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Posts Tagged ‘Cancer – General’

Lymphatic Cancer Metastasis Model

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

How Stress Affects Cancer’s Spread

A mouse study reveals how chronic stress remodels lymphatic vasculature to facilitate the spread of tumor cells.

By Catherine Offord | March 1, 2016

http://www.the-scientist.com/?articles.view/articleNo/45476/title/How-Stress-Affects-Cancer-s-Spread

http://www.the-scientist.com/images/News/March2016/lymph.gif

Green fluorescently-tagged nanospheres flow through a lymph vessel from an unstressed mouse (top) and a mouse that has been administered the stress hormone norepinephrine (bottom). Scale bar: 20 μmNATURE COMMUNICATIONS, LE ET AL.

Stress is implicated in increased tumor progression risk and poor survival in cancer patients. A number of recent studies have linked these effects to the promotion of tumor cell dissemination through the bloodstream via stress-induced pathways. Now, a mouse study led by researchers in Australia has revealed the mechanisms by which stress modulates cancer’s spread through another transport network open to tumor cells—the lymphatic system. The findings were published today (March 1) in Nature Communications.

Chronic stress in mice remodels lymph vasculature to promote tumour cell dissemination

Caroline P. LeCameron J. NowellCorina Kim-FuchsEdoardo Botteri, …., Andreas MöllerSteven A. Stacker Erica K. Sloan
Nature Communications  7,  Article number:10634    doi:10.1038/ncomms10634

Chronic stress induces signalling from the sympathetic nervous system (SNS) and drives cancer progression, although the pathways of tumour cell dissemination are unclear. Here we show that chronic stress restructures lymphatic networks within and around tumours to provide pathways for tumour cell escape. We show that VEGFC derived from tumour cells is required for stress to induce lymphatic remodelling and that this depends on COX2 inflammatory signalling from macrophages. Pharmacological inhibition of SNS signalling blocks the effect of chronic stress on lymphatic remodelling in vivo and reduces lymphatic metastasis in preclinical cancer models and in patients with breast cancer. These findings reveal unanticipated communication between stress-induced neural signalling and inflammation, which regulates tumour lymphatic architecture and lymphogenous tumour cell dissemination. These findings suggest that limiting the effects of SNS signalling to prevent tumour cell dissemination through lymphatic routes may provide a strategy to improve cancer outcomes.

In everyday life, we encounter stressful experiences that pose a threat to physiological homeostasis. These threats trigger stress responses, including activation of the sympathetic nervous system (SNS), which leads to elevated local and systemic levels of catecholaminergic neurotransmitters that signal to cells1. Stress-induced SNS signalling is important to enhance alertness and physiological functions for rapid reaction to threat2. However, chronic periods of stress can be detrimental to health by increasing inflammation and promoting the progression of diseases including cancer3, 4, 5, 6. Clinical studies have linked experience of stressful events to poor cancer survival7, 8. This is supported by preclinical studies that show chronic stress promotes cancer progression3, 4, 6. These studies found that stress recruits inflammatory cells to tumours and increases the formation of blood vessels3, 6, which may provide routes for tumour cell dissemination. In addition to dissemination through blood vessels, cancer cells also escape from tumours through lymphatic vasculature9, 10, 11.

The lymphatic system plays an important role in immune function and therefore can influence the trajectory of disease progression. Under normal physiological conditions, the lymphatic system maintains homeostasis by directing cells and solutes from the interstitial fluid of peripheral tissues through lymphatic vessels and into lymph nodes, where they undergo immune examination12, 13. In addition, the lymphatic system aids in the resolution of inflammation by transporting immune cells away from sites of infection14. In cancer, the lymphatic system contributes to disease progression by providing a pathway for tumour cell escape while also being a rich source of chemokines that can promote the invasive properties of tumour cells15. Furthermore, tumour-draining lymph nodes and associated lymphatic endothelium have been shown to develop an immunosuppressive environment, which promotes immune tolerance to the cancer and facilitates tumour growth and spread16, 17, 18. The importance of the lymphatic system in cancer progression is supported by vast clinical data that show tumour-associated lymphatic vessel density (LVD), tumour cell invasion into lymphatic vasculature and the presence of tumour cells in lymph nodes are each associated with increased clinical tumour stage and reduced disease-free survival19, 20,21.

The lymphatic system is innervated by fibres of the SNS22, and acute SNS activity has been shown to increase lymphatic vessel contraction23, 24 and lymphocyte output into lymphatic circulation25. However, little is known about whether stress-induced SNS signalling affects tumour lymphatic vasculature and the consequences this may have on cancer progression.

In this study, we show that chronic stress increases intratumoural LVD while also inducing dilation and increasing flow in lymphatic vessels that drain metastatic tumour cells into lymphatic circulation. Inhibition of COX2 activity blocked the effect of stress on lymphatic vascular remodelling, and showed a key role for macrophage-mediated inflammation in the effects of stress. In addition, we show a critical role for tumour cell-derived VEGFC in the effects of stress on lymphatic vasculature. In both clinical and preclinical studies we demonstrate that disrupting SNS regulation of lymphatics, by blocking β-adrenoceptor signalling, protects against lymphatic dissemination and cancer progression. These findings identify stress signalling as a regulator of lymphatic remodelling and provide evidence for the feasibility of clinically targeting SNS regulation of lymphatics to prevent tumour cell dissemination through lymphatic routes.

Figure 1: Chronic stress remodels tumour-associated lymphatic architecture to promote lymph node metastasis.

Chronic stress remodels tumour-associated lymphatic architecture to promote lymph node metastasis.

http://www.nature.com/ncomms/2016/160301/ncomms10634/images_article/ncomms10634-f1.jpg

(a) Schematic representation of the chronic stress paradigm. (b) Quantification and representative images of tumour LVD (LYVE-1+, green; nuclear, blue) immunostaining of MDA-MB-231 orthotopic tumours. Scale bar, 200μm (n=5). (c) Quantification of MDA-MB-231 primary tumour size in control or stressed BALB/c nu/nu mice over time (n=5 at each time point). (d) Quantification and representative images of tumour-draining lymphatic vessel diameter (LV, blue) in mice with MDA-MB-231 tumours. Scale bar, 1mm (ngreater than or equal to7). (e) Left: skin flap preparation after injection of Patent Blue V dye into the primary tumour (PT) showing the dye taken up into the tumour-draining LV and into the tumour-draining axillary lymph node (AxLN). The LV is adjacent to a blood vessel (BV). Right top panel: epifluorescence image of mCherry-tagged MDA-MB-231 tumour cells (TCs, red) that had spontaneously disseminated from orthotopic PT and were present in the tumour-draining LV that contained microspheres (green) and was adjacent to an autofluorescent BV. Right lower panel: corresponding maximum projection of multiphoton image. Scale bar, 100μm (Supplementary Movie 1). (f) Representative in vivo bioluminescence image of orthotopic MDA-MB-231 breast cancer model showing PT, and spontaneous metastasis to draining lymph node (LN) and lung 21 days after tumour cell injection. (g) Representative images of LN and lung metastasis and quantification of metastasis by ex vivo bioluminescence (BLI) imaging in control versus stressed mice with MDA-MB-231 tumours (n=5). (h) Metastasis in vivo over time (n=5 at each time point). (i) LN metastasis in mice that were negative or positive for tumour cells in collecting lymphatic vessels (ngreater than or equal to13). (j) Ex vivo quantification of bioluminescence from LN at day 28 of 66cl4 tumour progression from control or stressed mice (n=5). (k) Area of lymph node metastasis when primary tumour diameter reached 12mm in control or stressed MMTV-PyMT mice (ngreater than or equal to8). Experiments were completed 2–4 times. All data represent mean±s.e. **P<0.01 and ***P<0.001 by Student’s t-test or Mann–Whitney U-test (post hocBonferroni correction).

 

Figure 7: Stress-induced lymphatic remodelling

Stress-induced lymphatic remodelling.

http://www.nature.com/ncomms/2016/160301/ncomms10634/images_article/ncomms10634-f7.jpg

Stress remodels lymphatic vasculature through a tumour neural-inflammatory axis to promote lymphogenous tumour cell dissemination and metastasis. Tumour cell-derived VEGFC is necessary for stress-enhanced lymphatic remodelling but is not directly activated by β-adrenoceptor signalling. Tumour-associated macrophages respond to β-adrenoceptor signalling to produce inflammatory molecules such as PGE2, which may then signal to tumour cells to produce VEGFC required for lymphatic remodelling. These effects may be clinically blocked using BBs, anti-VEGFC therapeutics (αVEGFC) or COX2 inhibitors (COX2i). E, epinephrine; NE, norepinephrine; β-AR, β-adrenoceptor.

