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Supplementary Figure 2 from Identification of a Novel Biomarker, SEMA5A, for Non–Small Cell Lung Carcinoma in Nonsmoking Women

Supplementary Table 1 from Identification of a Novel Biomarker, SEMA5A, for Non–Small Cell Lung Carcinoma in Nonsmoking Women

Supplementary Figure 1 from Identification of a Novel Biomarker, SEMA5A, for Non–Small Cell Lung Carcinoma in Nonsmoking Women

Background: Although cigarette smoking is the major risk factor for lung cancer, only 7% of female lung cancer patients in Taiwan have a history of smoking. The genetic mechanisms of carcinogenesis in nonsmokers are unclear, but semaphorins have been suggested to play a role as lung tumor suppressors. This report is a comprehensive analysis of the molecular signature of nonsmoking female lung cancer patients in Taiwan, with a particular focus on the semaphorin gene family.Methods: Sixty pairs of tumor and adjacent normal lung tissue specimens were analyzed by using Affymetrix U133plus2.0 expression arrays. Differentially expressed genes in tumor tissues were identified by a paired t test and validated by reverse transcriptase-PCR and immunohistochemistry. Functional analysis was conducted by using Ingenuity Pathway Analysis as well as gene set enrichment analysis and sigPathway algorithms. Kaplan-Meier survival analyses were used to evaluate the association of SEMA5A expression and clinical outcome.Results: We identified 687 differentially expressed genes in non–small cell lung carcinoma (NSCLC). Many of these genes, most notably the semaphorin family, were participants in the axon guidance signaling pathway. The downregulation of SEMA5A in tumor tissue, both at the transcriptional and translational levels, was associated with poor survival among nonsmoking women with NSCLC.Conclusions: In summary, several semaphorin gene family members were identified as potential therapeutic targets, and SEMA5A may be useful as a prognostic biomarker for NSCLC, which may also be gender specific in Taiwanese patients.Impact: A novel biomarker for NSCLC is identified. Cancer Epidemiol Biomarkers Prev; 19(10); 2590–7. ©2010 AACR.

Supplementary Table 2 from Identification of a Novel Biomarker, SEMA5A, for Non–Small Cell Lung Carcinoma in Nonsmoking Women

Supplementary Table S1. Comparison of fold change of gene expression in ADAM9 knockdown and brain-metastatic cell sublines (Bm2 and Bm7) with parental cells.

The transmembrane cell adhesion protein ADAM9 has been implicated in cancer cell migration and lung cancer metastasis to the brain, but the underpinning mechanisms are unclear and clinical support has been lacking. Here, we demonstrate that ADAM9 enhances the ability of tissue plasminogen activator (tPA) to cleave and stimulate the function of the promigratory protein CDCP1 to promote lung metastasis. Blocking this mechanism of cancer cell migration prolonged survival in tumor-bearing mice and cooperated with dexamethasone and dasatinib (a dual Src/Abl kinase inhibitor) treatment to enhance cytotoxic treatment. In clinical specimens, high levels of ADAM9 and CDCP1 correlated with poor prognosis and high risk of mortality in patients with lung cancer. Moreover, ADAM9 levels in brain metastases derived from lung tumors were relatively higher than the levels observed in primary lung tumors. Our results show how ADAM9 regulates lung cancer metastasis to the brain by facilitating the tPA-mediated cleavage of CDCP1, with potential implications to target this network as a strategy to prevent or treat brain metastatic disease. Cancer Res; 74(18); 5229–43. ©2014 AACR.

Background Breast cancer is a prevalent disease in women, with high prevalence worldwide. The hypoxic microenvironment of solid tumors develops during the progress of carcinogenesis and leads to greater malignancy and treatment resistance. Recently, accumulating evidence indicates that non-coding RNAs, such as circular RNAs (circRNAs), play a pivotal role in altering cellular functions. However, the underlying mechanisms of circRNAs in breast cancer are still unclear. Therefore, the purpose of this study was to investigate the role of a tumor-suppressive circRNA, circAAGAB, in breast cancer by assuming down-regulation of circAAGAB under hypoxia and the properties of a tumor suppressor. Methods Firstly, circAAGAB was identified from expression profiling by next generation sequencing. Next, the stability of circAAGAB increased by interacting with the RNA binding protein FUS. Moreover, cellular and nuclear fractionation showed that most circAAGAB resided in the cytoplasm and that it up-regulated KIAA1522, NKX3-1, and JADE3 by sponging miR-378 h. Lastly, the functions of circAAGAB were explored by identifying its down-stream genes using Affymetrix microarrays and validated by in vitro assays. Results The results showed that circAAGAB reduced cell colony formation, cell migration, and signaling through p38 MAPK pathway, as well as increased radiosensitivity. Conclusion These findings suggest that the oxygen-responsive circAAGAB acts as a tumor suppressor in breast cancer, and may contribute to the development of a more specific therapeutic regimen for breast cancer.

Background: Cognitive frailty integrating impaired cognitive domains and frailty dimensions has not been explored. Objective: This study aimed to explore 1) associations among frailty dimensions and cognitive domains over time and 2) the extended definitions of cognitive frailty for predicting all-cause mortality. Methods: This four-year cohort study recruited 521 older adults at baseline (2011–2013). We utilized 1) generalized linear mixed models exploring associations of frailty dimensions (physical dimension: modified from Fried et al.; psychosocial dimension: integrating self-rated health, mood, and social relationship and support; global frailty: combining physical and psychosocial frailty) with cognition (global and domain-specific) over time and 2) time-dependent Cox proportional hazard models assessing associations between extended definitions of cognitive frailty (cognitive domains-frailty dimensions) and all-cause mortality. Results: At baseline, the prevalence was 3.0% for physical frailty and 37.6% for psychosocial frailty. Greater physical frailty was associated with poor global cognition (adjusted odds ratio = 1.43–3.29, β: –1.07), logical memory (β: –0.14 to –0.10), and executive function (β: –0.51 to –0.12). Greater psychosocial frailty was associated with poor global cognition (β: –0.44) and attention (β: –0.15 to –0.13). Three newly proposed definitions of cognitive frailty, “mild cognitive impairment (MCI)-psychosocial frailty,” “MCI-global frailty,” and “impaired verbal fluency-global frailty,” outperformed traditional cognitive frailty for predicting all-cause mortality (adjusted hazard ratio = 3.49, 6.83, 3.29 versus 4.87; AIC = 224.3, 221.8, 226.1 versus 228.1). Conclusion: Notably, extended definitions of cognitive frailty proposed by this study better predict all-cause mortality in older adults than the traditional definition of cognitive frailty, highlighting the importance of psychosocial frailty to reduce mortality in older adults.

