Screening of stress enhancer based on analysis of gene expression profiles: enhancement of hyperthermia-induced tumor necrosis by an MMP-3 inhibitor

Comprehensive multi-omics analysis reveals WEE1 as a synergistic lethal target with hyperthermia through CDK1 super-activation

Hyperthermic intraperitoneal chemotherapy's role in ovarian cancer remains controversial, hindered by limited understanding of hyperthermia-induced tumor cellular changes. This limits developing potent combinatory strategies anchored in hyperthermic intraperitoneal therapy (HIPET). Here, we perform a comprehensive multi-omics study on ovarian cancer cells under hyperthermia, unveiling a distinct molecular panorama, primarily characterized by rapid protein phosphorylation changes. Based on the phospho-signature, we pinpoint CDK1 kinase is hyperactivated during hyperthermia, influencing the global signaling landscape. We observe dynamic, reversible CDK1 activity, causing replication arrest and early mitotic entry post-hyperthermia. Subsequent drug screening shows WEE1 inhibition synergistically destroys cancer cells with hyperthermia. An in-house developed miniaturized device confirms hyperthermia and WEE1 inhibitor combination significantly reduces tumors in vivo. These findings offer additional insights into HIPET, detailing molecular mechanisms of hyperthermia and identifying precise drug combinations for targeted treatment. This research propels the concept of precise hyperthermic intraperitoneal therapy, highlighting its potential against ovarian cancer.

Single-cell gene regulatory network prediction by explainable AI

The molecular heterogeneity of cancer cells contributes to the often partial response to targeted therapies and relapse of disease due to the escape of resistant cell populations. While single-cell sequencing has started to improve our understanding of this heterogeneity, it offers a mostly descriptive view on cellular types and states. To obtain more functional insights, we propose scGeneRAI, an explainable deep learning approach that uses layer-wise relevance propagation (LRP) to infer gene regulatory networks from static single-cell RNA sequencing data for individual cells. We benchmark our method with synthetic data and apply it to single-cell RNA sequencing data of a cohort of human lung cancers. From the predicted single-cell networks our approach reveals characteristic network patterns for tumor cells and normal epithelial cells and identifies subnetworks that are observed only in (subgroups of) tumor cells of certain patients. While current state-of-the-art methods are limited by their ability to only predict average networks for cell populations, our approach facilitates the reconstruction of networks down to the level of single cells which can be utilized to characterize the heterogeneity of gene regulation within and across tumors.

Role of cytokines and chemokines in alcohol-induced tumor promotion

Excessive chronic alcohol consumption has become a worldwide health problem. The oncogenic effect of chronic alcohol consumption is one of the leading concerns. The mechanisms of alcohol-induced tumorigenesis and tumor progression are largely unknown, although many factors have been implicated in the process. This review discusses the recent progress in this research area with concentration on alcohol-induced dysregulation of cytokines and chemokines. Based on the available evidence, we propose that alcohol promotes tumor progression by the dysregulation of the cytokine/chemokine system. In addition, we discuss specific transcription factors and signaling pathways that are involved in the action of these cytokines/chemokines and the oncogenic effect of alcohol. This review provides novel insight into the mechanisms of alcohol-induced tumor promotion.

ART, cognitive science, and technology transfer

Three computational examples illustrate how cognitive science can introduce new approaches to the analysis of large datasets. The first example addresses the question: how can a neural system learning from one example at a time absorb information that is inconsistent but correct, as when a family pet is called Spot and dog and animal, while rejecting similar incorrect information, as when the same pet is called wolf? How does this system transform such scattered information into the knowledge that dogs are animals, but not conversely? The second example asks: how can a real-time system, initially trained with a few labeled examples and a limited feature set, continue to learn from experience when confronted with oceans of additional information, without eroding reliable early memories? How can such individual systems adapt to their unique application contexts? The third example asks: how can a neural system that has made an error refocus attention on environmental features that it had initially ignored? Three models that address these questions, each based on the distributed adaptive resonance theory (dART) neural network, are applied to a spatial testbed created from multimodal remotely sensed data. The article summarizes key design elements of ART models, and provides links to open-source code for each system and the testbed dataset. WIREs Cogn Sci 2013, 4:707-719. doi: 10.1002/wcs.1260 CONFLICT OF INTEREST: The author has declared no conflicts of interest for this article. For further resources related to this article, please visit the WIREs website.