 

These findings suggest that it may be important to identify stressed individuals who may be particularly susceptible to lymphogenous dissemination. One approach may be through transcriptional profiling using a stress signature55. Alternatively, as cancer is often a highly stressful experience, it is plausible that SNS intervention may be generally useful to improve cancer outcome. In support of that contention, we found here that clinical BB use was linked to a significant reduction in lymph node metastasis (and reduced distant metastasis) in a cancer cohort without prior evaluation of stress levels.

Stress regulation of lymphatic vasculature may have evolved to promote survival during times of threat. Co-ordinated regulation of the fight-or-flight stress response with increased lymphatic function may have provided an evolutionary advantage by enhancing immune surveillance and activating a rapid immune response to physical threat. However, the findings presented here demonstrate that SNS-regulated lymphatic function can have adverse effects in the context of chronic diseases such as cancer. Importantly, these findings identify multiple points of clinical intervention to limit these adverse effects of stress.

 

“Stress not only affects your well-being, but it also affects your biology,” said study coauthor Erica Sloan, a cancer researcher at Monash University in Melbourne. “Our study particularly highlights the early steps of tumor cell dissemination into the lymphatic system.”

“This is an excellent contribution,” said Kari Alitalo, a professor of translational cancer biology at the University of Helsinki, Finland, who was not involved in the study. “It’s certainly a very refreshing, novel aspect of biology that they explore in this paper.”

Chronic stress, mediated partly through the sympathetic nervous system, has been associated in cancer patients with a number of physiological changes that promote metastasis (the spread of cancer), including the promotion of blood vessel formation and the recruitment of inflammatory cells like macrophages.

To investigate whether stress could also induce changes in lymph vasculature, the researchers subjected various types of mammary tumor–bearing mice—including strains genetically engineered to develop tumors spontaneously, as well as animals given tumor transplants—to a paradigm designed to induce chronic stress: confinement in a tight space. Comparing stressed mice to controls that bore the same cancerous tumors but had been kept in normal cage conditions, the researchers found no difference in primary tumor growth, but significant differences in lymph vasculature architecture and the frequency of metastases.

“We found that stress helps to build new lymphatic freeways out of the tumor [and] modulates how quickly lymph flows through lymph vessels,” said Sloan, adding that “stress increases the speed limit on these little lymphatic highways and helps cells transit more quickly out of the tumor.”

Since tumor cell dissemination is a key step in cancer metastasis, the team wanted to test whether dissemination through the lymphatic system could be reduced by blocking stress signaling pathways. The researchers turned to beta-blockers—cheap, widely available drugs commonly used to treat hypertension—which inhibit signaling of norepinephrine (or noadrenaline), a stress hormone already implicated in cancer progression risk.

Administering beta-blockers to tumor-bearing mice, the researchers were able to minimize changes in the density of lymph vessels at the primary tumor site, and subsequently reduce metastasis to the lymph nodes. By contrast, artificially stimulating norepinephrine receptors increased both lymph vessel density and metastasis. Through a series of further experiments, the team demonstrated important roles for macrophages involved in inflammatory signaling and a set of tumor-secreted vascular endothelial growth factors (VEGFs) in the regulation of lymph vasculature remodeling and tumor cell dissemination.

“It’s an important step in understanding how stress pathways can influence metastasis,” said Anil Sood, a professor of translational research at MD Anderson Cancer Center in Houston, Texas, who was not involved in the research. “It really helps us to understand the possible mechanisms by which sympathetic nervous system pathways can affect how lymphatics may be remodeled.”

The study also included an analysis of observational data from a cohort of nearly 1,000 breast cancer patients in Milan, which corroborate the team’s findings in mice: patients taking beta-blockers showed a significantly lower incidence of lymph node and distant metastases, even once potentially confounding factors such as age and treatment type had been taken into account.

But Alitalo cautioned against drawing strong conclusions from these data. “Stress biology is complex,” he said. “In laboratory conditions with mice, it’s easier to define and measure stress. In real life, these things fluctuate a lot, especially in cancer patients.” He added that beta-blockers show “no specificity to the lymphatic system, so [their] effects as such could be transduced via a variety of pathways.”

Sloan and colleagues are now working to further resolve the molecular mechanisms involved in stress-induced remodeling of the tumor microenvironment in mice, and are investigating potential interactions between beta-blockers and standard cancer treatments, with a view to using the drugs to tackle stress-related metastasis risk in the clinic.

“This is something that, when we treat cancer, we should be considering,” Sloan said. “By actually addressing stress in the patient, we’re giving our cancer therapies a better chance to work.”

C.P. Le et al., “Chronic stress in mice remodels lymph vasculature to promote tumour cell dissemination,” Nature Communications, http://dx.doi.org:/10.1038/ncomms10634,2016.

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Nanoparticle Delivery to Cancer Drug Targets

Curator: Larry H. Bernstein, MD, FCAP

UPDATED 8/05/2022

 

 

 

Image for unlabelled figure

Lipid-based drug delivery (LBDD) systems have gained much importance in the recent years due to their ability to improve the solubility and bioavailability of drugs with poor water solubility9. The absorption of drug from lipid based formulation depends on numerous factors, including particle size, degree of emulsification, rate of dispersion and precipitation of drug upon dispersion4 and 10.
Diagram of liposome showing a phospholipid bilayer surrounding an aqueous interior
This diagram shows several ways in which transport across the BBB works. For nanoparticle delivery across the BBB, the most common mechanisms are receptor-mediated transcytosis and adsorptive transcytosis
Wikipedia
Targeted Polymeric Nanotherapeutics
Author: Jeff Hrkach

New drug-delivery strategies will lead to safer, more effective treatments for previously intractable diseases.

This paper provides an overview of steps being taken by BIND Biosciences Inc. to translate innovative research conducted at the Massachusetts Institute of Technology (MIT) and Harvard Medical School into novel, targeted, polymeric nanotherapeutics.

Figure 1 Schematic diagram of a BIND targeted polymeric nanoparticle.
Schematic diagram of a BIND targeted polymeric nanoparticle.

Drugs delivered by nanoparticles hold promise for targeted treatment of many diseases, including cancer. However, the particles have to be injected into patients, which has limited their usefulness so far.

Now, researchers from MIT and Brigham and Women’s Hospital (BWH) have developed a new type of nanoparticle that can be delivered orally and absorbed through the digestive tract, allowing patients to simply take a pill instead of receiving injections.

The BIND Targeted Nanoparticle
BIND Biosciences Inc. (BIND), a biopharmaceutical company that was founded upon the research of two pioneers in nanoparticle drug delivery, Professor Robert Langer of MIT and Professor Omid Farokhzad of Brigham and Women’s Hospital of the Harvard Medical School, has developed methods of engineering targeted nanoparticles composed of biodegradable and biocompatible polymers with precise biophysicochemical properties optimized to deliver drugs for specific therapeutic applications (Gu et al., 2008).

The foundational research by Langer and Farokhzad put BIND in a position to pursue the development of targeted polymeric nanotherapeutics for treating several diseases. BIND’s lead program is focused on translating their innovative academic findings into improved treatments for patients with cancer. The BIND technology offers a unique combination of long-circulating nanoparticles with the capability of targeting diseased cells specifically and releasing drugs from nanoparticles in a programmable, controlled way.

Figure 1 is a schematic diagram of a BIND targeted nanoparticle. The targeting ligand enables the nano-particle to recognize specific proteins or receptors on the surface of cells involved in disease, or in the surrounding extracellular matrix, and bind, with high specificity and avidity, to its intended cellular target site. Many types of cancer have been shown to have cell-surface receptors that are highly expressed on the cancer cells (e.g., prostate cancer [prostate-specific membrane antigen, PSMA], breast cancer [human epidermal growth factor receptor 2, HER-2], and lung cancer [epidermal growth factor receptor, EGFR]), and many drugs are being evaluated that might improve treatment outcomes.

Surface Functionalization
Surface functionalization imparted by a PEG component shields the targeted nanoparticles from MPS immune clearance, while providing an attachment site for the targeting ligand on the particle surface at precise, controlled levels through proprietary linkage strategies. A key to the successful development of BIND targeted nanoparticles is the optimization of the nanoparticle surface, which requires a precise balance between the targeting ligand and PEG coverage so the nanoparticle surface is masked enough to provide circulation times long enough to reach the disease site and enough targeting ligand on the surface to effectively bind to the target cell surface receptors. This delicate balance requires precise control over the nanoparticle production process. It also requires the discovery and selection of ligands that are potent and specific enough to bind selectively to the targeted disease cells while remaining bound to the nanoparticle surface.