Many studies have shown the associations between colorectal cancer (CRC) and gut microbiome. The deep learning models have the potential to detect CRC earlier than the conventional stool screening test. However, the results are very inconsistent, which impedes the application of prediction using gut microbiomes as biomarkers. Therefore, this study aims to construct a novel deep learning (DL) pipeline to better classify CRC, colorectal adenoma, and healthy groups using microbiome data. Tissue or stool samples with sequence data and/or taxonomy profiles from 16 studies were collected from the NCBI SRA database or supplementary data provided in studies. Tumor-adjacent samples were excluded because of highly related to tumor samples. Sequence data were quality controlled and taxonomy assigned by EasyMAP based on the QIIME2 pipeline. All taxonomy profiles were merged and normalized to relative abundance. In total, 136 CRC-associated genera were collected from 38 different region studies. Among the CRC-associated genera, 98 ones with high prevalence were selected as CRC biomarkers. Taxonomy profiles were feature-selected by the CRC biomarkers. A phylogenetic tree of 98 CRC biomarkers was constructed by ete3 package and NCBI taxonomy database. Features in taxonomy profiles were sorted and converted into a 10x10 array by phylogenetic-based order. Samples labeled as healthy, adenoma, or CRC were randomly split into train, validation, and test datasets by 8:1:1. The 2D convolutional neural network DL model was trained with a feature array of the samples in the training dataset. Model performance was evaluated by the test dataset. Moreover, Saliency map was calculated to identify highly contributed features. Our results showed that, by combining the tissue and stool data, the DL model illustrated excellent performance with 81% AUC and 60% accuracy for the test dataset in classifying health, adenoma, and CRC groups. Two-class DL model performed even higher with 85% AUC and 78% accuracy in classifying health and CRC groups. For a model with only stool samples, the model in classifying health and CRC groups achieved comparable results with 84% AUC and 76% accuracy. Finally, CRC biomarkers that highly contributed to the DL model were identified by saliency map. In summary, we developed a new pipeline for CRC classification using 16s rRNA gut microbiome data and identified CRC-specific gut microbiome genera. The pipeline and biomarkers could be used as a non-invasive tool for the early detection of CRC. Citation Format: Nai-Shun Liao, Yuan-Mao Hung, Yi-Jian Tsai, Nam Nhut Phan, Pei-Chun Chen, Liang-Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu, Eric Y. Chuang. A novel deep learning pipeline for early detection of colorectal cancer and colorectal adenoma using gut microbiome data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3032.

Introduction: Oral cancer is a fatal cancer and the sixth most common neoplasm worldwide. Over 90% of oral cancer is oral squamous cell carcinoma (OSCC). OSCC is a global health problem because of its late diagnosis and high rate of relapse and metastasis. Currently, cumulative evidence has suggested the association between oral microbiome and oral cancer. However, the correlation between the oral microbiome and OSCC recurrence remained unclear. Therefore, we investigated the OSCC patients’ oral microbiota to understand the roles of oral microbiome in the recurrence of OSCC. Materials and Methods: To evaluate the role of the oral microbiome in the recurrence of oral cancer, we compared the oral bacterial composition of tumor samples from the OSCC patients with or without recurrence based on 16S rRNA amplicon sequencing of 54 oral swab samples. Then, the structures of the oral microbiome were analyzed to establish a prediction model for the recurrence of OSCC. To identify microbial signatures capable of distinguishing recurrence from non-recurrence, the 54 tumor samples from OSCC patients were used as a training dataset. Furthermore, 46 external tumor samples from other OSCC patients were used to validate the dataset. Results: The oral bacterial compositions differed in OSCC patients between with and without recurrence. Compared to nonrecurrence OSCC, periodontitis-related bacteria were enriched in OSCC recurrence. Functional analysis of the oral microbiome showed several functions associated with OSCC recurrence including amino acid metabolism, carbohydrate metabolism, lipid metabolism, glucose utilization, and drug resistance. Subsequently, we established a random forest prediction model with high accuracy (accuracy = 0.963) to discriminate OSCC recurrence from the original OSCC based on five specific microbial signatures. Moreover, the prediction model achieved an accuracy of 0.761 in another independent cohort (46 OSCC patients). On the other hand, the accuracy predicted by the current clinical-used model was 0.519 with the training dataset. Thus, our novel model could improve the prediction accuracy of OSCC recurrence. Conclusions: In this study, we elucidated the relationship between oral bacteria and the recurrence of OSCC. Moreover, we established a novel bacteria-based prediction model for the recurrence of OSCC. Thus, the present study provided a new insight and treatment strategy for the clinical prediction of OSCC recurrence. Citation Format: Wei-Ni Lyu, Mei-Chun Lin, Pei-Jen Lou, Liang-Chuan Lai, Mong-Hsun Tsai. Identification of microbial biomarkers to predict recurrence of oral squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5896.

Breast cancer is the most prevalent cancer among women, and the second major cause of cancer-related deaths in women worldwide. The hypoxic microenvironment of solid tumors is formed in the progress of carcinogenesis, which leads to more malignant and treatment resistance. Recently, circular RNAs (circRNA), a kind of noncoding RNA, were discovered to influence the progress of tumorigenesis, and were induced under hypoxia. However, the regulation and functions of hypoxia-induced circRNA in breast cancer remain unclear. Therefore, the purpose of this study is to identify the regulatory mechanism and its function of a hypoxia-induced circRNAs, circSFMBT2, in breast cancer cells. Firstly, hypoxia-responsive circRNA candidates in breast cancer MCF-7 cells under different oxygen concentrations were identified by RNA-sequencing. Among the differentially expressed circRNAs, circSFMBT2 was chosen for further experiments. The up-regulation of circSFMBT2 under hypoxia was validated by quantitative RT-PCR. The functional assays showed that overexpression of circSFMBT2 inhibited cell proliferation, migration, invasion, and epithelial-mesenchymal transition. Next, in order to investigate the regulatory mechanisms of circSFMBT2, nuclear and cytoplasm fractionation was performed. The results showed circSFMBT2 predominantly localized in the cytoplasm, indicating that the regulatory mechanism of circSFMBT2 might be via interaction with microRNA or RNA-binding proteins (RBP). In order to identify the RBPs, bioinformatic tools, RBPDB, ATtRACT, and RBPmap, were first used to predict the candidate RBPs and validated by RNA pulldown assays. The RNA-binding protein PABPC1 was proved to bind with circSFMBT2. On the other hand, the potential sponging microRNAs were predicted by ENCORI and miRDB, followed by qRT-PCR. No miRNAs were shown to bind with circSFMBT2. Lastly, the functions of circSFMBT2 were explored by identifying its downstream genes using Affymetrix microarrays. The top 10 differentially expressed genes were chosen for validation by quantitative RT-PCR. However, no genes showed significant changes in cells overexpressing circSFMBT2, implying the regulation of circSFMBT2 might not be at the transcriptional level. In summary, circSFMBT2 was able to inhibit the cellular function of breast cancer and bind to PABPC1. With a deeper understanding of the regulatory mechanisms of circSFMBT2, we hope to develop a novel treatment regime for breast cancer. Citation Format: Chia-Ming Liu, Yi-Chun Ke, Liang-Chuan Lai. Hypoxia-induced circular RNAcircSFMBT2 inhibits tumor malignancy in breast cancer cells. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3770.

