30 research outputs found
GSAE: an autoencoder with embedded gene-set nodes for genomics functional characterization
Bioinformatics tools have been developed to interpret gene expression data at
the gene set level, and these gene set based analyses improve the biologists'
capability to discover functional relevance of their experiment design. While
elucidating gene set individually, inter gene sets association is rarely taken
into consideration. Deep learning, an emerging machine learning technique in
computational biology, can be used to generate an unbiased combination of gene
set, and to determine the biological relevance and analysis consistency of
these combining gene sets by leveraging large genomic data sets. In this study,
we proposed a gene superset autoencoder (GSAE), a multi-layer autoencoder model
with the incorporation of a priori defined gene sets that retain the crucial
biological features in the latent layer. We introduced the concept of the gene
superset, an unbiased combination of gene sets with weights trained by the
autoencoder, where each node in the latent layer is a superset. Trained with
genomic data from TCGA and evaluated with their accompanying clinical
parameters, we showed gene supersets' ability of discriminating tumor subtypes
and their prognostic capability. We further demonstrated the biological
relevance of the top component gene sets in the significant supersets. Using
autoencoder model and gene superset at its latent layer, we demonstrated that
gene supersets retain sufficient biological information with respect to tumor
subtypes and clinical prognostic significance. Superset also provides high
reproducibility on survival analysis and accurate prediction for cancer
subtypes.Comment: Presented in the International Conference on Intelligent Biology and
Medicine (ICIBM 2018) at Los Angeles, CA, USA and published in BMC Systems
Biology 2018, 12(Suppl 8):14
Predicting drug response of tumors from integrated genomic profiles by deep neural networks
The study of high-throughput genomic profiles from a pharmacogenomics
viewpoint has provided unprecedented insights into the oncogenic features
modulating drug response. A recent screening of ~1,000 cancer cell lines to a
collection of anti-cancer drugs illuminated the link between genotypes and
vulnerability. However, due to essential differences between cell lines and
tumors, the translation into predicting drug response in tumors remains
challenging. Here we proposed a DNN model to predict drug response based on
mutation and expression profiles of a cancer cell or a tumor. The model
contains a mutation and an expression encoders pre-trained using a large
pan-cancer dataset to abstract core representations of high-dimension data,
followed by a drug response predictor network. Given a pair of mutation and
expression profiles, the model predicts IC50 values of 265 drugs. We trained
and tested the model on a dataset of 622 cancer cell lines and achieved an
overall prediction performance of mean squared error at 1.96 (log-scale IC50
values). The performance was superior in prediction error or stability than two
classical methods and four analog DNNs of our model. We then applied the model
to predict drug response of 9,059 tumors of 33 cancer types. The model
predicted both known, including EGFR inhibitors in non-small cell lung cancer
and tamoxifen in ER+ breast cancer, and novel drug targets. The comprehensive
analysis further revealed the molecular mechanisms underlying the resistance to
a chemotherapeutic drug docetaxel in a pan-cancer setting and the anti-cancer
potential of a novel agent, CX-5461, in treating gliomas and hematopoietic
malignancies. Overall, our model and findings improve the prediction of drug
response and the identification of novel therapeutic options.Comment: Accepted for presentation in the International Conference on
Intelligent Biology and Medicine (ICIBM 2018) at Los Angeles, CA, USA.
Currently under consideration for publication in a Supplement Issue of BMC
Genomic
Adverse Events of Extracorporeal Ultrasound-Guided High Intensity Focused Ultrasound Therapy
High-intensity focused ultrasound (HIFU) is considered to be an alternative to surgery. Extracorporeal ultrasound-guided HIFU (USgFU) has been clinically used to treat solid tumors. Preliminary trials in a small sample of a Western population suggested that this modality was safe. Most trials are performed in China thereby providing comprehensive data for understanding the safety profile. The aim of this study was to evaluate adverse events of USgFU therapy.Clinical data were searched in 2 Chinese databases. Adverse events of USgFU were summarized and compared with those of magnetic resonance-guided HIFU (MRgFU; for uterine, bone or breast tumor) and transrectal ultrasound-guided HIFU (for prostate cancer or benign prostate hyperplasia). USgFU treatment was performed using 7 types of device. Side effects were evaluated in 13262 cases. There were fewer adverse events in benign lesions than in malignant lesions (11.81% vs. 21.65%, p<0.0001). Rates of adverse events greatly varied between the disease types (0-280%, p<0.0001) and between the applied HIFU devices in both malignant (10.58-44.38%, p<0.0001) and benign lesions (1.67-17.57%, p<0.0001). Chronological analysis did not demonstrate a decrease in the rate of adverse events. Based upon evaluable adverse events, incidences in USgFU were consistent with those in MRgFU or transrectal HIFU. Some side effects frequently occurred following transrectal HIFU were not reported in USgFU. Several events including intrahepatic metastasis, intraoperative high fever, and occlusions of the superior mesenteric artery should be of particular concern because they have not been previously noted. The types of adverse events suggested that they were ultrasonic lesions.The frequency of adverse events depended on the location of the lesion and the type of HIFU device; however, side effects of USgFU were not yet understood. USgFU did not decrease the incidence of adverse events compared with MRgFU
