Bone Metastases Lesion Segmentation on Breast Cancer Bone Scan Images with Negative Sample Training.

The use of deep learning methods for the automatic detection and quantification of bone metastases in bone scan images holds significant clinical value. A fast and accurate automated system for segmenting bone metastatic lesions can assist clinical physicians in diagnosis. In this study, a small internal dataset comprising 100 breast cancer patients (90 cases of bone metastasis and 10 cases of non-metastasis) and 100 prostate cancer patients (50 cases of bone metastasis and 50 cases of non-metastasis) was used for model training. Initially, all image labels were binary. We used the Otsu thresholding method or negative mining to generate a non-metastasis mask, thereby transforming the image labels into three classes. We adopted the Double U-Net as the baseline model and made modifications to its output activation function. We changed the activation function to SoftMax to accommodate multi-class segmentation. Several methods were used to enhance model performance, including background pre-processing to remove background information, adding negative samples to improve model precision, and using transfer learning to leverage shared features between two datasets, which enhances the model's performance. The performance was investigated via 10-fold cross-validation and computed on a pixel-level scale. The best model we achieved had a precision of 69.96%, a sensitivity of 63.55%, and an F1-score of 66.60%. Compared to the baseline model, this represents an 8.40% improvement in precision, a 0.56% improvement in sensitivity, and a 4.33% improvement in the F1-score. The developed system has the potential to provide pre-diagnostic reports for physicians in final decisions and the calculation of the bone scan index (BSI) with the combination with bone skeleton segmentation.

Clinical evaluation of a multitarget fecal immunochemical test-sDNA test for colorectal cancer screening in a high-risk population: a prospective, multicenter clinical study.

Colorectal cancer (CRC) is a major malignancy threatening the health of people in China and screening could be effective for preventing the occurrence and reducing the mortality of CRC. We conducted a multicenter, prospective clinical study which recruited 4,245 high-risk CRC individuals defined as having positive risk-adapted scores or fecal immunochemical test (FIT) results, to evaluate the clinical performance of the multitarget fecal immunochemical and stool DNA (FIT-sDNA) test for CRC screening. Each participant was asked to provide a stool sample prior to bowel preparation, and FIT-sDNA test and FIT were performed independently of colonoscopy. We found that 186 (4.4%) were confirmed to have CRC, and 375 (8.8%) had advanced precancerous neoplasia among the high CRC risk individuals. The sensitivity of detecting CRC for FIT-sDNA test was 91.9% (95% CI, 86.8-95.3), compared with 62.4% (95% CI, 54.9-69.3) for FIT (P < 0.001). The sensitivity for detecting advanced precancerous neoplasia was 63.5% (95% CI, 58.3-68.3) for FIT-sDNA test, compared with 30.9% (95% CI, 26.3-35.6) for FIT (P < 0.001). Multitarget FIT-sDNA test detected more colorectal advanced neoplasia than FIT. Overall, these findings indicated that in areas with limited colonoscopy resources, FIT-sDNA test could be a promising further risk triaging modality to select patients for colonoscopy in CRC screening.

Skeleton Segmentation on Bone Scintigraphy for BSI Computation.

Bone Scan Index (BSI) is an image biomarker for quantifying bone metastasis of cancers. To compute BSI, not only the hotspots (metastasis) but also the bones have to be segmented. Most related research focus on binary classification in bone scintigraphy: having metastasis or none. Rare studies focus on pixel-wise segmentation. This study compares three advanced convolutional neural network (CNN) based models to explore bone segmentation on a dataset in-house. The best model is Mask R-CNN, which reaches the precision, sensitivity, and F1-score: 0.93, 0.87, 0.90 for prostate cancer patients and 0.92, 0.86, and 0.88 for breast cancer patients, respectively. The results are the average of 10-fold cross-validation, which reveals the reliability of clinical use on bone segmentation.

YM155 inhibits neuroblastoma growth through degradation of MYCN: A new role as a USP7 inhibitor.

Amplification of the MYCN gene (MNA) is observed in approximately 25 to 35% of neuroblastoma patients, and is a well-recognized marker of tumor aggressiveness and poor outcome. Targeting MYCN is a novel therapy strategy to induce tumor regression. Here, we discovered that a BIRC5/Survivin inhibitor, YM155, specifically inhibits MNA neuroblastoma cell growth in vitro. We found that YM155 promotes MYCN degradation in MNA cells. Further, we found that YM155 inhibits USP7 deubiquitinase activity in vitro, using Ub-aminomethylcoumarin (Ub-AMC) as substrate. Results from in vivo studies further demonstrated that YM155 significantly inhibited the tumor growth in MNA neuroblastoma xenograft model. Our data support a novel mechanism of action of YM155 in inhibition of growth of cancer cells through inducing MYCN degradation by inibition of activity of deubiquitinase like USP7.