Genetic instability of cancer cells often generates abundant somatic mutations, and these non-synonymous variations can produce mutated tumor-specific antigens (mTSAs), usually referred to as neoantigens. In addition to mutation-derived neoantigens, aberrantly expressed TSAs (aeTSAs), arising from epigenetic changes and cis- or trans-acting genetics, are also prospective materials for cancer immunotherapy. Since these neoantigens are highly immunogenic, they can activate T cells to trigger an immune response. So far, nevertheless, none of current neoantigen identification tools can identify and differentiate mTSAs and aeTSAs. Here, we demonstrated a comprehensive pipeline and online system to discover both mTSAs and aeTSAs from DNA-seq, RNA-seq, and liquid chromatography-MS/MS (LC-MS/MS) data. To identify potential mTSAs, somatic mutations are discovered and annotated. Afterward, missense mutations and flanking nucleotide bases are further translated into peptides. Quantification of gene expression is conducted to filter out those peptides with low expression levels if RNA-seq reads are provided as well. To identify aeTSAs, most of which originate from allegedly noncoding regions, an alignment-free approach is employed. The RNA-seq reads from tumor and normal tissues are chopped into short k-mer sequences. Those presenting in tumors but not normal tissues are kept, assembled into longer sequences, and translated into peptides then. LC-MS/MS peptides are optionally provided to improve the confidence of the results. Binding affinities between specific major histocompatibility complexes (MHC) and all translated peptides are predicted. Generally, if a tumor-specific peptide can successfully bind with the MHC on the surfaces of tumor cells, it will be defined as a potential neoantigen candidate. The databases associated with cancer proteomics such as Catalogue of Somatic Mutations in Cancer (COSMIC) database are also included in the system, providing information on common cancer variants. We applied the online system to identify 95 putative aeTSA candidates sharing among 13 patients with colorectal cancer, and on top of that 14 of them could be presented by HLA-A*11:01 & 11:02, which are common alleles in Asians. We also compared 246 putative mTSA candidates with peptides in COSMIC database and found 15 of them were common cancer variants, including KRAS and BRAF mutations, both of which are prognostic and predictive biomarkers in colorectal cancer. More importantly, initial evidence shows that these candidates are immunogenic on primary peripheral blood mononuclear cells. Overall, we propose a user-friendly and practical online system to identify and differentiate mTSAs and aeTSAs with optimized procedures. It integrates analysis results of various inputs, i.e., DNA-seq, RNA-seq, and LC-MS/MS data, which can improve the reliability of identified TSAs and provide valuable information for clinical investigators. Citation Format: Chia-Yu Sung, Chien-Yueh Lee, Chia-Hsin Wu, Kevin Chih-Yang Huang, Yu-Hsuan Tseng, Mong-Hsun Tsai, Liang-Chuan Lai, Tzu-Pin Lu, Kun-San Clifford Chao, Eric Y. Chuang. A comprehensive online system for identifying tumor neoantigens [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2065.

Introduction: Unraveling the underlying signaling pathways and multi-omics expression is vital for cancer research. We aim to construct an analytic deep learning (DL) pipeline toward the discovery of pathways and multi-omics signatures with high confidence from histopathological whole slide images (WSIs) for lung cancer. Methods: A total of 458 and 442 diagnostic WSIs from TCGA-LUAD and TCGA-LUSC cohorts, respectively, were preprocessed via steps including patch generation, color normalization, blurry removal, K-means clustering, and pre-trained Convolutional Neural Network (CNN) based feature extraction. The attention-based model was trained on the CNN-extracted features that provided the importance score for each cluster which was utilized for the final prediction of (1) pathway activities, (2) gene expression, and (3) protein expression. The model was first used to predict 1387 pathway activity scores using PARADIGM as the ground truth. The thresholds for Spearman’s correlation R >= 0.5 and R >= 0.45at p-value Results: The models demonstrated good performance in predicting pathway scores, genes, and proteins’ expression using the hold-out testing sets. For LUAD, the model successfully predicted important pathways such as interleukin-, uPAR-, and Sema4D-related and PIP3-activated AKT signaling pathways, which have been proven to be associated with LUAD. At the gene- and protein expression level, the model predicted IRF4, EREG, CCNA2, IL2RB, GRB2, CCNB1, STAT5A genes, and AKT protein, respectively, with high and significant correlation. Similarly, for LUSC, the model predicted highly correlated pathways such as the regulation of telomerase and inflammasomes as well as important genes including AIM2, SIN3A, EGFR, and ATM with significant correlation. Furthermore, the highly activated hot spots from the heat map could assist in decoding the model prediction for crucial tissue locations, eventually contributing to a better interpretation of the final output. Conclusion: The proposed attention-based DL pipeline not only provides high-resolution results at the pathways, and multi-omics levels, but offers a cost-effective approach that enables high throughput screening for potential targets rapidly and robustly via a single WSI. Citation Format: Han-Ru Chen, Nam Nhut Phan, Tzu-Pin Lu, Liang-Chuan Lai, Mong-Hsun Tsai, Amrita Chattopadhyay, Eric Y. Chuang. Prediction of pathway-omics signature of histopathology images via attention-based deep learning in lung adenocarcinoma and squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3177.

Hypoxia and angiogenesis play key roles in the pathogenesis of esophageal squamous cell carcinoma (ESCC), but regulators linking these two pathways to drive tumor progression remain elusive. Here we provide evidence of ADAM9's novel function in ESCC progression. Increasing expression of ADAM9 was correlated with poor clinical outcomes in ESCC patients. Suppression of ADAM9 function diminished ESCC cell migration and in vivo metastasis in ESCC xenograft mouse models. Using cellular fractionation and imaging, we found a fraction of ADAM9 was present in the nucleus and was uniquely associated with gene loci known to be linked to the angiogenesis pathway demonstrated by genome-wide ChIP-seq. Mechanistically, nuclear ADAM9, triggered by hypoxia-induced translocation, functions as a transcriptional repressor by binding to promoters of genes involved in the negative regulation of angiogenesis, and thereby promotes tumor angiogenesis in plasminogen/plasmin pathway. Moreover, ADAM9 suppresses plasminogen activator inhibitor-1 gene transcription by interacting with its transcription factors at the promoter. Our findings uncover a novel regulatory mechanism of ADAM9 as a transcriptional regulator in angiogenesis and highlight ADAM9 as a promising therapeutic target for ESCC treatment.

Many research articles are published on regenerative medicine every year. However, only a small proportion of these articles provide experimental methods on organ/tissue differentiation. Therefore, we developed a database – ATTRACTIVE (An auTo-updating daTabase foR experimentAl protoCols in regeneraTIVe mEdicine) – that collects journal articles with differentiation methods in regenerative medicine and updates itself automatically on a regular basis. Since the number of articles in regenerative medicine was insufficient and unbalanced, which limited the performance of the supervised learning algorithms, we proposed an algorithm that combines cosine similarity and linear discriminant functions to classify articles based on their titles and abstracts more efficiently. The results show that our proposed methods out-performed other machine learning algorithms such as k-nearest neighbors, support vector machine, and long short-term memory methods. The classification accuracy reached 94.62%, even with a small and unbalanced dataset. Lastly, we incorporated our classifier into the database for automatic updates. The database is available at http://attractive.cgm.ntu.edu.tw/ .

Rationale and ObjectiveGut microbiota have been targeted by alternative therapies for non-communicable diseases. We examined the gut microbiota of a healthy Taiwanese population, identified various bacterial drivers in different demographics, and compared them with dialysis patients to associate kidney disease progression with changes in gut microbiota.Study DesignThis was a cross-sectional cohort study.Settings and ParticipantsFecal samples were obtained from 119 healthy Taiwanese volunteers, and 16S rRNA sequencing was done on the V3-V4 regions to identify the bacterial enterotypes. Twenty-six samples from the above cohort were compared with fecal samples from 22 peritoneal dialysis and 16 hemodialysis patients to identify species-level bacterial biomarkers in the dysbiotic gut of chronic kidney disease (CKD) patients.ResultsSpecific bacterial species were identified pertaining to different demographics such as gender, age, BMI, physical activity, and sleeping habits. Dialysis patients had a significant difference in gut microbiome composition compared to healthy controls. The most abundant genus identified in CKD patients was Bacteroides, and at the species level hemodialysis patients showed significant abundance in B. ovatus, B. caccae, B. uniformis, and peritoneal dialysis patients showed higher abundance in Blautia producta (p ≤ 0.05) than the control group. Pathways pertaining to the production of uremic toxins were enriched in CKD patients. The abundance of the bacterial species depended on the type of dialysis treatment.ConclusionThis study characterizes the healthy gut microbiome of a Taiwanese population in terms of various demographics. In a case-control examination, the results showed the alteration in gut microbiota in CKD patients corresponding to different dialysis treatments. Also, this study identified the bacterial species abundant in CKD patients and their possible role in complicating the patients’ condition.

