Identification of novel targets for breast cancer by exploring gene switches on a genome scale

Comparative expression of trophoblast cell-surface antigen 2 (TROP2) in the different molecular subtypes of invasive breast carcinoma: An immunohistochemical study of 94 therapy-naive primary breast tumors

BACKGROUND

Sacituzumab govitecan, targeting trophoblast cell-surface antigen 2 (TROP2), is approved for the treatment of triple-negative and hormone receptor-positive/HER2-negative breast cancers. However, detailed studies comparing TROP2 protein expression in the different molecular subtypes of breast cancer are limited, and definitive evidence supporting the use of TROP2 as a biomarker for predicting response to this agent in patients with breast cancer is currently lacking.

OBJECTIVE

To compare the expression of TROP2 in the different molecular subtypes of breast cancer.

METHODS

Immunohistochemical staining for TROP2 was performed on 94 therapy-naive primary invasive breast carcinomas, including 25 luminal A-like, 25 luminal B-like, 19 HER2-like, and 25 triple-negative tumors.

RESULTS

Intermediate to high levels of TROP2 expression were observed in the majority of carcinomas of each molecular subtype, with a wide range of expression in each subtype. Occasional tumors with low or absent TROP2 expression were encountered, including two metaplastic carcinomas which were completely negative for TROP2.

CONCLUSIONS

Our observations support the continued investigation of the efficacy of sacituzumab govitecan in all molecular subtypes of breast carcinoma. Furthermore, the observed wide range of expression of TROP2 suggests that TROP2 may have potential utility as a biomarker for predicting responsiveness to sacituzumab govitecan. If this proves to be the case, then immunohistochemical staining for TROP2 would be critical for identifying those patients whose tumors are completely negative for TROP2, since these patients may be least likely or unlikely to respond to this agent, and alternative therapies may be more appropriate in such instances.

Emerging Intrinsic Therapeutic Targets for Metastatic Breast Cancer

Breast cancer is now the most common cancer worldwide, and it is also the main cause of cancer-related death in women. Survival rates for female breast cancer have significantly improved due to early diagnosis and better treatment. Nevertheless, for patients with advanced or metastatic breast cancer, the survival rate is still low, reflecting a need for the development of new therapies. Mechanistic insights into metastatic breast cancer have provided excellent opportunities for developing novel therapeutic strategies. Although high-throughput approaches have identified several therapeutic targets in metastatic disease, some subtypes such as triple-negative breast cancer do not yet have an apparent tumor-specific receptor or pathway to target. Therefore, exploring new druggable targets in metastatic disease is a high clinical priority. In this review, we summarize the emerging intrinsic therapeutic targets for metastatic breast cancer, including cyclin D-dependent kinases CDK4 and CDK6, the PI3K/AKT/mTOR pathway, the insulin/IGF1R pathway, the EGFR/HER family, the JAK/STAT pathway, poly(ADP-ribose) polymerases (PARP), TROP-2, Src kinases, histone modification enzymes, activated growth factor receptors, androgen receptors, breast cancer stem cells, matrix metalloproteinases, and immune checkpoint proteins. We also review the latest development in breast cancer immunotherapy. Drugs that target these molecules/pathways are either already FDA-approved or currently being tested in clinical trials.

Functional Resilience of Mutually Repressing Motifs Embedded in Larger Networks

Elucidating the design principles of regulatory networks driving cellular decision-making has important implications for understanding cell differentiation and guiding the design of synthetic circuits. Mutually repressing feedback loops between 'master regulators' of cell fates can exhibit multistable dynamics enabling "single-positive" phenotypes: (high A, low B) and (low A, high B) for a toggle switch, and (high A, low B, low C), (low A, high B, low C) and (low A, low B, high C) for a toggle triad. However, the dynamics of these two motifs have been interrogated in isolation in silico, but in vitro and in vivo, they often operate while embedded in larger regulatory networks. Here, we embed these motifs in complex larger networks of varying sizes and connectivity to identify hallmarks under which these motifs maintain their canonical dynamical behavior. We show that an increased number of incoming edges onto a motif leads to a decay in their canonical stand-alone behaviors. We also show that this decay can be exacerbated by adding self-inhibition but not self-activation loops on the 'master regulators'. These observations offer insights into the design principles of biological networks containing these motifs and can help devise optimal strategies for the integration of these motifs into larger synthetic networks.

