r value increased gradually in both males (r = 0.3197 at L2, 0.4006 at L3, 0.5769 at L4) and females (r = 0.3771 at L2, 0.4557 at L3, 0.5251 at L4). Similarly, the area under the curve (AUC) values predicting low muscle mass were as follows: for males, AUC=0.582 at L2, 0.619 at L3, 0.728 at L4; for females, AUC=0.685 at L2, 0.733 at L3, 0.744 at L4. The cut-off point for PMI in males was 4.12 at L2, 6.25 at L3, and 8.48 at L4, while in females was 2.61 at L2, 4.47 at L3, 6.07 at L4. CONCLUSION: The Psoas muscle index can be used to assess the muscle mass status in patients with cACLD. Among the various levels that can be used, we recommend using the fourth inferior endplate of the lumbar spine, as it shows the highest correlation. Additionally, we suggest using a PMI cut-off point of 8.48 cm2/m2 for males and 6.07 cm2/m2 for females as a predictor of low muscle mass in Asian.

Combined Hounsfield units of hepatocellular carcinoma on computed tomography and PET as a noninvasive predictor of early recurrence after living donor liver transplantation: Time-to-recurrence survival analysis.

BACKGROUND: Liver transplantation is an effective treatment for preventing hepatocellular carcinoma (HCC) recurrence. This retrospective study aimed to quantitatively evaluate the attenuation in Hounsfield units (HU) on contrast-enhanced computed tomography (CECT) as a prognostic factor for hepatocellular carcinoma (HCC) following liver transplantation as a treatment. Our goal is to optimize its predictive ability for early tumor recurrence and compare it with the other imaging modality-positron emission tomography (PET). METHODS: In 618 cases of LDLT for HCC, only 131 patients with measurable viable HCC on preoperative CECT and preoperative positron emission tomography (PET) evaluations were included, with a minimum follow-up period of 6 years. Cox regression models were developed to identify predictors of postoperative recurrence. Performance metrics for both CT and PET were assessed. The correlation between these two imaging modalities was also evaluated. Survival analyses were conducted using time-dependent receiver operating characteristic (ROC) curve analysis and area under the curve (AUC) to assess accuracy and determine optimized cut-off points. RESULTS: Univariate and multivariate analyses revealed that both arterial-phase preoperative tumor attenuation (HU) and PET were independent prognostic factors for recurrence-free survival. Both lower arterial tumor enhancement (Cut-off value = 59.2, AUC 0.88) on CT and PET positive (AUC 0.89) increased risk of early tumor recurrence 0.5-year time-dependent ROC. Composites with HU < 59.2 and a positive PET result exhibited significantly higher diagnostic accuracy in detecting early tumor recurrence (AUC = 0.96). CONCLUSION: Relatively low arterial tumor enhancement values on CECT effectively predict early HCC recurrence after LDLT. The integration of CT and PET imaging may serve as imaging markers of early tumor recurrence in HCC patients after LDLT.

Combination of Sarcopenia and Anemia Predicts Worse Outcome in Elderly Patients With Diffuse Large B-Cell Lymphoma.

BACKGROUND/AIM: In diffuse large B-cell lymphoma (DLBCL), sarcopenia is associated with increased side-effects of chemotherapy and poor survival, especially in elderly patients. Anemia, a complex condition resulting from cancer itself and inflammation, might have a correlation with loss of muscle mass and might also indicate a worse outcome. In this study, we aimed to investigate the association of the skeletal muscle index (SMI) at the third lumbar vertebra (L3) with hemoglobin (Hb) levels and its predictive value for the outcome of DLBCL. PATIENTS AND METHODS: The study included patients, aged 70 or older, newly diagnosed with DLBCL who received immunochemotherapy. Sex-specific L3-SMI was measured by computed tomography, and Hb levels before treatment were recorded. The Kaplan-Meier method and Cox regression model were used to analyze survival and prognostic factors. RESULTS: Anemia was correlated with a low SMI. The presence of either low L3-SMI or anemia (Hb <10.5 g/l) indicated a poor prognosis for both progression-free and overall survival. A novel score combining L3-SMI, and Hb and lactate dehydrogenase levels as independent predictive factors was proposed for treatment response, progression-free and overall survival after adjusting for International Prognostic Index. CONCLUSION: This study highlights the importance of sarcopenia and anemia in patients with DLBCL, particularly in the elderly population. The proposed novel score combining L3-SMI, Hb, and lactate dehydrogenase may provide additional prognostic information for patients with DLBCL, aiding in treatment decisions and management.

Efficacy and Safety of Combined Ethanol-Lipiodol Mixture and Drug-Eluting Bead TACE for Large HCC.