Common gene expression patterns responsive to mild temperature hyperthermia in normal human fibroblastic cells

PURPOSE

Heat stress induces complex cellular responses, and its detailed molecular mechanisms still remain to be clarified. The objective of this study was to investigate the molecular mechanisms underlying cellular responses to mild hyperthermia (MHT) in normal human fibroblastic (NHF) cells.

MATERIALS AND METHODS

Cells were treated with MHT (41°C, 30 min) and then cultured at 37°C. Gene expression was determined by the GeneChip® system and bioinformatics tools.

RESULTS

Treatment of the NHF cell lines, Hs68 and OUMS-36, with MHT did not affect the cell viability or cell cycle. In contrast, many probe sets were differentially expressed by >1.5-fold in both cell lines after MHT treatment. Of the 1,196 commonly and differentially expressed probe sets analysed by k-means clustering, three gene clusters, Up-I, Down-I and Down-II, were observed. Interestingly, two gene networks were obtained from the up-regulated genes in cluster Up-I. The gene network E contained DDIT3 and HSPA5 and was mainly associated with the biological process of endoplasmic reticulum stress, while the network S contained HBEGF and LIF and was associated with the biological process of cell survival. Eighteen genes were validated by quantitative real-time polymerase chain reaction, consistent with the microarray data, in four kinds of NHF cells.

CONCLUSIONS

Common genes that were differentially expressed and/or acted within a gene network in response to MHT in NHF cells were identified. These findings provide the molecular basis for a further understanding of the mechanisms of the MHT response in NHF cells.

Gene expression in enhanced apoptosis of human lymphoma U937 cells treated with the combination of different free radical generators and hyperthermia

The effects of various free radicals derived from 6-formylpterin (6-FP), alpha-phenyl-tert-butyl nitrone (PBN) and 2,2'-azobis (2-amidinopropane) dihydrochloride (AAPH) combined with hyperthermia, on gene expression in similarly enhanced apoptosis of human lymphoma U937 cells were investigated using cDNA microarrays containing approximately 16,600 genes and computational gene expression analysis tools. When the cells were treated for 10 min at 44 degrees C (15% apoptosis level), 39 up-regulated and 3 down-regulated genes were identified. In the up-regulated genes, apoptosis- and unfolded protein response-associated genes were contained. The combined treatment with heat and either chemical enhanced apoptosis level (approximately 30%) and showed a chemical-specific gene expression pattern. Furthermore, the expression levels of selected genes were confirmed by a real-time quantitative PCR. The present results will provide a basis for further understanding the molecular mechanisms in enhancement of heat-induced apoptosis by different intracellular oxidative stress.

Early growth response-1 mediates downregulation of telomerase in cervical cancer

Early growth response (Egr)-1 is a transcription factor that triggers transcription of downstream genes within 15-30 min of various stimulations. These genes are expressed rapidly through specific promoter activation and mediate cell growth and angiogenesis. Following the previous computational identification of a site that was thought to be an Egr-1 consensus binding site at -273 to -281 in the human telomerase reverse transcriptase (hTERT) promoter region, the present study was conducted to evaluate the role of Egr-1 in the regulation of hTERT and telomerase in uterine cervical cancer. First, the expression of Egr-1 and hTERT at the mRNA level was examined in cervical cancer tissues. Egr-1 and hTERT were expressed much higher in cervical cancer tissues than in the normal cervix. However, a negative correlation was noted in the expression between Egr-1 and hTERT. By luciferase assay using hTERT promoter constructs, hTERT transcriptional activation was shown to be inhibited when Egr-1 was overexpressed. Furthermore, Egr-1 overexpression decreased hTERT protein production as well as hTERT mRNA as observed by western blotting analysis and real-time reverse transcription-polymerase chain reaction, respectively. The present study suggests that Egr-1 plays an important regulatory role in the transcriptional activation of hTERT.