Value of genomics- and radiomics-based machine learning models in the identification of breast cancer molecular subtypes: a systematic review and meta-analysis

Background

In the era of precision therapy, early classification of breast cancer (BRCA) molecular subtypes has clinical significance for disease management and prognosis. We explored the accuracy of machine learning (ML) models for early classification of BRCA molecular subtypes through a systematic review of the literature currently available.

Methods

We retrieved relevant studies published in PubMed, EMBASE, Cochrane, and Web of Science until 15 April 2022. A prediction model risk of bias assessment tool (PROBAST) was applied for the assessment of risk of bias of a genomics-based ML model, and the Radiomics Quality Score (RQS) was simultaneously used to evaluate the quality of this radiomics-based ML model. A random effects model was adopted to analyze the predictive accuracy of genomics-based ML and radiomics-based ML for Luminal A, Luminal B, Basal-like or triple-negative breast cancer (TNBC), and human epidermal growth factor receptor 2 (HER2). The PROSPERO of our study was prospectively registered (CRD42022333611).

Results

Of the 38 studies were selected for analysis, 14 ML models were based on gene-transcriptomic, with only 4 external validations; and 43 ML models were based on radiomics, with only 14 external validations. Meta-analysis results showed that c-statistic values of the ML based on radiomics for the identification of BRCA molecular subtypes Luminal A, Luminal B, Basal-like or TNBC, and HER2 were 0.76 [95% confidence interval (CI): 0.60-0.96], 0.78 (95% CI: 0.69-0.87), 0.89 (95% CI: 0.83-0.91), and 0.83 (95% CI: 0.81-0.86), respectively. The c-statistic values of ML based on the gene-transcriptomic analysis cohort for the identification of the previously described BRCA molecular subtypes were 0.96 (95% CI: 0.93-0.99), 0.96 (95% CI: 0.93-0.99), 0.98 (95% CI: 0.95-1.00), and 0.97 (95% CI: 0.96-0.98) respectively. Additionally, the sensitivity of the ML model based on radiomics for each molecular subtype ranged from 0.79 to 0.85, while the sensitivity of the ML model based on gene-transcriptomic was between 0.92 and 0.99.

Conclusions

Both radiomics and gene transcriptomics produced ideal effects on BRCA molecular subtype prediction. Compared with radiomics, gene transcriptomics yielded better prediction results, but radiomics was simpler and more convenient from a clinical point of view.

Antibody-drug conjugates targeting TROP-2: Clinical development in metastatic breast cancer

Antibody drug conjugates (ADCs) combine the potent cytotoxicity of chemotherapy with the antigen -specific targeted approach of antibodies into one single molecule. Trophoblast cell surface antigen 2 (TROP-2) is a transmembrane glycoprotein involved in calcium signal transduction and is expressed in multiple tumor types. TROP-2 expression is higher in HER2-negative breast tumors (HR+/HR-) and is associated with worse survival. Sacituzumab govitecan (SG) is a first-in-class TROP-2-directed ADC with an anti-TROP-2 antibody conjugated to SN-38, a topoisomerase inhibitor via a hydrolysable linker. This hydrolysable linker permits intracellular and extracellular release of the membrane permeable payload enabling the "bystander effect" contributing to the efficacy of this agent. There was significant improvement in progression free survival (PFS) and overall survival (OS) with SG versus chemotherapy in pretreated metastatic triple negative breast cancer (TNBC), resulting in regulatory approval. Common adverse events (AE) reported were neutropenia and diarrhea. SG also demonstrated clinical activity versus chemotherapy in a phase III trial of HR+/HER2-metastatic breast cancer (MBC) and is under evaluation in first-line metastatic and early stage TNBC as well. Datopotamab deruxtecan (Dato-DXd) is a TROP-2 ADC that differs from SG in that it has a cleavable tetrapeptide linker and a more potent topoisomerase inhibitor payload. This construct is highly stable in circulation with a longer half-life than SG, and undergoes cleavage in presence of intracellular lysosomal proteases. Dato-DXd demonstrated preliminary efficacy in unselected metastatic TNBC, with common AEs of low-grade nausea and stomatitis. Dato-DXd is being investigated in phase III studies in metastatic TNBC and HR+/HER2- MBC. These novel TROP-2 ADCs have the potential to deliver enhanced efficacy with reduced toxicity in MBC and possibly in early stage breast cancer (EBC).