Purpose: To evaluate treatment response, survival and safety of a novel TACE using combination of ethanol-Lipiodol mixture and drug-eluting beads in patients with large unresectable HCC, single tumor >8 cm or multiple tumors with the largest tumor diameter >5 cm and total tumor diameter >10 cm. Patients and Methods: Between June 2016 and February 2020, a total of 27 patients were enrolled in this retrospective cohort study. Treatment response was assessed at first month after the treatment; progression-free survival (PFS) and overall survival (OS) were evaluated. The prognostic factors associated with patient survival were statistically analyzed by the Cox regression model. Adverse events were recorded. Results: The maximum diameter of the tumors ranged from 5 cm to 17 cm (mean 10.48 cm). The objective response and disease control rates were 56% and 78%, respectively, at 1-month follow-up. The median survival time was 15.9 months (95% CI, 9.03-34.76 months). The OS rates were 76.9% at six months, 65.2% at one year and 44.8% at two years. AFP >400 ng/mL (p = 0.0306), maximum tumor size >10cm (p = 0.0240) were potential risk factors for OS. Regarding safety, major complications occurred in one patient (1/27, 3.7%), presenting with transient hepatic encephalopathy. Conclusion: Combined DEB-TACE appeared to have favorable objective tumor response. It can be an effective treatment option for large unresectable HCC.

Clinical Impact of Gadoxetic Acid-Enhanced Magnetic Resonance Imaging on Living Donor Liver Transplant.

BACKGROUND: Gadolinium-ethoxybenzyl-diethylene triamine pentaacetic acid (Gd-EOB-DTPA) is a newer magnetic resonance contrast that has the combined effect of conventional and liver-specific contrast. The use of Gd-EOB-DTPA may aid in management of patients with hepatocellular carcinoma (HCC) undergoing living donor liver transplant (LDLT). MATERIALS AND METHODS: We retrospectively reviewed all HCC patients who received LDLT with Gd-EOB-DTPA-enhanced magnetic resonance imaging (MRI) as part of a pretransplant evaluation between October 2012 and October 2016. The detection rate and impact on decision making were assessed between multidetector-row computed tomography (MDCT) and Gd-EOB-DTPA-enhanced MRI with pathology of the explanted liver being the reference standard. RESULTS: We analyzed 25 patients with 80 nodules. Gd-EOB-DTPA-enhanced MRI showed superior detection rate for HCCs than MDCT (76.1% vs 35.8%). Among the 25 patients, 16 had additional HCCs detected by Gd-EOB-DTPA-enhanced MRI, which led to changes in therapeutic decisions in 11 patients. The recurrence rate and mortality rate were 4% (1 of 25). In the same period in our institution, the mortality rate was 13.9% (25 of 180) for those who did not receive Gd-EOB-DTPA-enhanced MRI as part of the pretransplant evaluation. CONCLUSIONS: The use of Gd-EOB-DTPA-enhanced MRI can aid in characterization of indeterminate nodules and detect more HCCs and thus more adequate downstaging and pretransplant neoadjuvant treatment ensue, which may lower the recurrence rate after LDLT.

Portosystemic Shunt in Pediatric Living Donor Liver Transplant.

BACKGROUND: To evaluate the significance of portosystemic shunts and associated long-term outcomes in living donor liver transplant (LDLT) among pediatric patients. METHODS: Retrospective review of 121 pediatric patients who underwent LDLT between May 1994 and December 2015 at Taiwan Kaohsiung Chang Gung Memorial Hospital. Pre- and postoperative computed tomography images of the liver were reviewed, and portal vein complications were assessed. RESULTS: Ninety-seven pediatric patients were included in the study, and 70 had portosystemic shunts before transplant. Thirty-three patients have portal systemic shunt (PSS) 6 months after transplant (mean [SD] shunt size, 4.59 [1.98] mm). Thirty-seven patients' portosystemic shunts closed spontaneously (mean [SD] shunt size, 3.14 [1.06] mm). Smaller PSSs tend to close spontaneously with a cutoff point of 3.35 mm by receiver operating characteristic curve (P = .01). Patients with PSS have more portal vein complications than those without PSS (44.3% vs 11.1%, P = .02). Among PSS recipients, patients with portal vein complications tend to have larger PSS size (mean [SD], 4.14 [1.96] mm vs 3.59 [1.48] mm), although the difference is not statistically significant (P = .19). CONCLUSIONS: In pediatric patients, preoperative portosystemic shunts are significantly correlated with portal venous complications, some of which require minimal interventions after LDLT with good outcomes. Shunts larger than 3.35 mm tend to persist after transplant with increased portal venous complications.

