Polycyclic aromatic hydrocarbons (PAHs) emitted from combustion sources are known to be mutagenic, with more potent species also being carcinogenic. Previous studies show that PAHs can undergo ...complex transformations both in the body and in the atmosphere, yet these transformation processes are generally investigated separately.
Drawing from the literature in atmospheric chemistry and toxicology, we highlight the parallel transformations of PAHs that occur in the atmosphere and the body and discuss implications for public health. We also examine key uncertainties related to the toxicity of atmospheric oxidation products of PAHs and explore critical areas for future research.
We focus on a key mode of toxicity for PAHs, in which metabolic processes (driven by cytochrome P450 enzymes), leads to the formation of oxidized PAHs that can damage DNA. Such species can also be formed abiotically in the atmosphere from natural oxidation processes, potentially augmenting PAH toxicity by skipping the necessary metabolic steps that activate their mutagenicity. Despite the large body of literature related to these two general pathways, the extent to which atmospheric oxidation affects a PAH's overall toxicity remains highly uncertain. Combining knowledge and promoting collaboration across both fields can help identify key oxidation pathways and the resulting products that impact public health.
Cross-disciplinary research, in which toxicology studies evaluate atmospheric oxidation products and their mixtures, and atmospheric measurements examine the formation of compounds that are known to be most toxic. Close collaboration between research communities can help narrow down which PAHs, and which PAH degradation products, should be targeted when assessing public health risks. https://doi.org/10.1289/EHP9984.
Triple negative breast cancer (TNBC) is a heterogeneous group of tumors which lack estrogen receptor, progesterone receptor, and HER2 expression. Targeted therapies have limited success in treating ...TNBC, thus a strategy enabling effective targeted combinations is an unmet need. To tackle these challenges and discover individualized targeted combination therapies for TNBC, we integrated phosphoproteomic analysis of altered signaling networks with patient-specific signaling signature (PaSSS) analysis using an information-theoretic, thermodynamic-based approach. Using this method on a large number of TNBC patient-derived tumors (PDX), we were able to thoroughly characterize each PDX by computing a patient-specific set of unbalanced signaling processes and assigning a personalized therapy based on them. We discovered that each tumor has an average of two separate processes, and that, consistent with prior research, EGFR is a major core target in at least one of them in half of the tumors analyzed. However, anti-EGFR monotherapies were predicted to be ineffective, thus we developed personalized combination treatments based on PaSSS. These were predicted to induce anti-EGFR responses or to be used to develop an alternative therapy if EGFR was not present.In-vivo experimental validation of the predicted therapy showed that PaSSS predictions were more accurate than other therapies. Thus, we suggest that a detailed identification of molecular imbalances is necessary to tailor therapy for each TNBC. In summary, we propose a new strategy to design personalized therapy for TNBC using pY proteomics and PaSSS analysis. This method can be applied to different cancer types to improve response to the biomarker-based treatment.
Human tissue samples commonly preserved as formalin-fixed paraffin-embedded (FFPE) tissues after diagnostic or surgical procedures in the clinic represent an invaluable source of clinical specimens ...for in-depth characterization of signaling networks to assess therapeutic options. Tyrosine phosphorylation (pTyr) plays a fundamental role in cellular processes and is commonly dysregulated in cancer but has not been studied to date in FFPE samples. In addition, pTyr analysis that may otherwise inform therapeutic interventions for patients has been limited by the requirement for large amounts of frozen tissue. Here we describe a method for highly sensitive, quantitative analysis of pTyr signaling networks, with hundreds of sites quantified from one to two 10-μm sections of FFPE tissue specimens. A combination of optimized magnetic bead-based sample processing, optimized pTyr enrichment strategies, and tandem mass tag multiplexing enabled in-depth coverage of pTyr signaling networks from small amounts of input material. Phosphotyrosine profiles of flash-frozen and FFPE tissues derived from the same tumors suggested that FFPE tissues preserve pTyr signaling characteristics in patient-derived xenografts and archived clinical specimens. pTyr analysis of FFPE tissue sections from breast cancer tumors as well as lung cancer tumors highlighted patient-specific oncogenic driving kinases, indicating potential targeted therapies for each patient. These data suggest the capability for direct translational insight from pTyr analysis of small amounts of FFPE tumor tissue specimens. SIGNIFICANCE: This study reports a highly sensitive method utilizing FFPE tissues to identify dysregulated signaling networks in patient tumors, opening the door for direct translational insights from FFPE tumor tissue banks in hospitals.