Analyzing 16S ribosomal RNA (rRNA) sequences allows researchers to elucidate the prokaryotic composition of an environment. In recent years, third-generation sequencing technology has provided opportunities for researchers to perform full-length sequence analysis of bacterial 16S rRNA. RDP, SILVA, and Greengenes are the most widely used 16S rRNA databases. Many 16S rRNA classifiers have used these databases as a reference for taxonomic assignment tasks. However, some of the prokaryotic taxonomies only exist in one of the three databases. Furthermore, Greengenes and SILVA include a considerable number of taxonomies that do not have the resolution to the species level, which has limited the classifiers’ performance. In order to improve the accuracy of taxonomic assignment at the species level for full-length 16S rRNA sequences, we manually curated the three databases and removed the sequences that did not have a species name. We then established a taxonomy-based integrated database by considering both taxonomies and sequences from all three 16S rRNA databases and validated it by a mock community. Results showed that our taxonomy-based integrated database had improved taxonomic resolution to the species level. The integrated database and the related datasets are available at https://github.com/yphsieh/ItgDB.

The origin and fate of renal myofibroblasts is not clear after acute kidney injury (AKI). Here, we demonstrate that myofibroblasts were activated from quiescent pericytes (qPericytes) and the cell numbers increased after ischemia/reperfusion injury–induced AKI (IRI-AKI). Myofibroblasts underwent apoptosis during renal recovery but one-fifth of them survived in the recovered kidneys on day 28 after IRI-AKI and their cell numbers increased again after day 56. Microarray data showed the distinctive gene expression patterns of qPericytes, activated pericytes (aPericytes, myofibroblasts), and inactivated pericytes (iPericytes) isolated from kidneys before, on day 7, and on day 28 after IRI-AKI. Hypermethylation of the Acta2 repressor Ybx2 during IRI-AKI resulted in epigenetic modification of iPericytes to promote the transition to chronic kidney disease (CKD) and aggravated fibrogenesis induced by a second AKI induced by adenine. Mechanistically, transforming growth factor-β1 decreased the binding of YBX2 to the promoter of Acta2 and induced Ybx2 hypermethylation, thereby increasing α-smooth muscle actin expression in aPericytes. Demethylation by 5-azacytidine recovered the microvascular stabilizing function of aPericytes, reversed the profibrotic property of iPericytes, prevented AKI-CKD transition, and attenuated fibrogenesis induced by a second adenine-AKI. In conclusion, intervention to erase hypermethylation of pericytes after AKI provides a strategy to stop the transition to CKD.

BACKGROUND Cerebral cortical thickness is a neuroimaging biomarker to predict cognitive decline, and kidney dysfunction (KD) is associated with cortical thinning. OBJECTIVE This study aimed to investigate the effects of KD and cortical thinning on cognitive change in a prospective cohort study. METHODS A total of 244 non-demented participants were recruited from elderly health checkup program and received cognitive exams including Montreal Cognitive Assessment (MoCA) and different cognitive domains at baseline and three biannual follow-ups afterwards. KD was defined as having either glomerular filtration rate

Semaphorin 5A (SEMA5A), which was originally identified as an axon guidance molecule in the nervous system, has been subsequently identified as a prognostic biomarker for lung cancer in nonsmoking women. SEMA5A acts as a tumor suppressor by inhibiting the proliferation and migration of lung cancer cells. However, the regulatory mechanism of SEMA5A is not clear. Therefore, the purpose of the present study was to explore the roles of different domains of SEMA5A in its tumor‑suppressive effects in lung adenocarcinoma cell lines. First, it was revealed that overexpression of full length SEMA5A or its extracellular domain significantly inhibited the proliferation and migration of both A549 and H1299 cells using MTT, colony formation and gap closure assays. Next, microarray analyses were performed to identify genes regulated by different domains of SEMA5A. Among the differentially expressed genes, the most significant function of these genes that were enriched was the 'Interferon Signaling' pathway according to Ingenuity Pathway Analysis. The activation of the 'Interferon Signaling' pathway was validated by reverse transcription‑quantitative PCR and western blotting. In summary, the present study demonstrated that the extracellular domain of SEMA5A could upregulate genes in interferon signaling pathways, resulting in suppressive effects in lung adenocarcinoma cells.

Chemical reactions that directly convert carbon-hydrogen (C–H) bonds to carbon-oxygen (C–O) bonds provide a powerful means to rapidly synthesize valuable organic compounds. However, achieving multiple C–H bond oxygenation reactions at the same time is challenging, particularly because of the risk of overoxidation. Here, we report the selective oxygenation of two or three contiguous C–H bonds, enabling the conversion of simple alkylarenes to diols, triols, or their corresponding acetates. The reactions are achieved using electrophotocatalysis—a process that utilizes both light and electricity to activate a single catalyst—to promote the oxidation reactions. The rapid increase in molecular complexity achieved by these multiple oxygenations enables the synthesis of some compounds of pharmaceutical interest by dramatically shorter sequences than previously achieved.

Thymic carcinoma (TC) is the most aggressive thymic epithelial neoplasm. TC patients with microsatellite instability, whole-genome doubling, or alternative tumor-specific antigens from gene fusion are most likely to benefit from immunotherapies. However, due to the rarity of this disease, how to prioritize the putative biomarkers and what constitutes an optimal treatment regimen remains largely unknown. Therefore, we integrated genomic and transcriptomic analyses from TC patients and revealed that frameshift indels in KMT2C and CYLD frequently produce neoantigens. Moreover, a median of 3 fusion-derived neoantigens was predicted across affected patients, especially the CATSPERB-TC2N neoantigens that were recurrently predicted in TC patients. Lastly, potentially actionable alterations with early levels of evidence were uncovered and could be used for designing clinical trials. In summary, this study shed light on our understanding of tumorigenesis and presented new avenues for molecular characterization and immunotherapy in TC.

Whole-genome doubling (WGD) is an early macro-evolutionary event in tumorigenesis, involving the doubling of an entire chromosome complement. However, its impact on breast cancer subtypes remains unclear. Here, we performed a comprehensive and quantitative analysis of WGD and its influence on breast cancer subtypes in patients from Taiwan and consequently highlight the genomic association between WGD and homologous recombination deficiency (HRD). A higher manifestation of WGD was reported in triple-negative breast cancer, conferring high chromosomal instability (CIN), while HER2 + tumors exhibited early WGD events, with widely varied CIN levels, compared to luminal-type tumors. An association of higher activity of de novo indel signature 2 with WGD and HRD in Taiwanese breast cancer patients was reported. A control test between WGD and pseudo non-WGD samples was further employed to support this finding. The study provides a better comprehension of tumorigenesis in breast cancer subtypes, thus assisting in personalized treatment. Wu, Hsieh et al. analyze Taiwanese breast cancer patient samples using whole-exome sequencing to examine the heterogeneity and homogeneity in the timing and dependencies of somatic aberrations across disease subtypes. The authors focus on somatic alterations and related features that correlate with whole genome doubling, including homologous recombination deficiencies.