The polymer matrix, the bulk of the nanoparticle composition, encapsulates the drug in a matrix of clinically safe, validated biodegradable and biocompatible polymers that can be designed to provide appropriate particle size, drug-loading level, drug-release profile, and other critical properties. A variety of drugs or therapeutic payloads can be incorporated into the targeted nanoparticles, including small molecules, peptides, proteins, and nucleic acids, such as siRNA.

Composite magnetic nanoparticle drug delivery system
US 20120265001 A1
ABSTRACT

A composite magnetic nanoparticle drug delivery system provides targeted controlled release chemotherapies for cancerous tumors and inflammatory diseases. The magnetic nanoparticle includes a biocompatible and biodegradable polymer, a magnetic nanoparticle, the biological targeting agent human serum albumin, and a therapeutic pharmaceutical composition. The composite nanoparticles are prepared by oil-in-oil emulsion/solvent evaporation and high shear mixing. An externally applied magnetic field draws the magnetic nanoparticles to affected areas. The biological targeting agent draws the nanoparticles into the affected tissues. Polymer degradation provides controlled time release delivery of the pharmaceutical agent.

WO2012051220A1
Patent Drawing
Patent Drawing
Nanoparticle delivery systems for cancer therapy: advances in clinical and preclinical research.
Nanoparticle drug delivery systems exploit the abnormal characteristics of tumour tissues to selectively target their payloads to cancer cells, either by passive, active or triggered targeting.
Drug delivery and nanoparticles: Applications and hazards
The use of nanotechnology in medicine and more specifically drug delivery is set to spread rapidly. Currently many substances are under investigation for drug delivery and more specifically for cancer therapy. Interestingly pharmaceutical sciences are using nanoparticles to reduce toxicity and side effects of drugs and up to recently did not realize that carrier systems themselves may impose risks to the patient. The kind of hazards that are introduced by using nanoparticles for drug delivery are beyond that posed by conventional hazards imposed by chemicals in classical delivery matrices. For nanoparticles the knowledge on particle toxicity as obtained in inhalation toxicity shows the way how to investigate the potential hazards of nanoparticles. The toxicology of particulate matter differs from toxicology of substances as the composing chemical(s) may or may not be soluble in biological matrices, thus influencing greatly the potential exposure of various internal organs. This may vary from a rather high local exposure in the lungs and a low or neglectable exposure for other organ systems after inhalation. However, absorbed species may also influence the potential toxicity of the inhaled particles. For nanoparticles the situation is different as their size opens the potential for crossing the various biological barriers within the body. From a positive viewpoint, especially the potential to cross the blood brain barrier may open new ways for drug delivery into the brain. In addition, the nanosize also allows for access into the cell and various cellular compartments including the nucleus. A multitude of substances are currently under investigation for the preparation of nanoparticles for drug delivery, varying from biological substances like albumin, gelatine and phospholipids for liposomes, and more substances of a chemical nature like various polymers and solid metal containing nanoparticles. It is obvious that the potential interaction with tissues and cells, and the potential toxicity, greatly depends on the actual composition of the nanoparticle formulation. This paper provides an overview on some of the currently used systems for drug delivery. Besides the potential beneficial use also attention is drawn to the questions how we should proceed with the safety evaluation of the nanoparticle formulations for drug delivery. For such testing the lessons learned from particle toxicity as applied in inhalation toxicology may be of use. Although for pharmaceutical use the current requirements seem to be adequate to detect most of the adverse effects of nanoparticle formulations, it can not be expected that all aspects of nanoparticle toxicology will be detected. So, probably additional more specific testing would be needed.

Recent years have witnessed unprecedented growth of research and applications in the area of nanoscience and nanotechnology. There is increasing optimism that nanotechnology, as applied to medicine, will bring significant advances in the diagnosis and treatment of disease. Anticipated applications in medicine include drug delivery, both in vitro and in vivo diagnostics, nutraceuticals and production of improved biocompatible materials (Duncan 2003; De Jong et al 2005; ESF 2005; European Technology Platform on Nanomedicine 2005; Ferrari 2005). Engineered nanoparticles are an important tool to realize a number of these applications. It has to be recognized that not all particles used for medical purposes comply to the recently proposed and now generally accepted definition of a size ≤100 nm (The Royal Society and Royal Academy of Engineering 2004). However, this does not necessarily has an impact on their functionality in medical applications. The reason why these nanoparticles (NPs) are attractive for medical purposes is based on their important and unique features, such as their surface to mass ratio that is much larger than that of other particles, their quantum properties and their ability to adsorb and carry other compounds. NPs have a relatively large (functional) surface which is able to bind, adsorb and carry other compounds such as drugs, probes and proteins. However, many challenges must be overcome if the application of nanotechnology is to realize the anticipated improved understanding of the patho-physiological basis of disease, bring more sophisticated diagnostic opportunities, and yield improved therapies. Although the definition identifies nanoparticles as having dimensions below 0.1 μm or 100 nm, especially in the area of drug delivery relatively large (size >100 nm) nanoparticles may be needed for loading a sufficient amount of drug onto the particles. In addition, for drug delivery not only engineered particles may be used as carrier, but also the drug itself may be formulated at a nanoscale, and then function as its own “carrier” (Cascone et al 2002; Baran et al 2002; Duncan 2003; Kipp 2004). The composition of the engineered nanoparticles may vary. Source materials may be of biological origin like phospholipids, lipids, lactic acid, dextran, chitosan, or have more “chemical” characteristics like various polymers, carbon, silica, and metals. The interaction with cells for some of the biological components like phospholipids will be quite different compared to the non biological components such as metals like iron or cadmium. Especially in the area of engineered nanoparticles of polymer origin there is a vast area of possibilities for the chemical composition.

Although solid NPs may be used for drug targeting, when reaching the intended diseased site in the body the drug carried needs to be released. So, for drug delivery biodegradable nanoparticle formulations are needed as it is the intention to transport and release the drug in order to be effective. However, model studies to the behavior of nanoparticles have largely been conducted with non-degradable particles. Most data concerning the biological behavior and toxicity of particles comes from studies on inhaled nanoparticles as part of the unintended release of ultrafine or nanoparticles by combustion derived processes such as diesel exhaust particles (reviewed by Oberdörster 1996; Donaldson et al 2001, 2004; Borm 2002;Donaldson and Stone 2003; Dreher 2004; Kreyling et al 2004; Oberdörster, Oberdörster et al 2005). Research has demonstrated that exposure to these combustion derived ultrafine particles/nanoparticles is associated with a wide variety of effects (Donaldson et al 2005) including pulmonary inflammation, immune adjuvant effects (Granum and Lovik 2002) and systemic effects including blood coagulation and cardiovascular effects (Borm and Kreyling 2004;Oberdorster, Oberdörster et al 2005). Since the cut-off size for both ultrafine and nanoparticles (100 nm) is the same, now both terms are used as equivalent. Based on the adverse effects of ultrafine particles as part of environmental pollution, engineered nanoparticles may be suspected of having similar adverse effects. It is the purpose of this review to use this database on combustion derived nanpoarticles (CDNP) obtained by inhalation toxicology and epidemiology and bridge the gap to engineered nanoparticles.

Nanoparticles and drug delivery

Drug delivery and related pharmaceutical development in the context of nanomedicine should be viewed as science and technology of nanometer scale complex systems (10–1000 nm), consisting of at least two components, one of which is a pharmaceutically active ingredient (Duncan 2003; Ferrari 2005), although nanoparticle formulations of the drug itself are also possible (Baran et al 2002; Cascone et al 2002; Duncan 2003; Kipp 2004). The whole system leads to a special function related to treating, preventing or diagnosing diseases sometimes called smart-drugs or theragnostics (LaVan et al 2003). The primary goals for research of nano-bio-technologies in drug delivery include:

  • More specific drug targeting and delivery,
  • Reduction in toxicity while maintaining therapeutic effects,
  • Greater safety and biocompatibility, and
  • Faster development of new safe medicines.

The main issues in the search for appropriate carriers as drug delivery systems pertain to the following topics that are basic prerequisites for design of new materials. They comprise knowledge on (i) drug incorporation and release, (ii) formulation stability and shelf life (iii) biocompatibility, (iv) biodistribution and targeting and (v) functionality. In addition, when used solely as carrier the possible adverse effects of residual material after the drug delivery should be considered as well. In this respect biodegradable nanoparticles with a limited life span as long as therapeutically needed would be optimal.

Table 1  presents some of the types of chemical structures and possibilities for the preparation of nanoscale materials used as pharmaceutical carrier system (reviewed in Borm and Muller-Schulte 2006). Certainly none of the so far developed carriers fulfill all the parameters mentioned above to the full extent; the progress made in nanotechnology inter alia emerging from the progress in the polymer-chemistry, however, can provide an intriguing basis to tackle this issue in a promising way.