Heat-induced MMP-1 expression is mediated by TRPV1 through PKCalpha signaling in HaCaT cells

BACKGROUND

Matrix metalloproteinase-1 (MMP-1) is considered a key initiator of collagen degradation in inflammatory responses. A heat-gated channel, transient receptor potential vanilloid type 1 (TRPV1), induces release of proinflammatory mediators. TRPV1 channels have been localized to the epidermis and we have recently suggested that they act as mediators of heat-induced MMP-1. The aim of this study was to investigate the signaling of TRPV1 in MMP-1 regulation by heat shock in human epidermal keratinocytes.

METHODS

Heat shock-induced MMP-1 expression was decreased by treatment with TRPV1 inhibitor. The heat-induced MMP-1 expression was suppressed by Gö6976 [calcium-dependent inhibitor] and staurosporine (ST, broad-spectrum PKC inhibitor), while rottlerin (ROT, calcium-independent PKCdelta inhibitor) had no effect. Also, transfection of PKCalpha siRNA decreased MMP-1 expression, whereas MMP-1 expression was not significantly affected in cells transfected with negative control siRNA, PKCbeta siRNA or PKCdelta siRNA.

RESULTS

We demonstrated that heat shock failed to induce MMP-1 expression in HaCaT cells cultured in calcium-free media. The heat-induced [Ca(2+)](i) increase was inhibited by Gö6976 and ST, but not by ROT. We also found that heat-induced phosphorylation of ERK, JNK and p38 MAPK in HaCaT cells, but capsazepine and ruthenium red had no effect on this activation. In addition to the role of TRPV1 in heat-induced MMP-1 expression, we also found that heat increased TRPV1 proteins in human skin in vivo.

CONCLUSIONS

Our results suggest that TRPV1 mediates heat shock-induced MMP-1 expression via calcium-dependent PKCalpha signaling in HaCaT cells.

Transient receptor potential vanilloid-1 mediates heat-shock-induced matrix metalloproteinase-1 expression in human epidermal keratinocytes

Transient receptor potential vanilloid-1 (TRPV1), a heat-gated channel, was recently found on human keratinocytes and the activation of epidermal TRPV1 was known to induce release of proinflammatory mediators. However, the functional consequences of TRPV1 activation in cutaneous physiology and pathology have not been elucidated clearly. In this study, we investigated the role of TRPV1 on the matrix metalloproteinase (MMP)-1 expression induced by heat shock in human epidermal keratinocytes. Heat shock induced the expression of MMP-1 mRNA and protein in a temperature-dependent manner in an immortalized human keratinocyte cell line (HaCaT) and normal human epidermal keratinocytes (NHK). Heat-shock-induced MMP-1 expression was decreased by treatment of the TRPV1 inhibitors (capsazepine and ruthenium red) or knockdown of TRPV1 using RNA interference in HaCaT cells. Overexpression of TRPV1 greatly increased heat-shock-induced MMP-1 promoter activity in HEK 293 cells. Furthermore, direct activation of TRPV1 by capsaicin, a TRPV1 agonist, increased MMP-1 expression. We found that heat shock induced calcium influx through TRPV1 and that extracellular calcium was necessary for heat-shock-induced MMP-1 expression in HaCaT cells. Taken together, our results suggest that heat-shock-induced MMP-1 expression is mediated by activation of TRPV1 and is dependent on a calcium-dependent signaling process in human epidermal keratinocytes.

Increased Body Temperature After Reperfused Acute Myocardial Infarction Is Associated With Adverse Left Ventricular Remodeling

BACKGROUND

Fever is frequently observed in patients with acute myocardial infarction (AMI); however, its prognostic significance remains to be determined. We sought to determine the prognostic significance of increased body temperature (BT) after AMI.