Gut microbiota have been targeted by alternative therapies for non-communicable diseases. We examined the gut microbiota of a healthy Taiwanese population, identified various bacterial drivers in different demographics, and compared them with dialysis patients to associate kidney disease progression with changes in gut microbiota.This was a cross-sectional cohort study.Fecal samples were obtained from 119 healthy Taiwanese volunteers, and 16S rRNA sequencing was done on the V3-V4 regions to identify the bacterial enterotypes. Twenty-six samples from the above cohort were compared with fecal samples from 22 peritoneal dialysis and 16 hemodialysis patients to identify species-level bacterial biomarkers in the dysbiotic gut of chronic kidney disease (CKD) patients.Specific bacterial species were identified pertaining to different demographics such as gender, age, BMI, physical activity, and sleeping habits. Dialysis patients had a significant difference in gut microbiome composition compared to healthy controls. The most abundant genus identified in CKD patients wasThis study characterizes the healthy gut microbiome of a Taiwanese population in terms of various demographics. In a case-control examination, the results showed the alteration in gut microbiota in CKD patients corresponding to different dialysis treatments. Also, this study identified the bacterial species abundant in CKD patients and their possible role in complicating the patients' condition.

Objectives To examine the association between metabolic syndrome (MetS) and successful aging among community-dwelling older adults. Methods Adults aged ≥ 65 years who participated in the senior health checkup program at National Taiwan University Hospital during 2011–2013 were recruited (N = 467 at baseline). The participants were followed after 4 years and 6 years. MetS was assessed at baseline. Successful aging was evaluated at baseline, 4-year follow-up, and 6-year follow-up. We adopted an extended definition of successful aging, which was defined as three major domains: physiological, psychological, and sociological and economic domains. Generalized linear mixed models were used to assess the association between MetS and successful aging adjusting for time (follow-up years), age, sex, years of education, alcohol consumption and MetS×time interaction term. Results The mean age of the study population was 72.9 (SD 5.5) years. The absence of baseline MetS had a positive effect on the probability of successful aging over six years. The absences of abdominal obesity, hyperglycemia, reduced high-density lipoprotein cholesterol, and hypertension were associated with the physiological successful aging. The absence of hypertension was the most significant predictor of physiological successful aging [aOR (95% CI) = 2.76 (1.67–4.58), pPtrend Conclusions We found that MetS is a risk factor of successful aging among community-dwelling older adults. Public health policy should aim at avoidance of MetS in order to facilitate successful aging in older population.

Long non-coding RNAs (lncRNAs) have been found to participate in multiple genetic pathways in cancer. Also, mitochondria-associated lncRNAs have been discovered to modulate mitochondrial function and metabolism. Previously, we identified oxygen-responsive lncRNAs in MCF-7 breast cancer cells under different oxygen concentrations. Among them, a novel mitochondria-encoded lncRNA, mitochondrial oxygen-responsive transcript 1 (MTORT1), was chosen for further investigation. Nuclear, cytoplasmic, and mitochondrial fractionation assays were performed to evaluate the endogenous expression levels of MTORT1 in breast cancer cells. In vitro proliferation and migration assays were conducted to investigate the functions of MTORT1 in breast cancer cells by knockdown of MTORT1. RNA immunoprecipitation and luciferase reporter assays were used to examine the physical binding between MTORT1 and microRNAs. Our results showed that MTORT1 had low endogenous expression levels in breast cancer cells and was mainly located in the mitochondria. Knockdown of MTORT1 enhanced cell proliferation and migration, implying a tumor suppressor role of this novel mitochondrial lncRNA. MTORT1 served as sponge of miR-26a-5p to up-regulate its target genes, CREB1 and STK4. Our findings shed some light on the characterization, function, and regulatory mechanism of the novel hypoxia-induced mitochondrial lncRNA MTORT1, which functions as a microRNA sponge and may inhibit breast cancer progression. These data suggest that MTORT1 may be a candidate for therapeutic targeting of breast cancer progression.

Esophageal cancer is one of the leading causes of cancer death in the male population of Eastern Asia. In addition, esophageal squamous cell carcinoma (ESCC) is the major type of esophageal cancer among the world. Owing to the poor overall 5-year survival rate, novel effective treatment strategies are needed. MicroRNAs are important gene regulators that are dysregulated in many cancer types. In our previous study, we applied next-generation sequencing to demonstrate that miR-338-5p was downregulated in the tumor tissue of patients with versus without recurrence. In this study, we further studied the roles of miR-338-5p in ESCC. The expression of endogenous miR-338-5p was at lower levels in ESCC cells compared with normal cells. Functional assays showed that miR-338-5p reduced cell proliferation, colony formation, migration and cisplatin resistance in an ESCC cell line, CE-81T. Potential target genes of miR-338-5p were identified by microarray and prediction tools, and 31 genes were selected. Among these, Fermitin family homolog 2 (FERMT2) plays an oncogenic role in ESCC, so it was chosen for further study. Luciferase assays showed the direct binding between miR-338-5p and the 3′ untranslated region of FERMT2. Silencing of FERMT2 inhibited cell proliferation, colony formation, migration and cisplatin resistance. Pathway analysis revealed that the integrin-linked protein kinase signaling pathway, in which FERMT2 participates, was significantly affected by a miR-338-5p mimic. Our results suggest that miR-338-5p may play an antioncogenic role in ESCC via repressing FERMT2.

Hypoxia plays a crucial role in the aggressiveness of solid tumors by driving multiple signaling pathways. Recently, long non-coding RNA (lncRNA) has been reported to promote or inhibit tumor aggressiveness by regulating gene expression. Previous studies in our laboratory found that the lncRNA NDRG1-OT1 is significantly up-regulated under hypoxia and inhibits its target gene NDRG1 at both the mRNA and protein levels. At the protein level, NDRG1-OT1 increases NDRG1 degradation via ubiquitin-mediated proteolysis. However, the repressive mechanism of NDRG1 at the RNA level is still unknown. Therefore, the purpose of this study was to study how NDRG1-OT1 transcriptionally regulates its target gene NDRG1. Luciferase reporter assays showed that NDRG1-OT1 decreased NDRG1 promoter activities. Mass spectrometry, bioinformatics tools, genetic manipulation, and immunoblotting were used to identify the interacting proteins. Surprisingly, different fragments of NDRG1-OT1 had opposite effects on NDRG1. The first quarter fragment (1-149 nt) of NDRG1-OT1 had no effect on the NDRG1 promoter; the second quarter fragment (150-263 nt) repressed NDRG1 by increasing the binding affinity of HNRNPA1; the third quarter fragment (264-392 nt) improved NDRG1 promoter activity by recruiting HIF-1α; the fourth quarter fragment (393-508 nt) down-regulated NDRG1 promoter activity via down-regulation of KHSRP under hypoxia. In summary, we have found a novel mechanism by which different fragments of the same lncRNA can cause opposite effects within the same target gene.

Hypoxia, a common process during tumor growth, can lead to tumor aggressiveness and is tightly associated with poor prognosis. Long noncoding RNAs (lncRNAs) are long ribonucleotides (>200 bases) with limited ability to translate proteins, and are known to affect many aspects of cellular function. One of their regulatory mechanisms is to function as a sponge for microRNA (miRNA) to modulate its biological functions. Previously, MALAT1 was identified as a hypoxia-induced lncRNA. However, the regulatory mechanism and functions of MALAT1 in breast cancer are still unclear. Therefore, we explored whether MALAT1 can regulate the functions of breast cancer cells through miRNAs. Our results showed the expression levels of MALAT1 were significantly up-regulated under hypoxia and regulated by HIF-1α and HIF-2α. Next, in contrast to previous reports, nuclear and cytoplasmic fractionation assays and fluorescence in situ hybridization indicated that MALAT1 was mainly located in the cytoplasm. Therefore, the labeling of MALAT1 as a nuclear marker should be done with the caveat. Furthermore, expression levels of miRNAs and RNA immunoprecipitation using antibody against AGO2 showed that MALAT1 functioned as a sponge of miRNA miR-3064-5p. Lastly, functional assays revealed that MALAT1 could promote cellular migration and proliferation of breast cancer cells. Our findings provide evidence that hypoxia-responsive long non-coding MALAT1 could be transcriptionally activated by HIF-1α and HIF-2α, act as a miRNA sponge of miR-3064-5p, and promote tumor growth and migration in breast cancer cells. These data suggest that MALAT1 may be a candidate for therapeutic targeting of breast cancer progression.