Table 1

Overview of nanoparticles and their applications in Life Sciences

Particle class Materials Application
Natural materials or derivatives Chitosan
Dextrane
Gelatine
Alginates
Liposomes
Starch
Drug/Gene delivery
Dendrimers Branched polymers Drug delivery
Fullerenes Carbon based carriers Photodynamics
Drug delivery
Polymer carriers Polylactic acid
Poly(cyano)acrylates
Polyethyleinemine
Block copolymers
Polycaprolactone
Drug/gene delivery
Ferrofluids SPIONS
USPIONS
Imaging (MRI)
Quantum dots Cd/Zn-selenides Imaging
In vitro diagnostics
Various Silica-nanoparticles
Mixtures of above
Gene delivery

Nanoparticle delivery system to tackle cancer

Directing drug treatment to tumors is a hit-or-miss activity. Considerable research efforts are going into improving targeted drug delivery. A new approach centers on nanotechnology
Nanoparticle delivery system to tackle cancer 

Cancer drugs are injected into the bloodstream and move through the body seeking out fast-growing cancer cells. One consequence of chemotherapy is the unintended effect on different parts of the body, including messing up the digestive system. Such side effects can be minimized if the drug is better targeted.

Another consequence of the poor targeting of some chemo drugs is that they miss cancer cells entirely.

For these reasons, different research groups are focusing on drug delivery: finding smart ways to direct the anti-cancer drug to the required target. One such research team is led by Professor Warren Chan of the University of Texas.

Professor Chan thinks the answer to more effective targeting is the use of nanoparticles. In trials, the research group has used nanoparticles attached to strands of DNA that can, remarkably, change shape to gain improved access to cancerous tissue.

Interviewed by Pharmaceutical Processing, Professor Chan explains: “Your body is basically a series of compartments.” He added: “Think of it as a giant house with rooms inside. We’re trying to figure out how to get something that’s outside, into one specific room.”

The complication with the approach is based on different cancers. Because different types of cancer differ in morphology, and cancers at different stages equally vary, selecting the appropriate nanoparticle is important. Here the research group have been looking at nanoparticles of varying sizes and shapes, as well as different coatings.

The solution is to create nanoparticles that can change shape to meet different types of tumors. This structural alteration makes the technology more versatile and means treatments could be delivered more quickly, rather than waiting for test results to assess the size and shape of the tumor.

The shape-shifting has been achieved by constructing the nanoparticles from tiny fragments of metal and then attaching DNA to them. The DNA acts as a means for marking the cancer, and then allowing the chemotherapy drug to attack the tumor.

The research is published in the journal Proceedings of the National Academy of Sciences. The paper is titled “Tailoring nanoparticle designs to target cancer based on tumor pathophysiology.”

Tailoring nanoparticle designs to target cancer based on tumor pathophysiology

Significance

Nanotechnology is a promising approach for improving cancer diagnosis and treatment with reduced side effects. A key question that has emerged is: What is the ideal nanoparticle size, shape, or surface chemistry for targeting tumors? Here, we show that tumor pathophysiology and volume can significantly impact nanoparticle targeting. This finding presents a paradigm shift in nanomedicine away from identifying and using a universal nanoparticle design for cancer detection and treatment. Rather, our results suggest that future clinicians will be capable of tailoring nanoparticle designs according to the patient’s tumor characteristics. This concept of “personalized nanomedicine” was tested for detection of prostate tumors and was successfully demonstrated to improve nanoparticle targeting by over 50%.

 

Abstract

Nanoparticles can provide significant improvements in the diagnosis and treatment of cancer. How nanoparticle size, shape, and surface chemistry can affect their accumulation, retention, and penetration in tumors remains heavily investigated, because such findings provide guiding principles for engineering optimal nanosystems for tumor targeting. Currently, the experimental focus has been on particle design and not the biological system. Here, we varied tumor volume to determine whether cancer pathophysiology can influence tumor accumulation and penetration of different sized nanoparticles. Monte Carlo simulations were also used to model the process of nanoparticle accumulation. We discovered that changes in pathophysiology associated with tumor volume can selectively change tumor uptake of nanoparticles of varying size. We further determine that nanoparticle retention within tumors depends on the frequency of interaction of particles with the perivascular extracellular matrix for smaller nanoparticles, whereas transport of larger nanomaterials is dominated by Brownian motion. These results reveal that nanoparticles can potentially be personalized according to a patient’s disease state to achieve optimal diagnostic and therapeutic outcomes.

 

 

Curr Pharm Des. 2013;19(37):6560-74.
Mechanisms for targeted delivery of nanoparticles in cancer.
With the evolution of the “omics” era, our molecular understanding of cancer has exponentially increased, leading to the development of the concept of personalized medicine. Nanoparticle technology has emerged as a way to combine cancer specific targeting with multifunctionality, such as imaging and therapy, leading to advantages over conventional small molecule based approaches. In this review, we discuss the targeting mechanisms of nanoparticles, which can be passive or active. The latter utilizes small molecules, aptamers, peptides, and antibodies as targeting moieties incorporated into the nanoparticle surface to deliver personalized therapy to patients.
PMID: 23621529

 

 

Nanoparticle-based targeted drug delivery

Rajesh Singh1 and James W. Lillard Jr.1
Exp Mol Pathol. 2009 June ; 86(3): 215–223.     http://dx.doi.org:/10.1016/j.yexmp.2008.12.004

Nanotechnology could be defined as the technology that has allowed for the control, manipulation, study, and manufacture of structures and devices in the “nanometer” size range. These nano-sized objects, e.g., “nanoparticles”, take on novel properties and functions that differ markedly from those seen from items made of identical materials. The small size, customized surface, improved solubility, and multi-functionality of nanoparticles will continue to open many doors and create new biomedical applications. Indeed, the novel properties of nanoparticles offer the ability to interact with complex cellular functions in new ways. This rapidly growing field requires crossdisciplinary research and provides opportunities to design and develop multifunctional devices that can target, diagnose, and treat devastating diseases such as cancer. This article presents an overview of nanotechnology for the biologist and discusses the attributes of our novel XPclad© nanoparticle formulation that has shown efficacy in treating solid tumors, for single dose vaccination, and oral delivery of therapeutic proteins.

The development of a wide spectrum of nanoscale technologies is beginning to change the scientific landscape in terms of disease diagnosis, treatment, and prevention. These technological innovations, referred to as nanomedicines by the National Institutes of Health, have the potential to turn molecular discoveries arising from genomics and proteomics into widespread benefit for patients. Nanoparticles can mimic or alter biological processes (e.g., infection, tissue engineering, de novo synthesis, etc.). These devices include, but are not limited to, functionalized carbon nanotubes, nanomachines (e.g., constructed from interchangeable DNA parts and DNA scaffolds), nanofibers, self-assembling polymeric nanoconstructs, nanomembranes, and nano-sized silicon chips for drug, protein, nucleic acid, or peptide delivery and release, and biosensors and laboratory diagnostics.

Nanotechnology-based Drug Delivery in Cancer

Drug delivery in cancer is important for optimizing the effect of drugs and reducing toxic side effects. Several nanotechnologies, mostly based on nanoparticles, can facilitate drug delivery to tumors.

Hydrogels

Hydrogel-nanoparticles are based on proprietary technology that uses hydrophobic polysaccharides for encapsulation and delivery of drug, therapeutic protein, or vaccine antigen. A novel system using cholesterol pullulan shows great promise. In this regard, four cholesterol molecules gather to form a self-aggregating hydrophobic core with pullulan outside. The resulting cholesterol nanoparticles stabilize entrapped proteins by forming this hybrid complex. These particles stimulate the immune system and are readily taken up by dendritic cells. Alternatively, larger hydrogels can encapsulate and release monoclonal antibodies.

Curcumin, a substance found in the cooking spice turmeric, has long been known to have anti-cancer properties. Nevertheless, widespread clinical application of this relatively efficacious agent has been limited due to its poor solubility and minimal systemic bioavailability. This problem has been resolved by encapsulating curcumin in a polymeric nanoparticle, creating “nanocurcumin” (Bisht et al., 2007). Further, the mechanism of action of nanocurcumin on pancreatic cancer cells mirrors that of free curcumin, including induction of apoptosis, blockade of nuclear factor kappa B (NFκB) activation, and downregulation of pro-inflammatory cytokines (i.e., IL-6, IL-8 and TNF-α). Nanocurcumin provides an opportunity to expand the clinical repertoire of this efficacious agent by enabling soluble dispersion. Future studies utilizing nanocurcumin are warranted in preclinical in vivo models of cancer and other diseases that might benefit from the effects of curcumin.

