Immune Landscape of Invasive Ductal Carcinoma Tumor Microenvironment Identifies a Prognostic and Immunotherapeutically Relevant Gene Signature

Background: Invasive ductal carcinoma (IDC) is a clinically and molecularly distinct disease. Tumor microenvironment (TME) immune phenotypes play crucial roles in predicting clinical outcomes and therapeutic efficacy. Method: In this study, we depict the immune landscape of IDC by using transcriptome profiling and clinical characteristics retrieved from The Cancer Genome Atlas (TCGA) data portal. Immune cell infiltration was evaluated via single-sample gene set enrichment (ssGSEA) analysis and systematically correlated with genomic characteristics and clinicopathological features of IDC patients. Furthermore, an immune signature was constructed using the least absolute shrinkage and selection operator (LASSO) Cox regression algorithm. A random forest algorithm was applied to identify the most important somatic gene mutations associated with the constructed immune signature. A nomogram that integrated clinicopathological features with the immune signature to predict survival probability was constructed by multivariate Cox regression. Results: The IDC were clustered into low immune infiltration, intermediate immune infiltration, and high immune infiltration by the immune landscape. The high infiltration group had a favorable survival probability compared with that of the low infiltration group. The low-risk score subtype identified by the immune signature was characterized by T cell-mediated immune activation. Additionally, activation of the interferon-α response, interferon-γ response, and TNF-α signaling via the NFκB pathway was observed in the low-risk score subtype, which indicated T cell activation and may be responsible for significantly favorable outcomes in IDC patients. A random forest algorithm identified the most important somatic gene mutations associated with the constructed immune signature. Furthermore, a nomogram that integrated clinicopathological features with the immune signature to predict survival probability was constructed, revealing that the immune signature was an independent prognostic biomarker. Finally, the relationship of VEGFA, PD1, PDL-1, and CTLA-4 expression with the immune infiltration landscape and the immune signature was analyzed to interpret the responses of IDC patients to immunotherapy. Conclusion: Taken together, we performed a comprehensive evaluation of the immune landscape of IDC and constructed an immune signature related to the immune landscape. This analysis of TME immune infiltration landscape has shed light on how IDC respond to immunotherapy and may guide the development of novel drug combination strategies

Quantum Algorithm for Unsupervised Anomaly Detection

Anomaly detection, an important branch of machine learning, plays a critical role in fraud detection, health care, intrusion detection, military surveillance, etc. As one of the most commonly used unsupervised anomaly detection algorithms, the Local Outlier Factor algorithm (LOF algorithm) has been extensively studied. This algorithm contains three steps, i.e., determining the k-distance neighborhood for each data point x, computing the local reachability density of x, and calculating the local outlier factor of x to judge whether x is abnormal. The LOF algorithm is computationally expensive when processing big data sets. Here we present a quantum LOF algorithm consisting of three parts corresponding to the classical algorithm. Specifically, the k-distance neighborhood of x is determined by amplitude estimation and minimum search; the local reachability density of each data point is calculated in parallel based on the quantum multiply-adder; the local outlier factor of each data point is obtained in parallel using amplitude estimation. It is shown that our quantum algorithm achieves exponential speedup on the dimension of the data points and polynomial speedup on the number of data points compared to its classical counterpart. This work demonstrates the advantage of quantum computing in unsupervised anomaly detection

Elective affinities – Bioinformatic analysis of proteomic mass spectrometry data

Li X, Pizarro A, Grosser T. Elective affinities – Bioinformatic analysis of proteomic mass spectrometry data. Archives of Physiology and Biochemistry. 2009;115(5):311-319.Shotgun proteomic strategies based on the identification of proteolytic peptides by tandem mass spectrometry and sequence database searches have emerged as useful approaches for qualitative and quantitative measurement of proteins in large scale studies. Coincidentally, the automated analysis of the resulting mass spectrometry data has become increasingly challenging. Important steps in the analysis include the statistical validation of peptide and protein identifications, the extraction of quantitative information, and the interpretation of identified peptide and protein lists. This review discusses current informatics methods and software available to analyze shotgun proteomics data

Microfluidic Assay of Platelet Deposition on Collagen by Perfusion of Whole Blood from Healthy Individuals Taking Aspirin