In this study, we proposed a deep learning (DL) model for classifying individuals from mixtures of DNA samples using 27 short tandem repeats and 94 single nucleotide polymorphisms obtained through massively parallel sequencing protocol. The model was trained/tested/validated with sequenced data from 6 individuals and then evaluated using mixtures from forensic DNA samples. The model successfully identified both the major and the minor contributors with 100% accuracy for 90 DNA mixtures, that were manually prepared by mixing sequence reads of 3 individuals at different ratios. Furthermore, the model identified 100% of the major contributors and 50–80% of the minor contributors in 20 two-sample external-mixed-samples at ratios of 1:39 and 1:9, respectively. To further demonstrate the versatility and applicability of the pipeline, we tested it on whole exome sequence data to classify subtypes of 20 breast cancer patients and achieved an area under curve of 0.85. Overall, we present, for the first time, a complete pipeline, including sequencing data processing steps and DL steps, that is applicable across different NGS platforms. We also introduced a sliding window approach, to overcome the sequence length variation problem of sequencing data, and demonstrate that it improves the model performance dramatically.

Macrophages comprise the front line of defense against various pathogens. Classically activated macrophages (M1), induced by IFN-γ and LPS, highly express inflammatory cytokines and contribute to inflammatory processes. By contrast, alternatively activated macrophages (M2) are induced by IL-4 and IL-13, produce IL-10, and display anti-inflammatory activity. Adenylate kinase 4 (Ak4), an enzyme that transfers phosphate group among ATP/GTP, AMP, and ADP, is a key modulator of ATP and maintains the homeostasis of cellular nucleotides which is essential for cell functions. However, its role in regulating the function of macrophages is not fully understood. Here we report that Ak4 expression is induced in M1 but not M2 macrophages. Suppressing the expression of Ak4 in M1 macrophages with shRNA or siRNA enhances ATP production and decreases ROS production, bactericidal ability and glycolysis in M1 cells. Moreover, Ak4 regulates the expression of inflammation genes, including Il1b, Il6, Tnfa, Nos2, Nox2, and Hif1a, in M1 macrophages. We further demonstrate that Ak4 inhibits the activation of AMPK and forms a positive feedback loop with Hif1α to promote the expression of inflammation-related genes in M1 cells. Furthermore, RNA-seq analysis demonstrates that Ak4 also regulates other biological processes in addition to the expression of inflammation-related genes in M1 cells. Interestingly, Ak4 does not regulate M1/M2 polarization. Taken together, our study uncovers a potential mechanism linking energy consumption and inflammation in macrophages.

Long non-coding RNAs (lncRNAs) have been found to participate in multiple genetic pathways in cancer. Also, mitochondria-associated lncRNAs have been discovered to modulate mitochondrial function and metabolism. Previously, we identified oxygen-responsive lncRNAs in MCF-7 breast cancer cells under different oxygen concentrations. Among them, a novel mitochondria-encoded lncRNA, mitochondrial oxygen-responsive transcript 1 (MTORT1), was chosen for further investigation. Nuclear, cytoplasmic, and mitochondrial fractionation assays were performed to evaluate the endogenous expression levels of MTORT1 in breast cancer cells. In vitro proliferation and migration assays were conducted to investigate the functions of MTORT1 in breast cancer cells by knockdown of MTORT1. RNA immunoprecipitation and luciferase reporter assays were used to examine the physical binding between MTORT1 and microRNAs. Our results showed that MTORT1 had low endogenous expression levels in breast cancer cells and was mainly located in the mitochondria. Knockdown of MTORT1 enhanced cell proliferation and migration, implying a tumor suppressor role of this novel mitochondrial lncRNA. MTORT1 served as sponge of miR-26a-5p to up-regulate its target genes, CREB1 and STK4. Our findings shed some light on the characterization, function, and regulatory mechanism of the novel hypoxia-induced mitochondrial lncRNA MTORT1, which functions as a microRNA sponge and may inhibit breast cancer progression. These data suggest that MTORT1 may be a candidate for therapeutic targeting of breast cancer progression.

Human copy number variations (CNVs) and copy number alterations (CNAs) are DNA segments (>1000 base pairs) of duplications or deletions with respect to the reference genome, potentially causing genomic imbalance leading to diseases such as cancer. CNVs further cause genetic diversity in healthy populations and are predominant drivers of gene/genome evolution. Initiatives have been taken by the research community to establish large-scale databases to comprehensively characterize CNVs in humans. Exome Aggregation Consortium (ExAC) is one such endeavor that catalogs CNVs, of nearly 60 000 healthy individuals across five demographic clusters. Furthermore, large projects such as the Catalogue of Somatic Mutations in Cancer (COSMIC) and the Cancer Cell Line Encyclopedia (CCLE) combine CNA data from cancer-affected individuals and large panels of human cancer cell lines, respectively. However, we lack a structured and comprehensive CNV/CNA resource including both healthy individuals and cancer patients across large populations. CNVIntegrate is the first web-based system that hosts CNV and CNA data from both healthy populations and cancer patients, respectively, and concomitantly provides statistical comparisons between copy number frequencies of multiple ethnic populations. It further includes, for the first time, well-cataloged CNV and CNA data from Taiwanese healthy individuals and Taiwan Breast Cancer data, respectively, along with imported resources from ExAC, COSMIC and CCLE. CNVIntegrate offers a CNV/CNA-data hub for structured information retrieval for clinicians and scientists towards important drug discoveries and precision treatments. Database URL: http://cnvintegrate.cgm.ntu.edu.tw/

Precision epidemiology using genomic technologies allows for a more targeted approach to COVID-19 control and treatment at individual and population level, and is the urgent need of the day. It enables identification of patients who may be at higher risk than others to COVID-19-related mortality, due to their genetic architecture, or who might respond better to a COVID-19 treatment. The COVID-19 virus, similar to SARS-CoV, uses the ACE2 receptor for cell entry and employs the cellular serine protease TMPRSS2 for viral S protein priming. This study aspires to present a multi-omics view of how variations in the ACE2 and TMPRSS2 genes affect COVID-19 infection and disease progression in affected individuals. It reports, for both genes, several variant and gene expression analysis findings, through (i) comparison analysis over single nucleotide polymorphisms (SNPs), that may account for the difference of COVID-19 manifestations among global sub-populations; (ii) calculating prevalence of structural variations (copy number variations (CNVs) / insertions), amongst populations; and (iii) studying expression patterns stratified by gender and age, over all human tissues. This work is a good first step to be followed by additional studies and functional assays towards informed treatment decisions and improved control of the infection rate.