Alteration of Trop-2 expression in breast cancer cells by clinically used therapeutic agents and acquired tamoxifen resistance

Background

Sacituzumab govitecan is an antibody–drug conjugate that delivers SN-38, an active metabolite of irinotecan, to the target molecule, trophoblast cell-surface antigen 2 (Trop-2). It is a promising drug for triple-negative breast cancer and is anticipated to be effective for luminal breast cancer. The efficacy of the agent relies on the expression of Trop-2 rather than its intracellular function. However, conditions that alter the Trop-2 expression have not been well investigated.

Methods

We tested a range of clinically related treatments for their effect on Trop-2 expression in cultured breast cancer cell lines.

Results

The expression level of Trop-2 differed among cell lines, independent of their subtypes, and was highly variable on treatment with kinase inhibitors, tamoxifen, irradiation, and chemotherapeutic agents including irinotecan. While inhibitors of AKT, RSK, and p38 MAPK suppressed the Trop-2 expression, tamoxifen treatment significantly increased Trop-2 expression in luminal cancer cell lines. Notably, luminal cancer cells with acquired resistance to tamoxifen also exhibited higher levels of Trop-2. We identified transcription factor EB (TFEB) as a possible mechanism underlying tamoxifen-induced elevation of Trop-2 expression. Tamoxifen triggers dephosphorylation of TFEB, an active form of TFEB, and the effect of tamoxifen on Trop-2 was prevented by depletion of TFEB. A luciferase reporter assay showed that Trop-2 induction by TFEB was dependent on a tandem E-box motif within the Trop-2 promoter region.

Conclusions

Overall, these results suggest that the effectiveness of sacituzumab govitecan could be altered by concomitant treatment and that tamoxifen could be a favorable agent for combined therapy.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12282-022-01389-3.

Deciphering the molecular mechanism of the cancer formation by chromosome structural dynamics

Cancer reflects the dysregulation of the underlying gene network, which is strongly related to the 3D genome organization. Numerous efforts have been spent on experimental characterizations of the structural alterations in cancer genomes. However, there is still a lack of genomic structural-level understanding of the temporal dynamics for cancer initiation and progression. Here, we use a landscape-switching model to investigate the chromosome structural transition during the cancerization and reversion processes. We find that the chromosome undergoes a non-monotonic structural shape-changing pathway with initial expansion followed by compaction during both of these processes. Furthermore, our analysis reveals that the chromosome with a more expanding structure than those at both the normal and cancer cell during cancerization exhibits a sparse contact pattern, which shows significant structural similarity to the one at the embryonic stem cell in many aspects, including the trend of contact probability declining with the genomic distance, the global structural shape geometry and the spatial distribution of loci on the chromosome. In light of the intimate structure-function relationship at the chromosomal level, we further describe the cell state transition processes by the chromosome structural changes, suggesting an elevated cell stemness during the formation of the cancer cells. We show that cell cancerization and reversion are highly irreversible processes in terms of the chromosome structural transition pathways, spatial repositioning of chromosomal loci and hysteresis loop of contact evolution analysis. Our model draws a molecular-scale picture of cell cancerization from the chromosome structural perspective. The process contains initial reprogramming towards the stem cell followed by the differentiation towards the cancer cell, accompanied by an initial increase and subsequent decrease of the cell stemness.

Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis

Mycobacterium tuberculosis (MTB) displays the remarkable ability to transition in and out of dormancy, a hallmark of the pathogen’s capacity to evade the immune system and exploit susceptible individuals. Uncovering the gene regulatory programs that underlie the phenotypic shifts in MTB during disease latency and reactivation has posed a challenge. We develop an experimental system to precisely control dissolved oxygen levels in MTB cultures in order to capture the transcriptional events that unfold as MTB transitions into and out of hypoxia-induced dormancy. Using a comprehensive genome-wide transcription factor binding map and insights from network topology analysis, we identify regulatory circuits that deterministically drive sequential transitions across six transcriptionally and functionally distinct states encompassing more than three-fifths of the MTB genome. The architecture of the genetic programs explains the transcriptional dynamics underlying synchronous entry of cells into a dormant state that is primed to infect the host upon encountering favorable conditions.

Mycobacterium tuberculosis (MTB) persists within the host by counteracting disparate stressors including hypoxia. Peterson et al. report a transcriptional program that coordinates sequential state transitions to drive MTB in and out of hypoxia-induced dormancy. Among varied properties, this program encodes advanced preparedness to infect the host in favorable conditions.

Trop2 Promotes Multidrug Resistance by Regulating Notch1 Signaling Pathway in Gastric Cancer Cells

BACKGROUND Chemotherapy is widely used in gastric cancer treatment, but multidrug resistance remains a leading cause of chemotherapy failure. Trop2 is highly expressed in gastric tumor tissues and greatly influences cancer progression. However, little is known about the relationship between Trop2 and drug resistance in gastric cancer. MATERIAL AND METHODS In the present study, Trop2 was knocked down in BGC823 cells and overexpressed in HGC27. CCK-8 assay was performed to explore the relationship of Trop2 expression and cell proliferation treated with anticancer drugs. Flow cytometry was performed to assess the relationship between Trop2 and cell apoptosis after chemotherapy. Subcutaneous xenograft models were generated to explore the curative effect of DDP to GC in vivo. MRP1 and Notch1 expressions were assessed by Western blot. RESULTS Trop2 decreased cell proliferation inhibition and apoptosis after chemotherapeutic treatments. DDP showed stronger therapeutic effects on Trop2-knockdown tumor than control in vivo. MRP1 and Notch1 signaling pathway were confirmed to participate in Trop2-induced drug resistance. CONCLUSIONS Our findings suggest that Trop2 promotes the resistance of gastric cancer to chemotherapy by activating the Notch1 pathway.

Advanced microscopic evaluation of parallel type I and type II cell deaths induced by multi-functionalized gold nanocages in breast cancer

Despite aggressive surgical resections and combinatorial chemoradiations, certain highly malignant populations of tumor cells resurrect and metastasize. Mixed-grade cancer cells fail to respond to standard-of-care therapies by developing intrinsic chemoresistance and subsequently result in tumor relapse. Macroautophagy is a membrane trafficking process that underlies drug resistance and tumorigenesis in most breast cancers. Manipulating cellular homeostasis by a combinatorial nanotherapeutic model, one can evaluate the crosstalk between type I and type II cell death and decipher the fate of cancer therapy. Here, we present a multi-strategic approach in cancer targeting to mitigate the autophagic flux with subcellular toxicity via lysosome permeation, accompanied by mitochondrial perturbation and apoptosis. In this way, a nanoformulation is developed with a unique blend of a lysosomotropic agent, an immunomodulating sulfated-polysaccharide, an adjuvant chemotherapeutic agent, and a monoclonal antibody as a broad-spectrum complex for combinatorial nanotherapy of all breast cancers. To the best of our knowledge, this manuscript illustrates for the first time the applications of advanced microscopic techniques such as electron tomography, three-dimensional rendering and segmentation of subcellular interactions, and fate of the multifunctional therapeutic gold nanocages specifically targeted toward breast cancer cells.