In assessments of cancer risk from atmospheric polycyclic aromatic hydrocarbons (PAHs), scientists and regulators rarely consider the complex mixture of emitted compounds and degradation products, ...and they often represent the entire mixture using a single emitted compound—benzoapyrene. Here, we show that benzoapyrene is a poor indicator of PAH risk distribution and management: nearly 90% of cancer risk worldwide results from other PAHs, including unregulated degradation products of emitted PAHs. We develop and apply a global‐scale atmospheric model and conduct health impact analyses to estimate human cancer risk from 16 PAHs and several of their N‐PAH degradation products. We find that benzoapyrene is a minor contributor to the total cancer risks of PAHs (11%); the remaining risk comes from other directly emitted PAHs (72%) and N‐PAHs (17%). We show that assessment and policy‐making that relies solely on benzoapyrene exposure provides misleading estimates of risk distribution, the importance of chemical processes, and the prospects for risk mitigation. We conclude that researchers and decision‐makers should consider additional PAHs as well as degradation products.
Plain Language Summary
Nearly 90% of global human lung cancer risk from polycyclic aromatic hydrocarbons (PAHs) comes from compounds omitted by prior analyses and not regulated directly. PAHs in the atmosphere are a complex mixture, but regulators and researchers often represent them using a single compound, namely benzo(a)pyrene. We show that benzo(a)pyrene is a poor indicator of global PAH cancer risk; its use as a proxy leads to erroneous conclusions about high‐risk populations and atmospheric chemical processes. We find that approximately 17% of risk comes from PAHs that are produced in atmospheric reactions and are not regulated or routinely monitored. Regulators and researchers should focus on the entire mixture of PAHs in the atmosphere, and we recommend that benzo(a)pyrene not be used as a sole reference compound.
Key Points
Benzoapyrene is a small contributor to human cancer risk of polycyclic aromatic hydrocarbons (PAHs) worldwide (11%)
Using benzoapyrene as a surrogate compound leads to erroneous conclusions about high‐risk populations and the importance of uncertain chemical processes
Science and policy could be improved by considering a wider group of both emitted PAHs as well as their degradation products
Neoadjuvant chemotherapy (NAC) remains the cornerstone of the treatment for triple negative breast cancer (TNBC), with the goal of complete eradication of disease. However, for patients with residual ...disease after NAC, recurrence and mortality rates are high and the identification of novel therapeutic targets is urgently needed. We quantified tyrosine phosphorylation (pTyr)-mediated signaling networks in chemotherapy sensitive (CS) and resistant (CR) TNBC patient-derived xenografts (PDX), to gain novel therapeutic insights. The antitumor activity of SFK inhibition was examined in vivo. Treated tumors were further subjected to phosphoproteomic and RNAseq analysis, to identify the mechanism of actions of the drug. We identified Src Family Kinases (SFKs) as potential therapeutic targets in CR TNBC PDXs. Treatment with dasatinib, an FDA approved SFK inhibitor, led to inhibition of tumor growth in vivo. Further analysis of post-treatment PDXs revealed multiple mechanisms of actions of the drug, confirming the multi-target inhibition of dasatinib. Analysis of pTyr in tumor specimens suggested a low prevalence of SFK-driven tumors, which may provide insight into prior clinical trial results demonstrating a lack of dasatinib antitumor activity in unselected breast cancer patients. Taken together, these results underscore the importance of pTyr characterization of tumors, in identifying new targets, as well as stratifying patients based on their activated signaling networks for therapeutic options. Our data provide a strong rationale for studying SFK inhibitors in biomarker-selected SFK-driven TNBC.