Micelles and liposomes

Block-copolymer micelles are spherical super-molecular assemblies of amphiphilic copolymer. The core of micelles can accommodate hydrophobic drugs, and the shell is a hydrophilic brush-like corona that makes the micelle water soluble, thereby allowing delivery of the poorly soluble contents. Camptothecin (CPT) is a topoisomerase I inhibitor that is effective against cancer, but clinical application of CPT is limited by its poor solubility, instability, and toxicity. Biocompatible, targeted sterically stabilized micelles (SSM) have been used as nanocarriers for CPT (CPT-SSM). CPT solubilization in SSM is expensive yet reproducible and is attributed to avoidance of drug aggregate formation. Furthermore, SSM composed of PEGylated phospholipids are attractive nanocarriers for CPT delivery because of their size (14 nm) and ability to extravasate through the leaky microvasculature of tumors and inflamed tissues. This passive targeting results in high drug concentration in tumors and reduced drug toxicity to the normal tissues (Koo et al., 2006).

Stealth micelle formulations have stabilizing PEG coronas to minimize opsonization of the micelles and maximize serum half-life. Currently, SP1049C, NK911, and Genexol-PM have been approved for clinical use (Sutton et al., 2007). SP1049C is formulated as doxorubicin (DOX)-encapsulated pluronic micelles. NK911 is DOX-encapsulated micelles from a copolymer of PEG-DOX-conjugated poly(aspartic acid), and Genexol-PM is a paclitaxelencapsulated PEG-PLA micelle formulation. Polymer micelles have several advantages over other drug delivery systems, including increased drug solubility, prolonged circulation halflife, selective accumulation at tumor sites, and lower toxicity. However, at the present time this technology lacks tumor specificity and the ability to control the release of the entrapped agents. Indeed, the focus of nano-therapy has gradually shifted from passive targeting systems (e.g., micelles) to active targeting.

Super paramagnetic iron oxide particles can be used in conjunction with magnetic resonance imaging (MRI) to localize the tumor as well as for subsequent thermal ablation. This has been used, for example, to target glioblastoma multiforme (GBM), a primary malignant tumor of the brain with few effective therapeutic options. The primary difficulty in treating GBM lies in the difficulty of delivering drugs across the BBB. However, nanoscale liposomal iron oxide preparations were recently shown to improve passage across the BBB (Jain, 2007).

 

Nanomaterial formulation

Nanomaterials have been successfully manipulated to create a new drug-delivery system that can solve the problem of poor water solubility of most promising currently available anticancer drugs and, thereby, increase their effectiveness. The poorly soluble anticancer drugs require the addition of solvents in order for them to be easily absorbed into cancer cells. Unfortunately, these solvents not only dilute the potency of the drugs but create toxicity. Researchers from the University of California Los Angeles California Nanosystem Institute have devised a novel approach using silica-based nanoparticles to deliver the anticancer drug CPT and other water insoluble drugs to cancer cells (Lu et al., 2007). The method incorporates the hydrophobic anticancer drug CPT into the pores of fluorescent mesoporous silica nanoparticles and delivers the particles into a variety of human cancer cells to induce cell death. The results suggest that the mesoporous silica nanoparticles might be used as a vehicle to overcome the insolubility of many anticancer drugs.

Nanosystems

Novel nanosystems can be pre-programmed to alter their structure and properties during the drug delivery process, allowing for more effective extra- and intra-cellular delivery of encapsulated drug (Wagner, 2007). This is achieved by the incorporation of molecular sensors that respond to physical or biological stimuli, including changes in pH, redox potential, or enzymes. Tumor-targeting principles include systemic passive targeting and active receptor targeting. Physical forces (e.g., electric or magnetic fields, ultrasound, hyperthermia, or light) may contribute to focusing and triggering activation of nano systems. Biological drugs delivered with programmed nanosystems also include plasmid DNA, siRNA, and other therapeutic nucleic acids.

Using a degradable, polyamine ester polymer, polybutanediol diacrylate co amino pentanol (C32), a diptheria toxin suicide gene (DT-A) driven by a prostate-specific promoter was directly injected into normal prostate and prostate tumors in mice (Peng et al., 2007). This C32/DT-A system resulted in significant size reduction, apoptosis in 50% of normal prostate. However, a single injection of C32/DT-A triggered apoptosis in 80% of tumor cells present in the tissue. It is expected that multiple nanoparticle injection would trigger a great percentage of prostate tumor cells to undergo apoptosis. These results suggest that local delivery of polymer/DT-A nanoparticles may have application in the treatment of benign prostatic hypertrophy and prostate cancer.

Multidrug resistance (MDR) of tumor cells is known to develop through a variety of molecular mechanisms. Glucosylceramide synthase (GCS) is responsible for the activation of the pro-apoptotic mediator, ceramide, to a nonfunctional moiety, glucosylceramide. This molecule is over-expressed by many MDR tumor types and has been implicated in cell survival in the presence of chemotherapy. A study has investigated the therapeutic strategy of co-administering ceramide with paclitaxel in an attempt to restore apoptotic signaling and overcome MDR in a human ovarian cancer cell line using modified poly(epsiloncaprolactone) (PEO-PCL) nanoparticles to encapsulate and deliver the therapeutic agents for enhanced efficacy (van Vlerken and Amiji, 2006). Results show that MDR cancer cells can be completely eradicated by this approach. Using this approach, MDR cells can be resensitized to a dose of paclitaxel near the IC50 of non-MDR cells. Molecular analysis of activity verified the hypothesis that the efficacy of this therapeutic approach is due to a restoration in apoptotic signaling, showing the promising potential for clinical use of this therapeutic strategy to overcome MDR.

Nanocells

Indiscriminate drug distribution and severe toxicity of systemic administration of chemotherapeutic agents can be overcome through encapsulation and cancer cell targeting of chemotherapeutics in 400 nm nanocells, which can be packaged with significant concentrations of chemotherapeutics of different charge, hydrophobicity, and solubility (MacDiarmid et al., 2007). Targeting of nanocells via bispecific antibodies to receptors on cancer cell membranes results in endocytosis, intracellular degradation, and drug release. Doses of drugs delivered via nanocells are ∼1,000 times less than the dose of the free drug required for equivalent tumor regression. It produces significant tumor growth inhibition and regression in mouse xenografts and lymphoma in dogs, despite administration of minute amounts of drug and antibody. Indeed, reduced dosage is a critical factor for limiting systemic toxicity. Clinical trials are planned for testing this method of drug delivery.

Dendrimers

In early studies, dendrimer-based drug delivery systems focused on encapsulating drugs. However, it was difficult to control the release of drugs associated with dendrimers. Recent developments in polymer and dendrimer chemistry have provided a new class of molecules called dendronized polymers, which are linear polymers that bear dendrons at each repeat unit. Their behavior differs from that of linear polymers and provides drug delivery advantages because of their enhanced circulation time. Another approach is to synthesize or conjugate the drug to the dendrimers so that incorporating a degradable link can be further used to control the release of the drug.

DOX was conjugated to a biodegradable dendrimer with optimized blood circulation time through the careful design of size and molecular architecture (Lee et al., 2006). Specifically, the DOX-dendrimer controlled drug-loading through multiple attachment sites, solubility through PEGylation, and drug release through the use of pH-sensitive hydrazone dendrimer linkages. In culture, DOX-dendrimers were >10 times less toxic than free DOX toward colon carcinoma cells. Upon intravenous administration to tumor bearing mice, tumor uptake of DOX-dendrimers were nine-fold higher than intravenous free DOX and caused complete tumor regression and 100% survival of the mice after 60 days.

Nanotubes Even though it was previously possible to attach drug molecules directly to antibodies, attaching more than a handful of drug molecules to an antibody significantly limits its targeting ability because the chemical bonds that are used tend to impede antibody activity. A number of nanoparticles have been investigated to overcome this limitation. Tumor targeting single-walled carbon nano-tube (SWCNT) have been synthesized by covalently attaching multiple copies of tumor-specific monoclonal antibodies (MAbs), radiation ion chelates and fluorescent probes (McDevitt et al., 2007). A new class of anticancer compound was created that contains both tumor-targeting antibodies and nanoparticles called fullerenes (C60). This delivery system can be loaded with several molecules of an anticancer drug, e.g., Taxol® (Ashcroft et al., 2006). It is possible to load as many as 40 fullerenes onto a single skin cancer antibody called ZME-108, which can be used to deliver drugs directly into melanomas. Certain binding sites on the antibody are hydrophobic (water repelling) and attract the hydrophobic fullerenes in large numbers so multiple drugs can be loaded into a single antibody in a spontaneous manner. No covalent bonds are required, so the increased payload does not significantly change the targeting ability of the antibody. The real advantage of fullerene-based therapies vs. other targeted therapeutic agents is likely to be fullerene’s potential to carry multiple drug payloads, such as taxol plus other chemotherapeutic drugs. Cancer cells can become drug resistant, and one can cut down on the possibility of their escaping treatment by attacking them with more than one kind of drug at a time. The first fullerene immuno-conjugates have been prepared and characterized as an initial step toward the development of fullerene immunotherapy.