METHODS AND RESULTS

We examined 156 consecutive patients with reperfused first anterior AMI. Axillary BT was serially measured every 6 hours for a week. Patients were divided into quartiles by peak BT from the lowest to highest levels. Peak BT within the first week showed a significant positive correlation with peak C-reactive protein level (P < .0001), but not with peak creatine kinase level. There were positive correlations of peak BT with the incidence of pump failure (P = .022), left ventricular (LV) aneurysm (P = .029), and readmission for heart failure (P = .006). Higher peak BT was associated with greater LV end-diastolic volume (P = .031), greater end-systolic volume (P = .008), and lower LV ejection fraction (P = .014) 2 weeks after AMI. Multiple logistic regression analyses revealed that peak BT quartile was an independent predictor of in-hospital cardiac events (odds ratio = 1.61/quartile, P = .008). Furthermore, peak BT quartile was a significant predictor of readmission for heart failure by Cox proportional hazard model analysis (P = .048).

CONCLUSIONS

Increased BT after AMI was associated with a worse clinical outcome and infarct expansion, suggesting a relationship between systemic inflammatory response and LV remodeling.

Cancer immunotherapy based on intracellular hyperthermia using magnetite nanoparticles: a novel concept of "heat-controlled necrosis" with heat shock protein expression

Heat shock proteins (HSPs) are highly conserved proteins whose syntheses are induced by a variety of stresses, including heat stress. Since the expression of HSPs, including HSP70, protects cells from heat-induced apoptosis, HSP expression has been considered to be a complicating factor in hyperthermia. On the other hand, recent reports have shown the importance of HSPs, such as HSP70, HSP90 and glucose-regulated protein 96 (gp96), in immune reactions. If HSP expression induced by hyperthermia is involved in tumor immunity, novel cancer immunotherapy based on this novel concept can be developed. In such a strategy, a tumor-specific hyperthermia system, which can heat the local tumor region to the intended temperature without damaging normal tissue, would be highly advantageous. To achieve tumor-specific hyperthermia, we have developed an intracellular hyperthermia system using magnetite nanoparticles. This novel hyperthermia system can induce necrotic cell death via HSP expression, which induces antitumor immunity. In the present article, cancer immunology and immunotherapy based on hyperthermia, and HSP expression are reviewed and discussed.

Time-course data analysis of gene expression profiles reveals purR regulon concerns in organic solvent tolerance in Escherichia coli

A time-course gene-expression profile was generated for Escherichia coli TK31 when it was exposed to an organic solvent mixture, and classified by fuzzy adaptive resonance theory (Fuzzy ART). It was found that the purR regulon plays an important role in the organic solvent tolerance (OST) of E. coli.

Analysis of gene expression in apoptosis of human lymphoma U937 cells induced by heat shock and the effects of α-phenyl N-tert-butylnitrone (PBN) and its derivatives

Hyperthermia, a modality of cancer therapy, has been known as a stress to induce apoptosis. However, the molecular mechanism of heat shock-induced apoptosis, especially on roles of intracellular oxidative stress, is not fully understood. First, when human lymphoma U937 cells were treated with heat shock (44 degrees C, 30 min), the fraction of apoptosis, revealed by phosphatidylserine externalization, increased gradually and peaked at 6 hr after the treatment. In contrast, intracellular superoxide formation increased early during the heat shock treatment and peaked at 30 min after the treatment. When the cells were treated with heat shock in the presence of alpha -phenyl-N-tert-butylnitrone (PBN) and its derivatives, which are potent antioxidants, the DNA fragmentation was inhibited in an order according to the agents' hydrophobicity. PBN showing the highest inhibitory effects suppressed not only intracellular superoxide formation but also various apoptosis indicators. cDNA microarray was employed to analyze gene expression associated with heat shock-induced apoptosis, and the time-course microarray analysis revealed 5 groups showing changes in their pattern of gene expression. Among these genes, c-jun mRNA expression showed more than 40 fold increase 2 hr after heat treatment. The expression level of c-jun mRNA verified by quantitative real-time PCR was about 20 fold increase, and c-jun expression was similarly suppressed by PBN and its derivatives. These results suggest that the change of c-jun expression is an excellent molecular marker for apoptosis mediated by intracellular oxidative stress induced by heat shock.