Li R, Fries S, Li X, Grosser T, Diamond SL. Microfluidic Assay of Platelet Deposition on Collagen by Perfusion of Whole Blood from Healthy Individuals Taking Aspirin. Clinical Chemistry. 2013;59(8):1195-1204.**BACKGROUND** Microfluidic devices can create hemodynamic conditions for platelet assays. We validated an 8-channel device in a study of interdonor response to acetylsalicylic acid (ASA, aspirin) with whole blood from 28 healthy individuals. **METHODS** Platelet deposition was assessed before treatment or 24 h after ingestion of 325 mg ASA. Whole blood (plus 100 μmol/L H-d-Phe-Pro-Arg-chloromethylketone to inhibit thrombin) was further treated ex vivo with ASA (0–500 μmol/L) and perfused over fibrillar collagen for 300 s at a venous wall shear rate (200 s−1). **RESULTS** Ex vivo ASA addition to blood drawn before aspirin ingestion caused a reduction in platelet deposition [half-maximal inhibitory concentration (IC50) approximately 10–20 μmol/L], especially between 150 and 300 s of perfusion, when secondary aggregation mediated by thromboxane was expected. Twenty-seven of 28 individuals displayed smaller deposits (45% mean reduction; range 10%–90%; P < 0.001) from blood obtained 24 h after ASA ingestion (no ASA added ex vivo). In replicate tests, an R value to score secondary aggregation [deposition rate from 150 to 300 s normalized by rate from 60 to 150 s] showed R < 1 in only 2 of 28 individuals without ASA ingestion, with R > 1 in only 3 of 28 individuals after 500 μmol/L ASA addition ex vivo. At 24 h after ASA ingestion, 21 of 28 individuals displayed poor secondary aggregation (R < 1) without ex vivo ASA addition, whereas the 7 individuals with residual secondary aggregation (R > 1) displayed insensitivity to ex vivo ASA addition. Platelet deposition was not correlated with platelet count. Ex vivo ASA addition caused similar inhibition at venous and arterial wall shear rates. **CONCLUSIONS** Microfluidic devices quantified platelet deposition after ingestion or ex vivo addition of aspirin

Stimulation of chondrocytes and chondroinduced mesenchymal stem cells by osteoinduced mesenchymal stem cells under a fluid flow stimulus on an integrated microfluidic device

The aim of the present study was to investigate the stimulation of osteoinduced mesenchymal stem cells (MSCs) into chondrogenically predifferentiated MSCs and chondrocytes in a mechanical environment. A novel two-layer microfluidic chip was used to mimic the interstitial flow in the superficial zones of articular cartilage. The morphology, proliferation rate and the expression of collagen I, collagen II and aggrecan of chondrocytes and chondro-MSCs were investigated. The results revealed that the cells in the bottom layer were influenced by the top layer's osteoinduced MSCs and the bottom layer's shear flow. The expression of collagen I, which may signify the effect of the shear stress on the dedifferentiation change, was weakened by the stimulation of osteoinduced MSCs on the top layer. The expression of collagen II and aggrecan was increased in the fluidic environment by osteoinduced MSCs. These results indicate that osteoinduced MSCs have a significant effect on the phenotype of chondro-MSCs and chondrocytes in the fluidic microenvironment. The present study described a simple and promising way to rapidly evaluate cell responses to other cells in a fluidic environment, which may help to better promote the utilization of MSCs and chondrocytes in tissue engineering

Standard-Free Absolute Quantitation of Antibody Deamidation Degradation and Host Cell Proteins by Coulometric Mass Spectrometry

Proteomic absolute quantitation strategies mainly rely on the use of synthetic stable isotope-labeled peptides or proteins as internal standards, which are highly costly and time-consuming to synthesize. To circumvent this limitation, we recently developed a coulometric mass spectrometry (CMS) approach for absolute quantitation of proteins without the use of standards, based on the electrochemical oxidation of oxidizable surrogate peptides, followed by mass spectrometry measurement of the peptide oxidation yield. Previously, CMS was only applied for single-protein quantitation. In this study, first, we demonstrated absolute quantitation of multiple proteins in a mixture (e.g., β-lactoglobulin B, α-lactalbumin, and carbonic anhydrase) by CMS in one run, without using any standards. The CMS quantitation result was validated with a traditional isotope dilution method. Second, CMS can be used for absolute quantitation of a low-level target protein in a mixture; for instance, 500 ppm of PLBL2, a problematic host cell protein (HCP), in the presence of a highly abundant monoclonal antibody (mAb) was successfully quantified by CMS with no use of standards. Third, taking one step further, this study demonstrated the unprecedented quantitative analysis of deamidated peptide products arising from the mAb heavy chain deamidation reaction. In particular, absolute quantitation of the deamidation succinimide intermediate which had not been performed before due to the lack of standard was conducted by CMS, for the first time. Overall, our data suggest that CMS has potential utilities for quantitative proteomics and biotherapeutic drug discovery