Combined Proteomic and Metabolomic Analysis of the Molecular Mechanism Underlying the Response to Salt Stress during Seed Germination in Barley.

Salt stress is a major abiotic stress factor affecting crop production, and understanding of the response mechanisms of seed germination to salt stress can help to improve crop tolerance and yield. The differences in regulatory pathways during germination in different salt-tolerant barley seeds are not clear. Therefore, this study investigated the responses of different salt-tolerant barley seeds during germination to salt stress at the proteomic and metabolic levels. To do so, the proteomics and metabolomics of two barley seeds with different salt tolerances were comprehensively examined. Through comparative proteomic analysis, 778 differentially expressed proteins were identified, of which 335 were upregulated and 443 were downregulated. These proteins, were mainly involved in signal transduction, propanoate metabolism, phenylpropanoid biosynthesis, plant hormones and cell wall stress. In addition, a total of 187 salt-regulated metabolites were identified in this research, which were mainly related to ABC transporters, amino acid metabolism, carbohydrate metabolism and lipid metabolism; 72 were increased and 112 were decreased. Compared with salt-sensitive materials, salt-tolerant materials responded more positively to salt stress at the protein and metabolic levels. Taken together, these results suggest that salt-tolerant germplasm may enhance resilience by repairing intracellular structures, promoting lipid metabolism and increasing osmotic metabolites. These data not only provide new ideas for how seeds respond to salt stress but also provide new directions for studying the molecular mechanisms and the metabolic homeostasis of seeds in the early stages of germination under abiotic stresses.

Fibroblast Activation Protein-α as a Target in the Bench-to-Bedside Diagnosis and Treatment of Tumors: A Narrative Review.

Fibroblast activation protein-α (FAP) is a type II integral serine protease that is specifically expressed by activated fibroblasts. Cancer-associated fibroblasts (CAFs) in the tumor stroma have an abundant and stable expression of FAP, which plays an important role in promoting tumor growth, invasion, metastasis, and immunosuppression. For example, in females with a high incidence of breast cancer, CAFs account for 50-70% of the cells in the tumor's microenvironment. CAF overexpression of FAP promotes tumor development and metastasis by influencing extracellular matrix remodeling, intracellular signaling, angiogenesis, epithelial-to-mesenchymal transition, and immunosuppression. This review discusses the basic biological characteristics of FAP and its applications in the diagnosis and treatment of various cancers. We review the emerging basic and clinical research data regarding the use of nanomaterials that target FAP.

Rapid screening for individualized chemotherapy optimization of colorectal cancer: A novel conditional reprogramming technology-based functional diagnostic assay.

BACKGROUND: In vitro patient tumor models such as patient-derived organoids (PDO) and conditionally reprogrammed (CR) cell culture are important for translational research and pre-clinical drug testing. In this study we present a personalized drug sensitivity test for late stage, potentially operable colorectal cancer (CRC) using patient-derived primary tumor cells isolated with i-CR technology, an optimized CR method. We explored the clinical feasibility of using i-CR platform to guide CRC chemotherapy, and established the correlation between in vitro drug sensitivity and patient clinical response. METHODS: Primary CRC tumor cells were isolated and cultured with the i-CR technology. NGS was performed and the WES and CNV results of i-CR cells were compared with that of the original patient tumor samples. In vitro drug screenings were done with guideline chemotherapy drugs for CRC. In vivo drug response was examined with paired PDX mouse models. A double-blind co-clinical cohort study was carried out and the clinical outcomes of the enrolled patients were compared with the i-CR results. RESULTS: i-CR platform could be used to rapidly propagate primary colorectal tumor cells that represent individual patient tumors effectively by keeping the clonal heterogeneity and the genetic characteristics. Chemotherapy drug screenings with i-CR cells were comparable with that of PDX models. More importantly, i-CR results showed high accordance with the clinical outcomes of the enrolled CRC patients. CONCLUSION: i-CR platform was capable to test and optimize therapeutic regimens pre-clinically, study cancer cell biology, and model tumor re-emergence to identify new targeted therapeutics from an effective personalized medicine standpoint.

