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Predicting pathological complete response (pCR) to neoadjuvant chemotherapy (NAC) in triple-negative breast cancer (TNBC) patients accurately is direly needed for clinical decision making. pCR is also regarded as a strong predictor of overall survival. In this work, we propose a deep learning system to predict pCR to NAC based on serial pathology images stained with hematoxylin and eosin and two immunohistochemical biomarkers (Ki67 and PHH3). To support human prior domain knowledge-based guidance and enhance interpretability of the deep learning system, we introduce a human knowledge-derived spatial attention mechanism to inform deep learning models of informative tissue areas of interest. For each patient, three serial breast tumor tissue sections from biopsy blocks were sectioned, stained in three different stains and integrated. The resulting comprehensive attention information from the image triplets is used to guide our prediction system for prognostic tissue regions.

The experimental dataset consists of 26 419 pathology image patches of 1000×1000 pixels from 73 TNBC patients treated with NAC. Image patches from randomly selected 43 patients are used as a training dataset and images patches from the rest 30 are used as a testing dataset. By the maximum voting from patch-level results, our proposed model achieves a 93% patient-level accuracy, outperforming baselines and other state-of-the-art systems, suggesting its high potential for clinical decision making.

The codes, the documentation and example data are available on an open source at: https://github.com/jkonglab/PCR_Prediction_Serial_WSIs_biomarkers

Supplementary data are available at Bioinformatics online.

 

Donor–π-acceptor (D–π-A) fluorophores consisting of a donor unit, a π linker, and an acceptor moiety have attracted attention in the last decade. In this study, we report the synthesis, characterization, optical properties, TD-DFT, and cytotoxicity studies of 17 near infrared (NIR) D–π-A analogs which have not been reported so far to the best of our knowledge. These fluorophores have chloroacrylic acid as the acceptor unit and various donor units such as indole, benzothiazole, benzo[ e ]indole, and quinoline. The fluorophores showed strong absorption in the NIR (700–970 nm) region due to their enhanced intramolecular charge transfer (ICT) between chloroacrylic acid and the donor moieties connected with the Vilsmeier–Haack linker. The emission wavelength maxima of the fluorophores were in between 798 and 870 nm. Compound 20 with a 4-quinoline donor moiety showed an emission wavelength above 1000 nm in the NIR II window. The synthesized fluorophores were characterized by 1 H NMR and 13 C NMR, and their optical properties were studied. Time dependent density functional theory (TD-DFT) calculations showed that the charge transfer occurs from the donor groups (indole, benzothiazole, benzo[ e ]indole, and quinoline) to the acceptor chloroacrylic acid moiety. Fluorophores with [HOMO] to [LUMO+1] transitions were shown to possess a charge separation character. The cytotoxicity of selected fluorophores, 4 , 7 , 10 and 12 was investigated against breast cancer cell lines and they showed better activity than the anti-cancer agent docetaxel. 

We report for the first time the usage of plasmonically enhanced Raman spectroscopy (PERS) to directly monitor the dynamics of pharmacologically generated hemeoxygenase-1 (HO-1) by evaluating the kinetics of formation of carbon monoxide (CO), one of the metabolites of HO-1 activation, in live cells during cisplatin treatment. Being an endogenous signaling molecule, CO plays an important role in cancer regression. Many aspects of HO-1's and CO's functions in biology are still unclear largely due to the lack of technological tools for the real-time monitoring of their dynamics in live cells and tissues. In this study, we found that, together with nuclear region-targeted gold nanocubes (AuNCs), cisplatin treatment can dramatically trigger the activation of HO-1 and thereby the rate and production of CO in mammalian cells in a dose-dependent manner. Though quantitative molecular data revealed that a lower concentration of cisplatin up-regulates HO-1 expression in cancer cells, PERS data suggest that it poorly facilitates the activation of HO-1 and thereby the production of CO. However, at a higher dose, cisplatin along with AuNCs could significantly enhance the activation of HO-1 in cancer cells, which could be probed in real-time by monitoring the CO generation by using PERS. Under the same conditions, the rate of formation of CO in healthy cells was relatively higher in comparison to the cancer cells. Additionally, molecular data revealed that AuNCs have the potential to suppress the up-regulation of HO-1 in cancer cells during cisplatin treatment at a lower concentration. As up-regulation of HO-1 has a significant role in cell adaptation to oxidative stress in cancer cells, the ability of AuNCs in suppressing the HO-1 overexpression will have a remarkable impact in the development of nanoformulations for combination cancer therapy. This exploratory study demonstrates the unique possibilities of PERS in the real-time monitoring of endogenously generated CO and thereby the dynamics of HO-1 in live cells, which could expedite our understanding of the signaling action of CO and HO-1 in cancer progression.