Polymersomes

Polymersomes, hollow shell nanoparticles, have unique properties that allow delivery of distinct drugs. Loading, delivery and cytosolic uptake of drug mixtures from degradable polymersomes were shown to exploit the thick membrane of these block copolymer vesicles, their aqueous lumen, and pH-triggered release within endolysosomes. Polymersomes break down in the acidic environments for targeted release of these drugs within tumor cell endosomes. While cell membranes and liposomes are created from a double layer of phospholipids, a polymersome is comprised of two layers of synthetic polymers. The individual polymers are considerably larger than individual phospholipids but have many of the same chemical features.

Polymersomes have been used to encapsulate paclitaxel and DOX for passive delivery to tumor-bearing mice (Ahmed et al., 2006). The large polymers making up the polymersome allows paclitaxel, which is water insoluble, to embed within the shell. DOX is water-soluble and stays within the interior of the polymersome until it degrades. The polymersome and drug combination spontaneously self-assembles when mixed together. Recently, studies have shown that cocktails of paclitaxel and DOX lead to better tumor regression that either drug alone, but previously there was no carrier system that could carry both drugs as efficiently to a tumor. Hence, this approach shows great promise.

Quantum dots

Single-particle quantum dots conjugated to tumor-targeting anti-human epidermal growth factor receptor 2 (HER2) MAb have been used to locate tumors using high-speed confocal microscopy (Tada et al., 2007). Following injection of quantum dot-MAb conjugate, six distinct stop-and-go steps were identified in the process as the particles traveled from the injection site to the tumor where they bound HER2. These blood-borne conjugates extravasated into the tumor, bound HER2 on cell membranes, entered the tumor cells and migrated to the perinuclear region. The image analysis of the delivery processes of single particles in vivo provided valuable information on MAb-conjugated therapeutic particles, which will be useful in increasing their anticancer therapeutic efficacy. However, the therapeutic utility of quantum dots remains undetermined.

XPclad® nanoparticles

The poor aqueous solubility of many drug candidates presents a significant problem in drug delivery and related requirements such as bioavailability and absorption. Recently, our laboratory has developed XPclad® nanoparticles that represent a novel formulation method that uses planetary ball milling to generate particles of uniform size (Figure 1), 100% loading efficiency of hydrophobic or hydrophilic drugs, subsequent coating for targeted delivery, and control of LogP for systemic, cutaneous, or oral administration of cancer drugs, vaccines, or therapeutic proteins (Figure 2).

The method for making XPclad® nanoparticles uses a novel and relatively inexpensive preparation technique (i.e., planetary ball milling), which allows for controlling the size of the particles (100 nm to 50 μm; ± 10% of mean size) with >99% loading efficiency, polymer- or ligand-coating for controlled-, protected-, and targeted-release and delivery of their contents. The nanoparticles produced thereby contain the desired biologically active agent(s) in a biopolymer excipient such as alginate, cellulose, starch or collagen and biologically active agents. Generally, there are two types of mills that have been employed for making particles: vibratory or planetary ball mills. The vibratory ball milling grinds powders by high velocity impact while planetary ball milling employs a grinding motion. Typically, planetary ball milling has been used only to generate micron-sized particles, while vibratory milling can yield nano-particles. However, the high impact resulting from the vibratory milling technique makes incorporating biologicals difficult. Planetary ball mills pulverize and mix materials ranging from soft and medium to extremely hard, brittle and fibrous materials. Both wet and dry grinding can be carried out. Minerals, ores, alloys, chemicals, glass, ceramics, plant materials, soil samples, sewage sludge, household and industrial waste and many other substances can be reduced in size simply, quickly and without loss. Planetary ball mills have been successfully used in many industrial and research sectors, particularly wherever there is high demand for purity, speed, fineness and reproducibility. The planetary ball mills produce extremely high centrifugal forces with very high pulverization energies and short grinding times. Because of the extreme forces exerted, the use of vibratory and planetary ball mills to formulate therapeutics has not been practiced until now. In general, XPclad® particle size can be engineered to range from 5 to 30 nm up to 10 to 60 μm by controlling the size and number of planetary balls, grinding speed, milling cycles, and centrifugal force by varying the revolutions per second and planetary jar velocity.

 

Nano delivery systems hold great potential to overcome some of the obstacles to efficiently target a number of diverse cell types. This represents an exciting possibility to overcome problems of drug resistance in target cells and to facilitate the movement of drugs across barriers (e.g., BBB). The challenge, however, remains the precise characterization of molecular targets and ensuring that these molecules only affect targeted organs. Furthermore, it is important to understand the fate of the drugs once delivered to the nucleus and other sensitive cells organelles.

UPDATED 8/05/2022

 

One step closer to cancer nanomedicine

High-throughput tool uncovers links between cell signaling and nanomaterial uptake
SCIENCE
21 Jul 2022
Vol 377Issue 6604
pp. 371-372
The promise of chemotherapeutic nanomedicine has tantalized clinicians and patients for decades. Nanoparticles (NPs) can directly target tumor cells, which would reduce the amount of chemotherapy administered and its systemic toxicity, increasing patient quality of life and extending utility of therapies with lifetime dosing limits. However, these hopes remain largely unrealized. Liposomal drug carriers, which make up nearly all clinically approved nanomedicines, have not extended overall patient survival compared with treatment with the drugs alone (1). These failures have been attributed to poor delivery to target cells (2) because NPs must first traverse a series of biological barriers (3). Although nanocarrier composition, surface chemistry, size, and shape have been optimized to promote cell entry, progress has been confounded by heterogeneity in cell uptake signaling (4). On page 384 of this issue, Boehnke et al. (5) uncover the reciprocal relationship between NP material properties and cell internalization using nanoPRISM, a high-throughput screening approach.
The nanoPRISM technology uses the profiling relative inhibition simultaneously in mixtures (PRISM) (6) method to generate a screening library of ∼500 cancer cell lines that are barcoded with distinct DNA sequences that permit identification of cells with high-throughput genomic sequencing. This cell library is combined with a panel of 35 different fluorescently labeled NPs with varying core compositions, surface chemistries, and diameters to identify synergistic interactions for cell uptake. PRISM-tagged cells are separated into four groups according to uptake level, and their DNA is sequenced to identify them and screen for key drivers of NP internalization that can be attributed to either NP characteristics or cell signaling.
Boehnke et al. compared the uptake efficiency of NPs conjugated to antibodies targeting epidermal growth factor receptor (EGFR) versus EGFR antibodies alone in cell lines that overexpress this receptor. NanoPRISM revealed differences in cellular uptake, most likely resulting from the steric hindrance of NP conjugation. These results suggest that nanoPRISM may be suitable for evaluating antibody-drug conjugates (ADCs), a growing therapeutic category.
Boehnke et al. also use nanoPRISM to interrogate NPs with compositions most commonly applied to nanomedicine: spherical liposomes made of lipid bilayers and solid lipid and polymer NPs consisting of disordered, spherical lipid or polymer aggregates. They also examine NPs with or without polyethylene glycol (PEG) modification, which is used to reduce systemic uptake and improve circulation time (7). They find that NP core composition is a primary determinant in cellular uptake. This unexpected finding upends years of work on modulating NP surface chemistries to alter protein adsorption patterns and subsequent cell adhesion (8). Although cells first detect NPs through their surface chemistry, the findings of Boehnke et al. support early studies that showed that NP stiffness and deformability, which are dictated by core composition, are stronger modulators of the uptake process (9).
The power of the nanoPRISM method is further illustrated by combining these findings with the Cancer Cell Line Encyclopedia, which quantifies mutational genomic signatures of common cancer cell lines. Boehnke et al. identify genomic signatures and signaling networks most correlated with NP internalization. Many of the results are not surprising, such as involvement of the solute carrier (SLC) transporter or adenosine triphosphate (ATP)–binding cassette (ABC) families, which have previously been implicated in NP cellular entry and transport. The nanoPRISM screens also highlight gene networks associated with the plasma membrane and extracellular matrix that contribute to NP cellular entry processes (see the figure).
However, the nanoPRISM method also reveals involvement of an understudied gene that has not been associated with NP internalization: SLC46A3. This encodes a lysosomal transmembrane protein linked to lipid catabolism (10) that influences lysosomal trafficking of ADCs (11). Expression of SLC46A3 negatively regulated liposomal and solid lipid NP cellular uptake, whereas polymer NPs that lack lipids were unaffected. SLC46A3 association with lipid-based NPs was evidenced even when NP surfaces were coated with nonlipid molecules. This further indicates the importance of NP core composition in cellular uptake processes and also suggests that cells can detect core composition through surface coatings, which better resemble a porous net than a wall. This could have important implications for predicting the efficacy of nucleic acid vaccines and therapies that use lipid-based carriers, such as COVID-19 mRNA vaccines. For example, SLC46A3 biomarker testing could be implemented to identify patients most likely to respond to lipid-based nanotherapeutics.
Signatures of cellular uptake
The nanoPRISM method combines cell and nanomaterial libraries to identify signatures associated with cellular internalization. The ABC and SLC protein families regulate uptake of lipid-based and polymer nanoparticles differentially, whereas vesicular trafficking, ECM, and focal adhesion pathways affected all types of nanoparticles. Core composition, not surface chemistry, was the strongest regulator of uptake behavior.