Conditionally reprogrammed colorectal cancer cells combined with mouse avatars identify synergy between EGFR and MEK or CDK4/6 inhibitors.

Preclinical models, including patient-derived xenograft (PDX) and organoid and primary cell culture, are essential for studies of cancer cell biology and facilitate translational research and individualization of therapy. We explored the optimum preclinical model by modifying the conventional conditional reprogramming (CR) system followed by screening effective targeted drug combinations against colorectal cancer (CRC). By modifying the ingredients of the culture medium used in a conventional CR system, a novel individualized CR system (termed i-CR) was established. Tumor samples from CRC patients were collected and PDX models were derived followed by high-throughput i-CR drug screening and validation of the effective targeted drug combinations. The i-CR system selectively expanded tumor cells rather than normal epithelial cells and facilitated high-throughput drug screening when combined with high-content imaging and quantitative analysis of cell proliferation. Using inhibitors targeting multiple signaling pathways identified by high-throughput i-CR drug screening, we discovered that inhibition of the EGFR and MEK or CDK4/6 pathways exerted a synergistic inhibitory effect against CRC, and we noted super-synergistic effects when EGFR, MEK, and CDK4/6 inhibitors were used simultaneously. These data were validated using paired PDX models, which showed marked inhibition of tumor growth. The novel i-CR system combined with PDX models will enable individualization of therapy and drug discovery, and strategies combining EGFR, MEK, and CDK4/6 inhibitors warrant clinical validation.

Distinct subpopulations of hepatitis C virus infectious cells with different levels of intracellular hepatitis C virus core protein.

Chronic infection by hepatitis C virus (HCV) is a major risk factor for the development of hepatocellular carcinoma (HCC). Despite the clear clinical importance of virus-associated HCC, the underlying molecular mechanisms remain largely unclarified. Oxidative stress, in particular, DNA lesions associated with oxidative damage, plays a major role in carcinogenesis, and is strongly linked to the development of many cancers, including HCC. However, in identifying hepatocytes with HCV viral RNA, estimates of the median proportion of HCV-infected hepatocytes have been found as high as 40% in patients with chronic HCV infection. In order to explore the gene alternation and association between different viral loads of HCV-infected cells, we established a method to dissect high and low viral load cells and examined the expression of DNA damage-related genes using a quantitative polymerase chain reaction array. We found distinct expression patterns of DNA damage-related genes between high and low viral load cells. This study provides a new method for future study on virus-associated gene expression research.

A subset of gastric cancers with EGFR amplification and overexpression respond to cetuximab therapy.

A preclinical trial identified 4 of 20 (20%) gastric cancer (GC) patient-derived xenografts responded to cetuximab. Genome-wide profiling and additional investigations revealed that high EGFR mRNA expression and immunohistochemistry score (3+) are associated with tumor growth inhibition. Furthermore, EGFR amplification were observed in 2/4 (50%) responders with average copy number 5.8 and >15 respectively. Our data suggest that a GC subtype with EGFR amplification and overexpression benefit from cetuximab treatment.

Overcoming erlotinib resistance with tailored treatment regimen in patient-derived xenografts from naïve Asian NSCLC patients.

Overall benefits of EGFR-TKIs are limited because these treatments are largely only for adenocarcinoma (ADC) with EGFR activating mutation. The treatments also usually lead to development of resistances. We have established a panel of patient-derived xenografts (PDXs) from treatment naïve Asian NSCLC patients, including those containing "classic" EGFR activating mutations. Some of these EGFR-mutated PDXs do not respond to erlotinib: LU1868 containing L858R/T790M mutations, and LU0858 having L858R mutation as well as c-MET gene amplification, both squamous cell carcinoma (SCC). Treatment of LU0858 with crizotinib, a small molecule inhibitor for ALK and c-MET, inhibited tumor growth and c-MET activity. Combination of erlotinib and crizotinib caused complete response, indicating the activation of both EGFR and c-MET promote its growth/survival. LU2503 and LU1901, both with wild-type EGFR and c-MET gene amplification, showed complete response to crizotinib alone, suggesting that c-MET gene amplification, not EGFR signaling, is the main oncogenic driver. Interestingly, LU1868 with the EGFR L858R/T790M, but without c-met amplification, had a complete response to cetuximab. Our data offer novel practical approaches to overcome the two most common resistances to EGFR-TKIs seen in the clinic using marketed target therapies.