Rationale: Lung adenocarcinoma (LUAD) is an aggressive disease with high propensity of metastasis. Among patients with early-stage disease, more than 30% of them may relapse or develop metastasis. There is an unmet medical need to stratify patients with early-stage LUAD according to their risk of relapse/metastasis to guide preventive or therapeutic approaches. In this study, we identified 4 genes that can serve both therapeutic and diagnostic (theranostic) purposes. Methods: Three independent datasets (GEO, TCGA, and KMPlotter) were used to evaluate gene expression profile of patients with LUAD by unbiased screening approach. Upon significant genes uncovered, functional enrichment analysis was carried out. The predictive power of their expression on patient prognosis were evaluated. Once confirmed their theranostic roles by integrated bioinformatics, we further conducted in vitro and in vivo validation. Results: We found that four genes (ADAM9, MTHFD2, RRM2, and SLC2A1) were associated with poor patient outcomes with an increased hazard ratio in LUAD. Knockdown of them, both separately and simultaneously, suppressed lung cancer cell proliferation and migration ability in vitro and prolonged survival time in metastatic tumor mouse models. Moreover, these four biomarkers were found to be overexpressed in tumor tissues from LUAD patients, and the total immunohistochemical staining scores correlated with poor prognosis. Conclusions: These results suggest that these four identified genes could be theranostic biomarkers for stratifying high-risk patients who develop relapse/metastasis in early-stage LUAD. Developing therapeutic approaches for the four biomarkers may benefit early-stage LUAD patients after surgery.

As next-generation sequencing technology has become more advanced, research on microbial 16S ribosomal DNA sequences has developed rapidly. Sequencing of 16S ribosomal DNA allows the composition of bacteria and archaea in a sample to be obtained and many analytical tools related to 16S ribosomal DNA sequences have been proposed; however, most do not include a user-friendly platform with a graphical user interface. Here, a comprehensive and easy-to-use online platform, Easy Microbiome Analysis Platform (EasyMAP), has been developed for analysis of 16S ribosomal DNA sequencing data. EasyMAP integrates the QIIME2, LefSe, and PICRUSt pipelines and includes temporal profiling analysis. Users can perform quality checks, taxonomy differential abundance analysis, microbial gene function prediction and longitudinal analysis with step-by-step guidance. EasyMAP is a user-friendly tool for comprehensive analysis of 16S ribosomal DNA sequencing data. The web server and documentation are freely available at http://easymap.cgm.ntu.edu.tw/.

Extracellular vesicles (EVs) of mesenchymal stem cells (MSCs) are secreted by live cells and possess the same regenerative potential and immunomodulatory ability as their parental cells. Clinical applications of MSC-EVs could overcome the shortage of MSCs for treatment of cancer and other diseases and impact the field of regenerative medicine from cellular to acellular therapy. For use of MSC-EVs as a clinical agent, various engineered EVs have been manufactured and their therapeutic effects on various diseases demonstrated in preclinical studies and clinical trials. However, MSC-EVs are heterogeneous, and many of their characteristics are still unknown. Many barriers still need to be surmounted before MSC-EVs can be used as biomedical agents.

Known as a selective δ1 opioid receptor (DOR1) antagonist, the 7-benzylidenenaltrexone (BNTX) is also a DOR1-independent immunosuppressant with unknown mechanisms. Here we investigated if BNTX could be beneficial for diseased MRL/lpr lupus mice. We treated mice with 0.5, 2, 5 or 10 mg/kg/day of BNTX for 2 weeks. At as low as 2 mg/kg/day, BNTX significantly improved splenomegaly and lymphadenopathy. Notably, B cell numbers, particularly autoreactive plasma cells, were preferentially reduced; moreover, BNTX enhanced surface expression of FcγRIIB, an immune complex (IC)-dependent apoptotic trigger of B cells. Consequently, serum autoantibody concentrations were significantly decreased, leading to diminished glomerular IC deposition and renal fibrosis, thereby improving proteinuria. Microarray and pathway analyses revealed heme oxygenase-1 (HO-1) and p38 MAPK as key mediators of BNTX-induced upregulation of FcγRIIB. Moreover, HO-1 expression was also induced by BNTX via p38 MAPK at renal proximal tubules to further cytoprotection. Taken together, we demonstrate that BNTX can alleviate lupus nephritis by reducing autoreactive B cells via FcγRIIB and by augmenting renal protection via HO-1. Accordingly, we propose a new strategy to treat lupus nephritis via such a dual immuno-renal targeting using either a single agent or combined agents to simultaneously deplete B cells and enhance renal protection.7-Benzylidenenaltrexone (BNTX) alleviates lupus nephritis in diseased MRL/lpr mice. BNTX reduces autoreactive plasma cell numbers and serum autoantibody titers. BNTX upregulates FcγRIIB levels via p38 MAPK and HO-1 to reduce B cell numbers. Reduction of immune complex deposition and fibrosis by BNTX improves proteinuria. BNTX induces HO-1 via p38 MAPK to enhance protection of renal proximal tubules.

// Chih-Hsien Wang 1, 2 , Ru-Wen Chang 3 , Chun-Yi Chang 4 , Ming-Shiou Wu 5 , Hsien-Li Kao 5 , Liang-Chuan Lai 3 , Tai-Horng Young 6 , Hsi-Yu Yu 1 , Yih-Sharng Chen 1 and Kuo-Chu Chang 3 1 Department of Surgery, National Taiwan University Hospital, Taipei 100, Taiwan 2 Department of Surgery, National Taiwan University Hospital, Hsinchu Branch, Hsinchu 300, Taiwan 3 Department of Physiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan 4 Department of Emergency Medicine, Taipei Veterans General Hospital, Chu-Tung Branch, Hsinchu 310, Taiwan 5 Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan 6 Institute of Biomedical Engineering, College of Medicine and Engineering, National Taiwan University, Taipei 100, Taiwan Correspondence to: Kuo-Chu Chang, email: kcchang1008@ntu.edu.tw Keywords: cardiac contractility; pressure-ejected volume curve; end-systolic elastance; left ventricular pressure; triangular aortic flow Received: June 20, 2017 Accepted: September 23, 2017 Published: October 10, 2017 ABSTRACT To quantitate the contractile mechanics of the heart, the ventricle is considered an elastic chamber with known end-systolic elastance ( E es ). E es can be calculated from a single pressure-ejected volume curve, which requires simultaneous records of left ventricular (LV) pressure and the aortic flow ( Q m ). In clinical settings, it is helpful to evaluate patients’ cardiac contractile status by using a minimally invasive approach to physiological signal monitoring, wherever possible, such as by using LV pressure alone. In this study, we evaluated a method for determining E es on the basis of the measured LV pressure and an assumed aortic flow with a triangular wave shape ( Q tri ). Q tri was derived using a fourth-order derivative of the LV pressure to approximate its corresponding Q m . Values of E es triQ obtained using Q tri were compared with those of E es mQ obtained from the measured Q m . Healthy rats (NC; n = 28) and rats with type 1 diabetes (DM; n = 26) and chronic kidney disease (CKD; n = 20) were examined. The cardiodynamic conditions in both the DM and CKD groups were characterized by a decline in E es mQ and E es triQ . A significant regression line for E es was observed ( P < 0.0001): E es triQ = 2.6214 + 1.0209 × E es mQ ( r 2 = 0.9870; n = 74). Our finding indicates that the systolic pumping mechanics of the heart can be derived from a single LV pressure recording together with the assumed Q tri .