A Scoring System for Predicting Microvascular Invasion in Hepatocellular Carcinoma Based on Quantitative Functional MRI.

Microvascular invasion (MVI) in hepatocellular carcinoma (HCC) is a histopathological marker and risk factor for HCC recurrence. We integrated diffusion-weighted imaging (DWI) and magnetic resonance (MR) image findings of tumors into a scoring system for predicting MVI. In total, 228 HCC patients with pathologically confirmed MVI who underwent surgical resection or liver transplant between November 2012 and March 2021 were enrolled retrospectively. Patients were divided into a right liver lobe group (n = 173, 75.9%) as the model dataset and a left liver lobe group (n = 55, 24.1%) as the model validation dataset. Multivariate logistic regression identified two-segment involved tumor (Score: 1; OR: 3.14; 95% CI: 1.22 to 8.06; p = 0.017); ADCmin ≤ 0.95 × 10-3 mm2/s (Score: 2; OR: 10.88; 95% CI: 4.61 to 25.68; p = 0.000); and largest single tumor diameter ≥ 3 cm (Score: 1; OR: 5.05; 95% CI: 2.25 to 11.30; p = 0.000), as predictive factors for the scoring model. Among all patients, sensitivity was 89.66%, specificity 58.04%, positive predictive value 68.87%, and negative predictive value 84.41%. For validation of left lobe group, sensitivity was 80.64%, specificity 70.83%, positive predictive value 78.12%, and negative predictive value 73.91%. The scoring model using ADCmin, largest tumor diameter, and two-segment involved tumor provides high sensitivity and negative predictive value in MVI prediction for use in routine functional MR.

Non-Contrast-Enhanced and Contrast-Enhanced Magnetic Resonance Angiography in Living Donor Liver Vascular Anatomy.

Background: Since the advent of a new generation of inflow-sensitive inversion recovery (IFIR) technology, three-dimensional non-contrast-enhanced magnetic resonance angiography is being used to obtain hepatic vessel images without applying gadolinium contrast agent. The purpose of this study was to explore the diagnostic efficacy of non-contrast-enhanced magnetic resonance angiography (non-CE MRA), contrast-enhanced magnetic resonance angiography (CMRA), and computed tomography angiography (CTA) in the preoperative evaluation of living liver donors. Methods: A total of 43 liver donor candidates who were evaluated for living donor liver transplantation completed examinations. Donors' age, gender, renal function (eGFR), and previous CTA and imaging were recorded before non-CE MRA and CMRA. CTA images were used as the standard. Results: Five different classifications of hepatic artery patterns (types I, III, V, VI, VIII) and three different classifications of portal vein patterns (types I, II, and III) were identified among 43 candidates. The pretransplant vascular anatomy was well identified using combined non-CE MRA and CMRA of hepatic arteries (100%), PVs (98%), and hepatic veins (100%) compared with CTA images. Non-CE MRA images had significantly stronger contrast signal intensity of portal veins (p < 0.01) and hepatic veins (p < 0.01) than CMRA. No differences were found in signal intensity of the hepatic artery between non-CE MRA and CMRA. Conclusion: Combined non-CE MRA and CMRA demonstrate comparable diagnostic ability to CTA and provide enhanced biliary anatomy information that assures optimum donor safety.

An integrated systematic approach for investigating microcurrent electrical nerve stimulation (MENS) efficacy in STZ-induced diabetes mellitus.

Diabetes mellitus (DM) is a major metabolic disorder and an increasing health problem worldwide. Effective non-invasive therapies for DM are still lacking. Here, we have developed Microcurrent electrical nerve stimulation (MENS), a non-invasive therapy, and tested on 46 mice clustered into five groups, such as control, STZ-induced DM, and MENS treatment groups. Experimental results show that MENS treatment is able to improve seven biochemical indexes (e.g., hemoglobin A1c and glucose level). To investigate the mechanisms of MENS treatment on STZ-induced DM, we selected six representative samples to perform microarray experiments for several groups and developed an integrated Hierarchical System Biology Model (HiSBiM) to analyze these omics data. The results indicate that MENS can affect fatty acid metabolism pathways, peroxisome proliferator-activated receptor (PPAR) signaling pathway and cell cycle. Additionally, the DM biochemical indexes and omics data profiles of MENS treatment were found to be consistent. We then compared the therapeutic effects of MENS with anti-diabetic compounds (e.g., quercetin, metformin, and rosiglitazone), using the HiSBiM four-level biological functions and processes of multiple omics data. The results show MENS and these anti-diabetic compounds have similar effect pathways highly correlated to the diabetes processes, such as the PPAR signaling pathway, bile secretion, and insulin signaling pathways. We believe that MENS is an effective and non-invasive therapy for DM and our HiSBiM is an useful method for investigating multiple omics data.