Nanosecond Electric Pulses Induce Early and Late Phases of DNA Damage and Cell Death in Cisplatin-Resistant Human Ovarian Cancer Cells
Chemoresistance is a challenge for management of ovarian cancer, and therefore the response of resistant cells to nanosecond electric pulses (nsEP) was explored. Human ovarian cancer cell line COC1 and the cisplatin-resistant subline COC1/DDP were subjected to nsEP (32βns, 10βkV/cm, 10βHz pulse repletion frequency, and 10βmin exposure duration), and then the cellular responses were followed. The percentages of dead cells and of comet-formed cells in the alkaline assay displayed two peak levels (i.e., 2 and 8βh after nsEP exposure), with the highest value noted at 8βh; the percentage of comet-formed cells in the neutral assay was increased at 8βh; the apoptotic percentage was increased at 8βh, with collapse of the mitochondrial membrane potential and the activation of caspase-3 and caspase-9. The comet assay demonstrated DNA single-strand break at 2βh and double-strand break at 8βh. nsEP resulted in lower cytotoxicity in COC1/DDP cells compared with COC1 cells. These findings indicated that nsEP induced early and late phases of DNA damage and cell death, and these two types of cell death may have distinct applications to treatments of chemoresistant ovarian cancers
Extracorporeal Ultrasound-Guided High Intensity Focused Ultrasound: Implications from the Present Clinical Trials
Extracorporeal ultrasound-guided high intensity focused ultrasound (HIFU) has been clinically used for 15 years, and over 36000 cases have been reported. However, there yet lacked a consensus in the clinical values, suggesting the necessity of checking clinical findings. Clinical trials were searched and data reevaluated. HIFU was hardly performed alone; almost all present anticancer means have been applied during an HIFU treatment, and a specific regimen varied between trials; there were heterogeneity and disagreement between trials. The complexity made it difficult to distinguish the effect of HIFU. Based upon evaluable data, the efficacy of HIFU was similar to that of radio frequency, chemoembolization, chemotherapy, radiotherapy, or hormone therapy; a combined therapy did not improve the efficacy. The survival rate of HIFU plus radiotherapy was lower than that of radical surgery in liver cancers. Adverse events had no downtrend in the past years. HIFU was not a standardized procedure where the intensity and insonation mode were modified constantly throughout a treatment, limiting an evaluation from the perspective of ultrasonics. These implied that HIFU should be applied as an alternative at most occasions. The present clinical trials had defects making against the understating of HIFU
An Advanced Orthotopic Ovarian Cancer Model in Mice for Therapeutic Trials
A nude mouse received subcutaneous injection of human ovarian cancer cells HO-8910PM to form a tumor, and then the tumor fragment was surgically transplanted to the ovary of a recipient mouse to establish an orthotopic cancer model. Tumors occurred in 100% of animals. A mouse displayed an ovarian mass, ascites, intraperitoneal spread, and lung metastasis at natural death. The mean survival time was 34.1Β±17.2 days, with median survival time of 28.5 days. The findings indicated that the present mouse model can reflect the biological behavior of advanced human ovarian cancers. This in vivo model can be used to explore therapeutic means against chemoresistance and metastasis, and an effective treatment would prolong the survival time
Pharmacokinetic profiles of cancer sonochemotherapy
<p><b>Introduction:</b> Sonochemotherapy is a promising strategy for the treatment of cancer, however, there is limited understanding of its pharmacokinetics (PK).</p> <p><b>Area covered:</b> The PK profile of sonochemotherapy is evaluated based on released data. Preclinical investigations suggest that the blood PK of sonochemotherapy is similar to chemotherapy when using free anticancer drugs. When using encapsulated drugs, a lower plasma level usually occurs; however, the ultrasonic release of drugs within a tumor may lead to drugs leaking into circulation, causing a rebound in the plasma drug level; a higher drug level is detected in certain healthy organs, however this depends mostly on the pharmaceutical formulation. Sonochemotherapy increases both the level and retention time of drugs in a tumor. Clinical trials of combined chemotherapy and high intensity focused ultrasound (HIFU) are evaluated from the perspective of preclinical PK: the intratumoral PK and drug interactions under insonation, and a protocol to set the interval between drug administration and insonation are lacking.</p> <p><b>Expert opinion:</b> Insonation can alter the PK properties of chemotherapeutics, which may exacerbate the system and/or organ toxicity of anticancer drugs. Directly employing the PK parameters validated in conventional chemotherapy plays an important role in unsatisfactory clinical outcomes of chemotherapy combined with HIFU.</p