// Kuo-Liang Chiu 1, 4, 5, * , Yu-Sen Lin 1, 8, * , Ting-Ting Kuo 7 , Chia-Chien Lo 7 , Yu-Kai Huang 7 , Hsien-Fang Chang 6 , Eric Y. Chuang 6 , Ching-Chan Lin 1, 9 , Wei-Chung Cheng 2, 3 , Yen-Nien Liu 10 , Liang-Chuan Lai 6, 11 and Yuh-Pyng Sher 1, 2, 7 1 Graduate Institute of Clinical Medical Science, China Medical University, Taichung 404, Taiwan 2 Graduate Institute of BioMedical Sciences, China Medical University, Taichung 404, Taiwan 3 Research Center for Tumor Medical Science, China Medical University, Taichung 404, Taiwan 4 Division of Chest Medicine, Department of Internal Medicine, Taichung Tzu-Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung 427, Taiwan 5 School of Post-Baccalaureate Chinese Medicine, Tzu Chi University, Hualien 970, Taiwan 6 Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei 100, Taiwan 7 Center for Molecular Medicine, China Medical University Hospital, Taichung 404, Taiwan 8 Division of Thoracic Surgery, China Medical University Hospital, Taichung 404, Taiwan 9 Division of Hematology and Oncology, China Medical University Hospital, Taichung 404, Taiwan 10 Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan 11 Graduate Institute of Physiology, National Taiwan University, Taipei 106, Taiwan * These authors contributed equally to this work Correspondence to: Yuh-Pyng Sher, email: ypsher@mail.cmu.edu.tw Liang-Chuan Lai, email: llai@ntu.edu.tw Keywords: lung cancer, ADAM9, EGFR, miR-1, CDCP1 Received: November 30, 2016 Accepted: April 19, 2017 Published: May 07, 2017 ABSTRACT MicroRNAs (miRNAs), which are endogenous short noncoding RNAs, can regulate genes involved in important biological and pathological functions. Therefore, dysregulation of miRNAs plays a critical role in cancer progression. However, whether the aberrant expression of miRNAs is regulated by oncogenes remains unclear. We previously demonstrated that a disintegrin and metalloprotease domain 9 (ADAM9) promotes lung metastasis by enhancing the expression of a pro-migratory protein, CUB domain containing protein 1 (CDCP1). In this study, we found that this process occurred via miR-1 down-regulation. miR-1 expression was down-regulated in lung tumors, but increased in ADAM9 -knockdown lung cancer cells, and was negatively correlated with CDCP1 expression as well as the migration ability of lung cancer cells. Luciferase-based reporter assays showed that miR-1 directly bound to the 3′-untranslated region of CDCP1 and inhibited its translation. Treatment with a miR-1 inhibitor restored CDCP1 protein levels and enhanced tumor cell mobility. Overexpression of miR-1 decreased tumor metastases and increased the survival rate in mice. ADAM9 knockdown reduced EGFR signaling and increased miR-1 expression. These results revealed that ADAM9 down-regulates miR-1 via activating EGFR signaling pathways, which in turn enhances CDCP1 expression to promote lung cancer progression.

Extracorporeal life support (ECLS) is a world-famous life-saving method. Until now, changes in arterial wave properties due to ECLS have remained unexamined. In this study, we determined the effects of ECLS on arterial wave properties and ventricular/arterial coupling in male Wistar rats with the measured aortic pressure alone. Ascending aortic pressure signals were measured before ECLS and at 30, 60, and 90 min after weaned off. The aortic pressure signal then calculated by fourth-order derivative to obtain an assumed triangular flow wave. The ratio of mean systolic pressure to mean diastolic pressure (Pms/Pmd), a parameter for evaluating the matching condition between myocardial oxygen demand and supply, was significantly higher after ECLS. The magnitude of forward pressure (|Pf|) augmented by ECLS prevailed over the backward pressure (|Pb|), leading to a decline in wave reflection factor. Pms/Pmd was positively linearly correlated with |Pf| (Pms/Pmd = 0.9177 + 0.0078 × |Pf|, r = 0.8677; P Pf| was a predominant factor responsible for the mismatch between the myocardial oxygen demand and supply in rats after ECLS phase of experiment.

Semaphorin 5A (SEMA5A), a member of the semaphorin family, plays an important role in axonal guidance. Previously, the authors identified another possible role of SEMA5A as a prognostic biomarker for non-smoking women with lung adenocarcinoma in Taiwan, and this phenomenon has been validated in other ethnic groups. However, the functional significance of SEMA5A in lung adenocarcinoma remains unclear. Therefore, we assessed the function of SEMA5A in three lung adenocarcinoma cell lines in this study. Kaplan-Meier Plotter for lung cancer was conducted for survival analyses. Reverse transcription-quantitative PCR (RT-qPCR) and western blot analysis were performed to investigate the expression and post-translational regulation of SEMA5A in lung adenocar-cinoma cell lines. A pre-designed PyroMark CpG assay and 5-aza-2′-deoxycytidine treatment were used to measure the methylation levels of SEMA5A. The biological functions of lung adenocarcinoma cells overexpressing SEMA5A were investigated by microarrays, and validated both in vitro (proliferation, colony formation and migration assays) and in vivo (tumor xenografts) experiments. The results revealed that the hypermethylation of SEMA5A and the cleavage of the extracellular domain of SEMA5A were responsible for the downregulation of the SEMA5A levels in lung adenocarcinoma cells (A549 and H1299) as compared to the normal controls. Functional analysis of SEMA5A-regulated genes revealed that they were involved in cellular growth and proliferation. The overexpression of SEMA5A in A549 and H1299 cells significantly decreased the proliferation (P

Background With advancements in high-throughput technologies, the cost of obtaining expression profiles of both mRNA and microRNA in the same individual has substantially decreased. Integrated analysis of these profiles can help to elucidate the functional effects of RNA expression in complex diseases, such as cancer. However, fundamental discrepancies are observed in the results from microRNA-mRNA target gene prediction algorithms, and few packages can be used to analyze microRNA and mRNA expression levels simultaneously. Results To address these issues, an R package, anamiR, was developed. A total of 10 experimental/prediction databases were integrated. Two analytical functions are provided in anamiR, including the single marker test and functional gene set enrichment analysis, and several parameters can be changed by users. Here we demonstrate the potential application of the anamiR package to 2 publicly available microarray datasets. Conclusion The anamiR package is effective for an integrated analysis of both RNA and microRNA profiles. By characterizing biological functions and signaling pathways, this package helps identify dysregulated genes/miRNAs from biological and medical experiments. The source code and manual of the anamiR package are freely available at https://bioconductor.org/packages/release/bioc/html/anamiR.html. Electronic supplementary material The online version of this article (10.1186/s12859-019-2870-x) contains supplementary material, which is available to authorized users.

Table S1. The total potential number of miRNA-gene pairs obtained by tallying different prediction algorithms. Table S2. Number of miRNA/gene interaction pairs in the prediction algorithms and experimentally validated databases included in the anamiR package. Table S3. Characteristics of anamiR and miRComb. Table S4. Pairs with negative correlation coefficients (GSE16558). Table S5. Pairs with negative correlation coefficients (GSE60371). Table S6. The default parameters used in the examples. Table S7. Top 5 interaction pairs with negative correlation coefficients in the 5 pathways identified by function-driven analysis. (DOCX 38 kb)

Additional file 1. Minimum standards of reporting checklist.

Integrated analysis of DNA variants and gene expression profiles may facilitate precise identification of gene regulatory networks involved in disease mechanisms. Despite the widespread availability of public resources, we lack databases that are capable of simultaneously providing gene expression profiles, variant annotations, functional prediction scores and pathogenic analyses. VariED is the first web-based querying system that integrates an annotation database and expression profiles for genetic variants. The database offers a user-friendly platform and locates gene/variant names in the literature by connecting to established online querying tools, biological annotation tools and records from free-text literature. VariED acts as a central hub for organized genome information consisting of gene annotation, variant allele frequency, functional prediction, clinical interpretation and gene expression profiles in three species: human, mouse and zebrafish. VariED also provides a novel scoring scheme to predict the functional impact of a DNA variant. With one single entry, all results regarding queried DNA variants can be downloaded. VariED can potentially serve as an efficient way to obtain comprehensive variant knowledge for clinicians and scientists around the world working on important drug discoveries and precision treatments.