N-Nitrosodimethylamine (NDMA) is a DNA-methylating agent that has been discovered to contaminate water, food, and drugs. The alkyladenine DNA glycosylase (AAG) removes methylated bases to initiate ...the base excision repair (BER) pathway. To understand how gene-environment interactions impact disease susceptibility, we study Aag-knockout (Aag−/−) and Aag-overexpressing mice that harbor increased levels of either replication-blocking lesions (3-methyladenine 3MeA) or strand breaks (BER intermediates), respectively. Remarkably, the disease outcome switches from cancer to lethality simply by changing AAG levels. To understand the underlying basis for this observation, we integrate a suite of molecular, cellular, and physiological analyses. We find that unrepaired 3MeA is somewhat toxic, but highly mutagenic (promoting cancer), whereas excess strand breaks are poorly mutagenic and highly toxic (suppressing cancer and promoting lethality). We demonstrate that the levels of a single DNA repair protein tip the balance between blocks and breaks and thus dictate the disease consequences of DNA damage.
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•AAG-initiated base excision repair modulates susceptibility to NDMA-induced disease•Low AAG increases susceptibility to methylation-induced mutations and liver cancer•High AAG activity sensitizes animals to hepatotoxicity and lethality from NDMA•Integration of phenotypes over time reveals progression of NDMA-induced pathologies
The environmental contaminant N-nitrosodimethylamine (NDMA) creates replication-blocking 3-methyladenine (3MeA) DNA lesions. Here, Kay et al. demonstrate that excision of 3MeA by the AAG glycosylase to initiate base excision repair prevents NDMA-induced mutations and cancer in the mouse liver, but excess AAG activity leads to hepatotoxicity and animal lethality.
Abstract
Background
Response to targeted therapy varies between patients for largely unknown reasons. Here, we developed and applied an integrative platform using mass spectrometry imaging (MSI), ...phosphoproteomics, and multiplexed tissue imaging for mapping drug distribution, target engagement, and adaptive response to gain insights into heterogeneous response to therapy.
Methods
Patient-derived xenograft (PDX) lines of glioblastoma were treated with adavosertib, a Wee1 inhibitor, and tissue drug distribution was measured with MALDI-MSI. Phosphoproteomics was measured in the same tumors to identify biomarkers of drug target engagement and cellular adaptive response. Multiplexed tissue imaging was performed on sister sections to evaluate spatial co-localization of drug and cellular response. The integrated platform was then applied on clinical specimens from glioblastoma patients enrolled in the phase 1 clinical trial.
Results
PDX tumors exposed to different doses of adavosertib revealed intra- and inter-tumoral heterogeneity of drug distribution and integration of the heterogeneous drug distribution with phosphoproteomics and multiplexed tissue imaging revealed new markers of molecular response to adavosertib. Analysis of paired clinical specimens from patients enrolled in the phase 1 clinical trial informed the translational potential of the identified biomarkers in studying patient’s response to adavosertib.
Conclusions
The multimodal platform identified a signature of drug efficacy and patient-specific adaptive responses applicable to preclinical and clinical drug development. The information generated by the approach may inform mechanisms of success and failure in future early phase clinical trials, providing information for optimizing clinical trial design and guiding future application into clinical practice.
Phosphorylation plays a fundamental role in cellular processes, and it is commonly dysregulated in cancer. Characterization of phosphorylation mediated signaling networks in tumors can inform ...therapeutic interventions. Additionally, analysis of phosphoproteome in response to drug candidates can help identify biomarkers for therapeutic response as well as lend direct insights into potential adaptive resistance mechanisms. However, quantification of phosphoproteome, especially the translationally relevant low abundant signals including tyrosine and pathway specific phosphorylation, is limited in the clinic. Here, we describe mass spectrometry based methods and their applications for quantitative analysis of low level phosphoproteome in preclinical models and patient tumors.;
;
In the first part, we describe a method for highly sensitive and quantitative analysis of tyrosine phosphorylation from 1 to 2 10-µm sections of formalin fixed paraffin embedded (FFPE) clinical tissue specimens, opening the doors for direct translational insights from FFPE tumor tissue banks in hospitals. In the second part, we present an integrative platform using mass spectrometry imaging, phosphoproteomics and multiplexed tissue imaging for mapping drug distribution, target engagement, and adaptive response to gain insights into heterogeneous response to therapy. In the last part of thesis, we demonstrate the application of quantitative tyrosine phosphorylation in identifying novel therapeutic targets in chemotherapy resistant triple negative breast cancer tumors. Together these approaches highlight the importance of low level phosphorylation signals to serve as biomarkers and inform novel therapeutic strategies.
Ph.D.
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