Exploring novel key regulators in breast cancer network

The breast cancer network constructed from 70 experimentally verified genes is found to follow hierarchical scale free nature with heterogeneous modular organization and diverge leading hubs. The topological parameters (degree distributions, clustering co-efficient, connectivity and centralities) of this network obey fractal rules indicating absence of centrality lethality rule, and efficient communication among the components. From the network theoretical approach, we identified few key regulators out of large number of leading hubs, which are deeply rooted from top to down of the network, serve as backbone of the network, and possible target genes. However, p53, which is one of these key regulators, is found to be in low rank and keep itself at low profile but directly cross-talks with important genes BRCA2 and BRCA3. The popularity of these hubs gets changed in unpredictable way at various levels of organization thus showing disassortive nature. The local community paradigm approach in this network shows strong correlation of nodes in majority of modules/sub-modules (fast communication among nodes) and weak correlation of nodes only in few modules/sub-modules (slow communication among nodes) at various levels of network organization.

The Potential Diagnostic Utility of TROP-2 in Thyroid Neoplasms

Objectives:

Human trophoblast cell-surface marker (TROP-2) has been reported to be overexpressed in various human carcinomas (CAs) and suggested to be a prognostic marker for some CAs. The diagnostic utility of TROP-2 in CAs has not been explored.

Methods:

Immunohistochemical evaluation of TROP-2 expression on tissue microarray sections of 136 thyroid neoplasms, surgical specimens of 61 atypical thyroid follicular-patterned lesions [including 33 papillary thyroid carcinomas (PTCs), 17 atypical follicular neoplasms (AFNs), and 11 adenomatoid nodules with focal nuclear atypia (ANFNA)], and 20 benign thyroid lesions, as well as 10 cytology specimens of PTCs was performed. For comparison, immunoassay for Hector Battifora mesothelial-1 (HBME-1), galectin-3, and cytokeratin 19 was performed on the 61 atypical thyroid follicular-patterned lesions.

Results:

Strong membranous staining with TROP-2 was seen in 94% (33/35) of classic PTCs and 81% (30/37) of confirmed follicular variant PTCs on tissue microarray and routine surgical sections, as well as 100% (10/10) of PTCs on cytology specimens; it was not observed in follicular adenomas (n=51) or CAs (n=37), AFNs or ANFNA (n=28), benign (n=20) or normal (n=15) thyroid tissue. In contrast, the expression of HBME-1 and galectin-3 was identified in 100% (33/33) of surgical cases of PTCs and in 57% (16/28) and 50% (14/28) of AFNs and ANFNA, respectively.

Conclusions:

Our findings demonstrate that a membranous TROP-2 staining pattern is highly specific for PTC, which may serve as a potential diagnostic marker aiding in the accurate classification of morphologically equivocal thyroid follicular-patterned lesions.

Characterization of transcription factor response kinetics in parallel

BACKGROUND

Transcription factors (TFs) are effectors of cell signaling pathways that regulate gene expression. TF networks are highly interconnected; one signal can lead to changes in many TF levels, and one TF level can be changed by many different signals. TF regulation is central to normal cell function, with altered TF function being implicated in many disease conditions. Thus, measuring TF levels in parallel, and over time, is crucial for understanding the impact of stimuli on regulatory networks and on diseases.

RESULTS

Here, we report the parallel analysis of temporal TF level changes due to multiple stimuli in distinct cell types. We have analyzed short-term dynamic changes in the levels of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kB), signal transducer and activator of transcription 3 (Stat3), cAMP response element-binding protein (CREB), glucocorticoid receptor (GR), and TATA binding protein (TBP), in breast and liver cancer cells after tumor necrosis factor-alpha (TNF-α) and palmitic acid (PA) exposure. In response to both stimuli, NF-kB and CREB levels were increased, Stat3 decreased, and TBP was constant. GR levels were unchanged in response to TNF-α stimulation and increased in response to PA treatment.