Gold nanoparticle-based colorimetric assays for coagulation-related proteins and their inhibition reactions.

In this paper, we describe two simple, label-free, homogenous assays using gold nanoparticles (Au NPs)-one to detect coagulation-related proteins and the other to screen inhibition reactions. The first nanosensor functions on the basis of the fact that thrombin catalyzes fibrinogen to form long-chain fibrins, which then induce aggregation of Au NPs. We applied this sensor to study the interactions of thrombin, inhibitors, cofactors, and antidotes. We further used thrombin-conjugated Au NPs (Thr-Au NPs) to analyze the levels of fibrinogen in plasma samples via fibrinogen-induced aggregation of Thr-Au NPs. The limit of detection (LOD; S/N=3) of this sensor for fibrinogen in plasma was 10nM. The Thr-Au NP probe provided quantitative results for fibrinogen in plasma samples that correlated (R(2)=0.97) with those obtained using a clinical von Clauss clotting rate assay. In addition, the Thr-Au NP-based sensor could be used to monitor thrombin concentrations in plasma samples under physiological conditions. Compared with conventional assays, these label-free assays offer several advantages, such as rapid and simple readout by the naked eye or by UV-vis absorption spectroscopy.

A label-free colorimetric detection of lead ions by controlling the ligand shells of gold nanoparticles.

We have developed a simple, colorimetric and label-free gold nanoparticle (Au NP)-based probe for the detection of Pb(2+) ions in aqueous solution, operating on the principle that Pb(2+) ions change the ligand shell of thiosulfate (S(2)O(3)(2-))-passivated Au NPs. Au NPs reacted with S(2)O(3)(2-) ions in solution to form Au(+).S(2)O(3)(2-) ligand shells on the Au NP surfaces, thereby inhibiting the access of 4-mercaptobutanol (4-MB). Surface-assisted laser desorption/ionization time-of-flight ionization mass spectrometry (SALDI-TOF MS) and inductively coupled plasma mass spectrometry (ICP-MS) measurements revealed that PbAu alloys formed on the surfaces of the Au NPs in the presence of Pb(2+) ions; these alloys weakened the stability of the Au(+).S(2)O(3)(2-) ligand shells, enhancing the access of 4-MB to the Au NP surfaces and, therefore, inducing their aggregation. As a result, the surface plasmon resonance (SPR) absorption of the Au NPs red-shifted and broadened, allowing quantitation of the Pb(2+) ions in the aqueous solution. This 4-MB/S(2)O(3)(2-)-Au NP probe is highly sensitive (linear detection range: 0.5-10 nM) and selective (by at least 100-fold over other metal ions) toward Pb(2+) ions. This cost-effective sensing system allows the rapid and simple determination of the concentrations of Pb(2+) ions in real samples (in this case, river water, Montana soil and urine samples).

Colorimetric assay for lead ions based on the leaching of gold nanoparticles.

A colorimetric, label-free, and nonaggregation-based gold nanoparticles (Au NPs) probe has been developed for the detection of Pb(2+) in aqueous solution, based on the fact that Pb(2+) ions accelerate the leaching rate of Au NPs by thiosulfate (S(2)O(3)(2-)) and 2-mercaptoethanol (2-ME). Au NPs reacted with S(2)O(3)(2-) ions in solution to form Au(S(2)O(3))(2)(3-) complexes on the Au NP surfaces, leading to slight decreases in their surface plasmon resonance (SPR) absorption. Surface-assisted laser desorption/ionization time-of-flight ionization mass spectrometry (SALDI-TOF MS) data reveals the formation of Pb-Au alloys on the surfaces of the Au NPs in the presence of Pb(2+) ions and 2-ME. The formation of Pb-Au alloys accelerated the Au NPs rapidly dissolved into solution, leading to dramatic decreases in the SPR absorption. The 2-ME/S(2)O(3)(2-)-Au NP probe is highly sensitive (LOD = 0.5 nM) and selective (by at least 1000-fold over other metal ions) toward Pb(2+) ions, with a linear detection range (2.5 nM-10 muM) over nearly 4 orders of magnitude. The cost-effective probe allows rapid and simple determination of the concentrations of Pb(2+) ions in environmental samples (Montana soil and river), with results showing its great practicality for the detection of lead in real samples.