Bidirectional interactions between indomethacin and the murine intestinal microbiota

Abstract The vertebrate gut microbiota have been implicated in the metabolism of xenobiotic compounds, motivating studies of microbe-driven metabolism of clinically important drugs. Here, we studied interactions between the microbiota and indomethacin, a nonsteroidal antiinflammatory drug (NSAID) that inhibits cyclooxygenases (COX) -1 and -2. Indomethacin was tested in both acute and chronic exposure models in mice at clinically relevant doses, which suppressed production of COX-1-and COX-2-derived prostaglandins and caused small intestinal (SI) damage. Deep sequencing analysis showed that indomethacin exposure was associated with alterations in the structure of the intestinal microbiota in both dosing models. Perturbation of the intestinal microbiome by antibiotic treatment altered indomethacin pharmacokinetics and pharmacodynamics, which is probably the result of reduced bacterial b-glucuronidase activity. Humans show considerable inter-individual differences in their microbiota and their responses to indomethacin -thus, the drug-microbe interactions described here provide candidate mediators of individualized drug responses

Binder-Free 3D Integrated Ni@Ni3Pt Air Electrode for Zn-Air Batteries

Developing an air electrode with high efficiency and stable performance is essential to improve the energy conversion efficiency and lifetime of zinc- air battery. Herein, Ni3Pt alloy is deposited on 3D nickel foam by a pulsed laser deposition method, working as a stable binder-free air electrode for rechargeable zinc-air batteries. The polycrystalline Ni3Pt alloy possesses high oxygen-conversion catalytic activity, which is highly desirable for the charge and discharge process in zinc-air battery. Meanwhile, this sample technique constructs an integrated and stable electrode structure, which not only has a 3D architecture of high conductivity and porosity but also produces a uniform Ni3Pt strongly adhering to the substrate, favoring rapid gas and electrolyte diffusion throughout the whole energy conversion process. Employed as an air electrode in zinc-air batteries, it exhibits a small charge and discharge gap of below 0.62 V at 10 mA cm−2, with long cycle life of 478 cycles under 10 min per cycle. Furthermore, benefitting from the structural advantages, a flexible device exhibits similar electrochemical performance even under the bending state. The high performance resulting from this type of integrated electrode in this work paves the way of a promising technique to fabricate air electrodes for zinc-air batteries

Small RNA and mRNA Sequencing Reveal the Roles of microRNAs Involved in Pomegranate Female Sterility

Female sterility is a key factor restricting plant reproduction. Our previous studies have revealed that pomegranate female sterility mainly arose from the abnormality of ovule development. MicroRNAs (miRNAs) play important roles in ovule development. However, little is known about the roles of miRNAs in female sterility. In this study, a combined high-throughput sequencing approach was used to investigate the miRNAs and their targeted transcripts involved in female development. A total of 103 conserved and 58 novel miRNAs were identified. Comparative profiling indicated that the expression of 43 known miRNAs and 14 novel miRNAs were differentially expressed between functional male flowers (FMFs) and bisexual flowers (BFs), 30 known miRNAs and nine novel miRNAs showed significant differences among different stages of BFs, and 20 known miRNAs and 18 novel miRNAs exhibited remarkable expression differences among different stages of FMFs. Gene ontology (GO) analyses of 144 predicted targets of differentially expressed miRNAs indicated that the “reproduction process” and “floral whorl development” processes were significantly enriched. The miRNA–mRNA interaction analyses revealed six pairs of candidate miRNAs and their targets associated with female sterility. Interestingly, pg-miR166a-3p was accumulated, whereas its predicted targets (Gglean012177.1 and Gglean013966.1) were repressed in functional male flowers (FMFs), and the interaction between pg-miR166a-3p and its targets (Gglean012177.1 and Gglean013966.1) were confirmed by transient assay. A. thaliana transformed with 35S-pre-pg-miR166a-3p verified the role of pg-miR166a-3p in ovule development, which indicated pg-miR166a-3p’s potential role in pomegranate female sterility. The results provide new insights into molecular mechanisms underlying the female sterility at the miRNA level