CONCLUSIONS

Our results show significant overlap in signaling initiated by TNF-α and by PA, with the exception that the events leading to PA-mediated cytotoxicity likely also include induction of GR signaling. These results further illuminate the dynamics of TF responses to cytokine and fatty acid exposure, while concomitantly demonstrating the utility of parallel TF measurement approaches in the analysis of biological phenomena.

Rapid fine conformational epitope mapping using comprehensive mutagenesis and deep sequencing

Knowledge of the fine location of neutralizing and non-neutralizing epitopes on human pathogens affords a better understanding of the structural basis of antibody efficacy, which will expedite rational design of vaccines, prophylactics, and therapeutics. However, full utilization of the wealth of information from single cell techniques and antibody repertoire sequencing awaits the development of a high throughput, inexpensive method to map the conformational epitopes for antibody-antigen interactions. Here we show such an approach that combines comprehensive mutagenesis, cell surface display, and DNA deep sequencing. We develop analytical equations to identify epitope positions and show the method effectiveness by mapping the fine epitope for different antibodies targeting TNF, pertussis toxin, and the cancer target TROP2. In all three cases, the experimentally determined conformational epitope was consistent with previous experimental datasets, confirming the reliability of the experimental pipeline. Once the comprehensive library is generated, fine conformational epitope maps can be prepared at a rate of four per day.

Trop-2 is a novel target for solid cancer therapy with sacituzumab govitecan (IMMU-132), an antibody-drug conjugate (ADC)

Trop-2 is a novel target for ADC therapy because of its high expression by many solid cancers. The rational development of IMMU-132 represents a paradigm shift as an ADC that binds a well-known moderately-cytotoxic drug, SN-38, to the anti-Trop-2 antibody. In vitro and in vivo studies show enhanced efficacy, while there is a gradual release of SN-38 that contributes to the overall effect. IMMU-132 is most efficacious at a high drug:antibody ratio (DAR) of 7.6:1, which does not affect binding and pharmacokinetics. It targets up to 136-fold more SN-38 to a human cancer xenograft than irinotecan, SN-38's prodrug. IMMU-132 delivers SN-38 in its most active, non-glucuronidated form, which may explain the lower frequency of severe diarrhea than with irinotecan. Thus, this ADC, carrying a moderately-toxic drug targeting Trop-2 represents a novel cancer therapeutic that is showing promising activity in patients with several metastatic cancer types, including triple-negative breast cancer, non-small-cell and small-cell lung cancers.

Estrogen and tamoxifen up-regulate FXYD3 on breast cancer cells: assessing the differential roles of ER α and ZEB1

Increased expression of the FXYD3 family of proteins has been associated with lung, colorectal, bladder and pancreatic cancers, and recent evidence suggests that elevated FXYD3 may promote tumor cell proliferation in breast cancer as well. However, factors involved in up-regulating the expression of FXYD3 in breast cancer have not been identified. We evaluated whether estrogen and the selective estrogen receptor modulator tamoxifen could regulate the expression of FXYD3 on breast cancer cells. Estrogen receptor (ER) α-positive MCF-7 and ER α-negative MDA-MB-231 human breast cancer cells used in our studies were treated with estrogen, tamoxifen or the combination of these agents. Relative expression of FXYD3 was assessed using fluorochrome-tagged antibodies and a fluorescence cytometer. We found that estrogen and tamoxifen, used alone or in combination, significantly increased FXYD3 on MCF-7 cells. FXYD3 levels did not increase compared to the control samples when ER α-negative 231 cells were treated with estrogen or tamoxifen, alone or in combination, indicating that ER α was required for the increased FXYD3 response. We showed that ER α associates with the transcription factor ZEB1 in MCF-7 cells, and that decreasing ZEB1 protein expression using siRNA disrupts the ability of estrogen, but not tamoxifen, to increase FXYD3 in MCF-7 cells. Our results indicate that there may be two mechanisms, both involving ER α and one requiring ZEB1, through which FXYD3 may be increased by estrogen and tamoxifen in breast cancer cells. Ongoing research endeavors are focusing on identifying cellular components through which estrogen and tamoxifen, alone or in combination, differentially regulate FXYD3 expression in human breast cancer cells.