GRAPHIC: V. ALTOUNIAN/SCIENCE

OPEN IN VIEWER

The results of the nanoPRISM screens are also confirmed in animal models, indicating that this technique could be used to identify the most promising formulations for downstream analysis, reducing preclinical animal testing demands. Such high-throughput approaches are critical to the rapid advancement of cancer nanomedicine, because US and European regulatory agencies have not established criteria for nanomedicine approval based on similarity to an existing product (12). Given the long timeline for drug development, which can span a decade or more, technologies to safely accelerate this process are desirable.
The nanoPRISM method represents a substantial advance over the less rigorous and qualitative studies of NP internalization that characterized the early years of the field. Studies that examined a few NP properties in a single cell line could not capture the complexities of NP cell entry. Combined with machine learning and iterative simulation and materials synthesis approaches, nanoPRISM could enable screening for nanomaterials that target specific cell types, similar to current biopanning methods for peptides or the systematic evolution of ligands by exponential enrichment (SELEX) method of aptamer discovery (13). Although the study of Boehnke et al. examines only 35 different NPs, additional nanomaterials could be added to the library, such as inorganic NPs (such as gold, silica, and carbon) and materials with complex geometries (such as DNA origamis). A limitation of nanoPRISM is its focus on cellular entry, the last step of the biodistribution process. However, it is easy to envision expanding this approach beyond cell uptake to study the relationship between NP material properties and gene expression in cell adhesion and trafficking. Additionally, with the template provided by Boehnke et al., similar methods could be integrated with microfluidics, organ-on-a-chip, or tumor organoid cultures to model other delivery barriers, such as circulation, extravasation, and tissue diffusion. Thus, the nanoPRISM approach could catalyze rapid materials optimization, accelerating nanocarrier design and bringing the promise of cancer nanomedicine closer to reality.

References and Notes

1
G. H. Petersen, S. K. Alzghari, W. Chee, S. S. Sankari, N. M. La-Beck, J. Control. Release 232, 255 (2016).
2
S. Wilhelm et al., Nat. Rev. Mater. 1, 16014 (2016).
3
S. Barua, S. Mitragotri, Nano Today 9, 223 (2014).
4
B. D. Chithrani, A. A. Ghazani, W. C. W. Chan, Nano Lett. 6, 662 (2006).
5
N. Boehnke et al., Science 377, eabm5551 (2022).
6
C. Yu et al., Nat. Biotechnol. 34, 419 (2016).
7
M. Eugene, Cell. Mol. Biol. 50, 209 (2004).
8
A. Albanese et al., ACS Nano 8, 5515 (2014).
9
X. Sun et al., Biomacromolecules 6, 2541 (2005).
10
J.-H. Kim et al., Nat. Commun. 12, 290 (2021).
11
K. J. Hamblett et al., Cancer Res. 75, 5329 (2015).
12
S. Soares, J. Sousa, A. Pais, C. Vitorino, Front Chem. 6, 360 (2018).
13
C. Tuerk, L. Gold, Science 249, 505 (1990).

 

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Thermodynamic Modeling for Cancer Cells

Author: Danut Dragoi, PhD

As scientific facts about cancers become more available, a physical modeling become more transparent as a basis to quantify various forms of energies involved in cancer cells interacting collectively with healthy cells. At this point in time the parametrization of a Hamiltonian equation is an important theoretical step of modeling cancer cells. Since some input parameters for a Hamiltonian or free energy thermodynamic functions are well known, recent SEM images of cancer cells can define, see link here  and in here. the use of a phenomenological approach that takes into consideration the thermodynamic Gibbs free energy function. The two pictures below taken from here  and from here  show that the cancer cell is an evolving spheroid covered with nano-tubes shaped tentacles that attache to the healthy cells.

Cancer Cell 3D Toulouse

Image SOURCE

http://www.24matins.fr/cancer-pancreas-decouverte-a-toulouse-281754

Cancer_cell_Vein

Image SOURCE

http://news.mit.edu/2015/cancer-cells-escape-blood-vessels-121

At the molecular level, the attaching tentacles have an opposite electric charge than the healthy cells, link in here,  and perhaps different handedness to accommodate a strong bond. In literature attempts to describe a living cell in resting state were done, see link in here . Because the cancer cell is an unstable system, growing cell(s), the process can be imagined as a non-equilibrium thermodynamic process. The authors of the paper, link in here, discuss the properties of cancer cells from a new perspective based on an analogy with phase transitions in physical systems. Similarities in terms of instabilities and attractor states are outlined and differences discussed. While physical phase transitions typically occur at or near thermodynamic equilibrium, a normal-to cancer (NTC) transition is a dynamical non-equilibrium phenomenon, which depends on both metabolic energy supply and local physiological conditions.

Assuming a dynamic equilibrium of a cancer cell with normal cell at a given moment in time t in its evolution we can adapt a Gibbs free thermodynamic function with addition of a misfit potential of different DNA strands and amino acids with different chiralities developed inside the cancer cell

G(U, T, S, P, V, R(+),L(-) ;t)=U-TS +PV+RT[ln(Xn)-ln(R(+)/L(-))]                 (1)

In expression (1) the variables have the usual known significance, link in here. The term RTln(Xn) is related with the chemical potential of component n. The R(+)=Right and L(-)=Left handedness variables are the percentage of DNA strands and/or chiral object / molecules right handed and left handed inside the cancer cell. The expression (1) is a time implicit form of Gibbs free energy for a cancer cell in which each term has some variation with time specific to cancer cells. For meaningful physical states not far from equilibrium, we select time to be sufficient small in order to have low contributions from the diverging terms. The last term in expression (1) was preferred in that way because in real situations, as the reference link here, shows that the DNA of every organism on Earth is a right-handed double helix. In same paper the authors explain what is the physical reason for organisms on Earth to have right handedness. Notice the components amino acids of a human DNA are all natural amino acids are  left handed except aspartame. However, the DNA strands do not keep the left handed character of each amino acid in composition of the DNA. As we know, for healthy living cells the handedness of DNA is right. 

Therefore, in relation (1) we differentiate two complex systems of enantiomers in a racemic mixture. As found in literature, link here, two enantiomers react with different reaction rates in a chemical reaction with a chiral catalyst or reagent, resulting in an enantioenriched sample of the less reactive enantiomer. This enantiomeric excess (ee) of the unreacted starting material continually rises as more product is formed, reaching 100% just before full completion of the reaction. In equation (1) the form of the last term is coming from enantiomeric excess (ee), R(+)/(R(+)+L(-))-L(-)/(R(+)+L(-)), in which each term is a probability to have an R(+) DNA and L(-) DNA within the cancer cell. From thermodynamic point of view, when we consider the energies in the Gibbs free energy expression, we need to take the logarithm of the probabilities as a difference, in which we get: ln(R(+)/(R(+)+L(-)))-ln( L(-)/(R(+)+L(-))=ln(R(+))-ln(R(+)+L(-))-ln(L(-))+ln(R(+)+L(-))=ln(R(+)/L(-)).

Knowing that for healthy living cells, like in a healthy pancreas cells, we have a shift in energy when a phase transition Normal to Cancer (NTC) state occurs. The link in here describes the NTC concept. A simple explanation of difference in energy of two chiral different objects is given here .