Convolutional neural network for human cancer types prediction by integrating protein interaction networks and omics data.

Many studies have proven the power of gene expression profile in cancer identification, however, the explosive growth of genomics data increasing needs of tools for cancer diagnosis and prognosis in high accuracy and short times. Here, we collected 6136 human samples from 11 cancer types, and integrated their gene expression profiles and protein-protein interaction (PPI) network to generate 2D images with spectral clustering method. To predict normal samples and 11 cancer tumor types, the images of these 6136 human cancer network were separated into training and validation dataset to develop convolutional neural network (CNN). Our model showed 97.4% and 95.4% accuracies in identification of normal versus tumors and 11 cancer types, respectively. We also provided the results that tumors located in neighboring tissues or in the same cell types, would induce machine make error classification due to the similar gene expression profiles. Furthermore, we observed some patients may exhibit better prognosis if their tumors often misjudged into normal samples. As far as we know, we are the first to generate thousands of cancer networks to predict and classify multiple cancer types with CNN architecture. We believe that our model not only can be applied to cancer diagnosis and prognosis, but also promote the discovery of multiple cancer biomarkers.

Sarcopenia adversely impacts postoperative complications in living-donor liver transplantation recipients.

Despite technological and immunological innovations, living-donor liver transplant (LDLT) recipients still face substantial risk of postoperative complications. Sarcopenia is being recognized more and more as a biomarker that correlates with poor outcomes in surgical patients. The purpose of this study was to evaluate the relationship between sarcopenia and significant surgical complications in LDLT recipients. This retrospective review included patients who had received LDLT at our institute from 2005 to 2017. Sarcopenia was assessed using the psoas muscle index (PMI) in cross-sectional images. ROC curve analysis was used to determine the ability of PMI to predict postoperative complications. Correlations between major postoperative complications and sarcopenia were evaluated using regression analysis. A total of 271 LDLT recipients were included. No significant differences were found between PMI and major postoperative complications in male patients. Female recipients with major postoperative complications had significantly lower mean PMI values (P = 0.028), and the PMI cut-off value was 2.63 cm2/m2. Postoperative massive pleural effusion requiring pigtail drainage occurred more frequently in the sarcopenia group than in the non-sarcopenia group (P = 0.003). 1-, 3-, 5- and 10-year overall survival rates in female were significantly poorer in the sarcopenia group (n = 14) compared with the non-sarcopenia group (n = 108), at 92.9% versus 97.2%, 85.7% versus 95.4%, 85.7% versus 92.5% and 70.1 versus 82.0%, respectively (P = 0.041) and 94.6%, 89.9%, 85.9% and 78.5% in male patients. Sarcopenia is associated with a significantly higher risk of major postoperative complications in females. PMI and sarcopenia together are predictive of major postoperative complications and survival rates in female LDLT recipients.

An Integrated Genomic Strategy to Identify CHRNB4 as a Diagnostic/Prognostic Biomarker for Targeted Therapy in Head and Neck Cancer.

Although many studies have shown the association between smoking and the increased incidence and adverse prognosis of head and neck squamous cell carcinoma (HNSCC), the mechanisms and pharmaceutical targets involved remain unclear. Here, we integrated gene expression signatures, genetic alterations, and survival analyses to identify prognostic indicators and therapeutic targets for smoking HNSCC patients, and we discovered that the FDA-approved drug varenicline inhibits the target for cancer cell migration/invasion. We first identified 18 smoking-related and prognostic genes for HNSCC by using RNA-Seq and clinical follow-up data. One of these genes, CHRNB4 (neuronal acetylcholine receptor subunit beta-4), increased the risk of death by approximately threefold in CHRNB4-high expression smokers compared to CHRNB4-low expression smokers (log rank, p = 0.00042; hazard ratio, 2.82; 95% CI, 1.55-5.14), former smokers, and non-smokers. Furthermore, we examined the functional enrichment of co-regulated genes of CHRNB4 and its 246 frequently occurring copy number alterations (CNAs). We found that these genes were involved in promoting angiogenesis, resisting cell death, and sustaining proliferation, and contributed to much worse outcomes for CHRNB4-high patients. Finally, we performed CHRNB4 gene editing and drug inhibition assays, and the results validate these observations. In summary, our study suggests that CHRNB4 is a prognostic indicator for smoking HNSCC patients and provides a potential new therapeutic drug to prevent recurrence or distant metastasis.