Trop2 and its overexpression in cancers: regulation and clinical/therapeutic implications

Trop2 is a transmembrane glycoprotein encoded by the Tacstd2 gene. It is an intracellular calcium signal transducer that is differentially expressed in many cancers. It signals cells for self-renewal, proliferation, invasion, and survival. It has stem cell-like qualities. Trop2 is expressed in many normal tissues, though in contrast, it is overexpressed in many cancers and the overexpression of Trop2 is of prognostic significance. Several ligands have been proposed that interact with Trop2. Trop2 signals the cells via different pathways and it is transcriptionally regulated by a complex network of several transcription factors. Trop2 expression in cancer cells has been correlated with drug resistance. Several strategies target Trop2 on cancer cells that include antibodies, antibody fusion proteins, chemical inhibitors, nanoparticles, etc. The in vitro studies and pre-clinical studies, using these various therapeutic treatments, have resulted in significant inhibition of tumor cell growth both in vitro and in vivo in mice. A clinical study is underway using IMMU-132 (hrS7 linked to SN38) in patients with epithelial cancers. This review describes briefly the various characteristics of cancer cells overexpressing Trop2 and the potential application of Trop2 as both a prognostic biomarker and as a therapeutic target to reverse resistance.

Robust prediction of anti-cancer drug sensitivity and sensitivity-specific biomarker

The personal genomics era has attracted a large amount of attention for anti-cancer therapy by patient-specific analysis. Patient-specific analysis enables discovery of individual genomic characteristics for each patient, and thus we can effectively predict individual genetic risk of disease and perform personalized anti-cancer therapy. Although the existing methods for patient-specific analysis have successfully uncovered crucial biomarkers, their performance takes a sudden turn for the worst in the presence of outliers, since the methods are based on non-robust manners. In practice, clinical and genomic alterations datasets usually contain outliers from various sources (e.g., experiment error, coding error, etc.) and the outliers may significantly affect the result of patient-specific analysis. We propose a robust methodology for patient-specific analysis in line with the NetwrokProfiler. In the proposed method, outliers in high dimensional gene expression levels and drug response datasets are simultaneously controlled by robust Mahalanobis distance in robust principal component space. Thus, we can effectively perform for predicting anti-cancer drug sensitivity and identifying sensitivity-specific biomarkers for individual patients. We observe through Monte Carlo simulations that the proposed robust method produces outstanding performances for predicting response variable in the presence of outliers. We also apply the proposed methodology to the Sanger dataset in order to uncover cancer biomarkers and predict anti-cancer drug sensitivity, and show the effectiveness of our method.

IPAF inflammasome is involved in interleukin-1β production from astrocytes, induced by palmitate; implications for Alzheimer's Disease

Inflammatory response has been strongly implicated in the pathogenesis of numerous diseases, including Alzheimer's disease (AD). However, little is known about the molecular mechanisms initiating the generation of inflammatory molecules in the central nervous system, such as interleukin-1β (IL-1β). Previously we identified that palmitate can induce primary astrocytes to produce cytokines, causing AD-like changes in primary neurons. Here we investigated and identified that palmitate induced the activation of ice protease-activating factor (IPAF)-apoptosis-associated speck-like protein containing a caspase activation and recruitment domains (CARD) (ASC) inflammasome in astrocytes leading to the maturation of IL-1β, thereby implicating that not only pathogen-related factors can activate the IPAF-ASC inflammasome. Moreover, downregulating IPAF (which was found to be regulated by cAMP response element-binding protein) in astrocytes through silencing to decrease IL-1β secretion from the astrocytes reduced the generation of amyloid-β42 by primary neurons. Furthermore, the expression levels of IPAF and ASC were found significantly elevated in a subgroup of sporadic AD patients, suggesting an involvement of the IPAF-ASC inflammasome in the inflammatory response associated with AD, and thus could be a potential therapeutic target for AD.

Palmitate induces transcriptional regulation of BACE1 and presenilin by STAT3 in neurons mediated by astrocytes

Deregulation of calcium has been implicated in neurodegenerative diseases, including Alzheimer's disease (AD). Previously, we showed that saturated free-fatty acid, palmitate, causes AD-like changes in primary cortical neurons mediated by astrocytes. However, the molecular mechanisms by which conditioned medium from astrocytes cultured in palmitate induce AD-like changes in neurons are unknown. This study demonstrates that this condition medium from astrocytes elevates calcium level in the neurons, which subsequently increases calpain activity, a calcium-dependent protease, leading to enhance p25/Cdk5 activity and phosphorylation and activation of the STAT3 (signal transducer and activator of transcription) transcription factor. Inhibiting calpain or Cdk5 significantly reduces the upregulation in nuclear level of pSTAT3, which we found to transcriptionally regulate both BACE1 and presenilin-1, the latter is a catalytic subunit of γ-secretase. Decreasing pSTAT3 levels reduced the mRNA levels of both BACE1 and presenilin-1 to near control levels. These data demonstrate a signal pathway leading to the activation of STAT3, and the generation of the amyloid peptide. Thus, our results suggest that STAT3 is an important potential therapeutic target of AD pathogenesis.

A multi-layer inference approach to reconstruct condition-specific genes and their regulation

An important topic in systems biology is the reverse engineering of regulatory mechanisms through reconstruction of context-dependent gene networks. A major challenge is to identify the genes and the regulations specific to a condition or phenotype, given that regulatory processes are highly connected such that a specific response is typically accompanied by numerous collateral effects. In this study, we design a multi-layer approach that is able to reconstruct condition-specific genes and their regulation through an integrative analysis of large-scale information of gene expression, protein interaction and transcriptional regulation (transcription factor-target gene relationships). We establish the accuracy of our methodology against synthetic datasets, as well as a yeast dataset. We then extend the framework to the application of higher eukaryotic systems, including human breast cancer and Arabidopsis thaliana cold acclimation. Our study identified TACSTD2 (TROP2) as a target gene for human breast cancer and discovered its regulation by transcription factors CREB, as well as NFkB. We also predict KIF2C is a target gene for ER-/HER2- breast cancer and is positively regulated by E2F1. The predictions were further confirmed through experimental studies.

AVAILABILITY

The implementation and detailed protocol of the layer approach is available at http://www.egr.msu.edu/changroup/Protocols/Three-layer%20approach%20 to % 20reconstruct%20condition.html.

Quantitative, solution-phase profiling of multiple transcription factors in parallel

Transcription factors are regulatory proteins that bind to specific sites of chromosomal DNA to enact responses to intracellular and extracellular stimuli. Transcription factor signalling networks are branched and interconnected so that any single transcription factor can activate many different genes and one gene can be activated by a combination of different transcription factors. Thus, trying to characterize a cellular response to a stimulus by measuring the level of only one transcription factor potentially ignores important simultaneous events that contribute to the response. Hence, parallel measurements of transcription factors are necessary to capture the breadth of valuable information about cellular responses that would not be obtained by measuring only a single transcription factor. We have sought to develop a new, scalable, flexible, and sensitive approach to analysis of transcription factor levels that complements existing parallel approaches. Here, we describe proof-of-principle analyses of purified human transcription factors and breast cancer nuclear extracts. Our assay can successfully quantify transcription factors in parallel with ~10-fold better sensitivity than current techniques. Sensitivity of the assay can be further increased by 200-fold through the use of PCR for signal amplification.