Moving all terms that do not include the R/L ratio on the left side of the equation (1) we get equation (2):

ΔG=-RTln(R(+)/L(+))                                                                            (2)

in which we distinguish two fundamental cases. First when G<0, metabolic reactions are going well as in a healthy organism, and second when G>0, metabolic reactions produce cancer. In the first case R(+)>L(-) as should be. For cancer living cell R(+)<L(-) we have G>0 where the cells are on unstable conditions. To cure them, we need to take energy from them in order to get them back to their original lower energy state. Surgery comes naturally here. We have to not forget that on each side of the transition NTC the physical and chemical coefficients have shifts that can be exploited in curing the cancer. As practice shows the cancer cells produce specific proteins that are used as identifiers of the cancers. Below the NTC transition those specific proteins are missing, indicating that the organism is healthy.

In general the lower the G is for a healthy human body the better.

From practical point of view, it is difficult to measure the ratio within the logarithm function. For this reason we introduce an approximation in which we use the measurements on the aspartame amino acid, that has both chiral forms among all natural amino-acids, see link in here , used by human living cells. Therefore the ratio R(+)/L(-) can be replaced in this approximation with D/L ratio for aspartame amino acid. Using appropriate samples and HPLC analytical method, which is a very sensitive method using micro-mole amounts of sample in solution, the D/L ratio can be easily determined and the G Gibbs free energy evaluated using equation (3):

ΔG=-RTln(D/L)                                                                                       (3)

Other experimental adjustments may be required for real situations, measurements and validations.

Other related articles published in this Open Access Online Scientific Journal include the following:

Pancreatic Cancer: a discovery in Toulouse that would slow its progression

Scientists discover how cancer cells escape blood vessels

SOURCE

Image SOURCE

http://www.24matins.fr/cancer-pancreas-decouverte-a-toulouse-281754

Image SOURCE

http://news.mit.edu/2015/cancer-cells-escape-blood-vessels-1216

Click to access arpita_upadaya_thesis.pdf

Click to access 1109.3033.pdf

Click to access Quantum%20Metabolism%20and%20Cancer%5B1%5D.pdf

Click to access thermo.pdf

http://phys.org/news/2014-09-dna-right-handed-helix.html

https://en.wikipedia.org/wiki/Kinetic_resolution

Click to access Quantum%20Metabolism%20and%20Cancer%5B1%5D.pdf

Click to access 5-stereoisomers.pdf

http://www.cancer.org/cancer/cancercauses/othercarcinogens/athome/aspartame

 

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Significance of Oncogenes

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

Epigenetics and Cancer Causing Genes

    Mar 13, 2015   https://www.linkedin.com/pulse/epigenetics-cancer-causing-genes-oncogenes-kleon-tona

 

Epigenetics and Cancer Causing Genes (Oncogenes)

 

I. Cancer Causing Genes?
I have read an article recently that explained cancer as just plain “bad luck.” I do not believe this to be the case. There are harmful initiators of cancer and it can be associated with unfortunate timing, exposures, poor protections, faulty adaptation and circumstances beyond control. There are approximately 2,619 known genes that are associated with cancer expression and I am confident that this number will change as more research continues. These types of genes are also called oncogenes. These genes can be directly or indirectly associated with cancer initiation, progression, expression, survival and demise.

II. Epigenetics?
Epigenetics plays an important role in the turn on or off signaling of these genes by influencing DNA protection mechanisms without altering the DNA sequencing. Epigenetics refers to high-level information residing above the genetic code. While each cell in the body is equipped with the same genetic manual, epigenetic instructions tell cells how to make a difference. These instructions determine the access to pages with genetic information by directing the way the DNA is packaged into chromatin. DNA organized in loose chromatin is readily available for gene expression. Conversely, DNA tightly packed into dense chromatin has the letters of genetic code effectively buried and unavailable for reading and transcription. Distinct epigenetic marks decide which sets of genes may be expressed and which genes are kept silent.

III. DNA Methylation Hypomethylation and Hypermethylation?
In previous articles (blogs), we discussed the methylation process of DNA. Simply, methylation is the mechanism by which DNA is in homeostasis (healthy sequencing) or in harmful dysfunctional sequencing. Hypomethylation (decreased or low) and Hypermethylation (increased or high) are the two extremes that initiate harmful consequences upon DNA and ultimately lead to and result in unfavorable conditions and change in DNA sequencing performance. Ultimately, this leads to unfavorable function and potentially bad signals altering cell health and survival, predisposing new cell lines to “bad” mutations.

DNA methylation patterns undergo complex changes in cancer. The total amount of methylated cytosine is usually decreased resulting in global (extensive) hypomethylation. Decreased cytosine methylation typically affects satellite DNA, repetitive sequences, and CpG sites. In genetics, CpG is a site where cytosine (C) lies next to guanine (G) in the DNA sequence. (The p indicates that C and G are connected by a phosphodiester bond.) Methylation of DNA occurs at any CpG site. The cause of reduced amount of methylcytosine observed in human tumors has not been determined and remains under investigation. Despite global hypomethylation, high activity of DNA methyltransferases has been detected in multiple human tumor types. This increase may be related to higher proliferation rate of malignant cells.
Besides global (extensive) hypomethylation, most cancers also show focal hypermethylation in distinct subsets of promoter-associated CpG islands as well. Affected genes are permanently silenced, since methylation marks are propagated through mitosis and are maintained in the malignant clone. Aberrant (diverging from normal) hypermethylation occurring in transformed cells serves as an alternative mechanism for inactivation of tumor suppressor genes. Hundreds to thousands of genes can be epigenetically silenced by CpG island hypermethylation in human cancer suggesting a general disturbance of epigenetic memory. Methylation affects individual cancer patients with varying extent. While some patients have minimal changes, others show concordant hypermethylation of multiple genes. This phenomenon was first described as CpG island methylator phenotype (CIMP) in colorectal cancer and confirmed in many other types of cancer and leukemia. Epigenetic DNA methylation changes in cancer appear to be considerably more frequent events than genetic mutations. Mass sequencing of more than 20,000 transcripts in breast and colorectal cancers revealed about 80 harmless and less than 15 potentially oncogenic mutations per tumor. Balanced methylation and protective epigenetics are essential in minimizing cancer-causing mutations.

IV. Not Just Bad Luck!
Cancer is, in fact, a scary diagnosis and it is unfortunate when it occurs. However, I would not term it “bad luck,” as this implies a powerless and hopeless end. The gift of life is filled with miraculous movements that defy the laws of nature. Protective epigenetics can be considered miraculous and spontaneous and is what becomes necessary to move toward favorable adaptations that increase health, longevity and survival. Moreover, it is the mechanism by which succeeding familial generations can benefit in protections against cancer. It’s not just about our own protective actions on gene expression but also for the protective adaptability of future generations. There is hope and record of individuals having spontaneous regression of cancer. I have treated many in my clinical career! Encourage the expression of your healthy genes by protective epigenetics!

Your Genetic Solution

V. For Your Interest and Exploration (2,619)

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Methylation and cancer epigenomics

Larry H. Bernstein, MD, FCAP, Curator

LPBI

UPDATED 12/12/2022

2015 DNA methylation research grant winners

https://www.diagenode.com/landingPages/display/dna-methylation-grant-applications

 

Persistency of Transgene Expression Mediated by Lentiviral Gene Delivery in Pluripotent Cell Lines

Suleiman Alhaji
Ph.D. Student, University Putra, Malaysia

My general objectives are to (1) determine the duration of reporter gene expression from pluripotent cell lines transduced by lentivirus and (2) to assess the epigenetic effects on the provirus. More specifically, I plan to (1) produce LV carrying Green Fluorescent Protein (GFP) reporter gene, (2) obtain and maintain the required cell lines including establishing primary mouse fibroblast as a control, 3) measure the duration of GFP expression from pluripotent and control cell lines transduced with the lentivirus, (4) exclude the loss of the integrated provirus as the factor for GFP silencing in transduced non-pluripotent cell lines, and (5) study the effects of epigenetics on the GFP gene and the regulatory sequence of the provirus.

Transgene integration by lentiviral (LV) vector in the host cell’s genome would theoretically generate a prolonged or permanent transgene expression. However, several citations have reported a decline in transgene expression in early progenitor cells and stem cells transduced by LV. We hypothesized that prolonged transgene expression can be achieved if the transgene is introduced into the cells before epigenetic markers are established in the genome, i.e during the pluripotency period. Therefore, the proposed study seeks to determine if this phenomenon would occur in pluripotent cell lines, focusing on mouse induced pluripotent stem (iPS) cells as the target cell, in a gene therapy context.

Two epigenetic analyses that will be performed on the promoter and transgene of the provirus are DNA methylation and chromatin modification. For DNA methylation profiling, the genomic DNA of the cell will be treated with bisulfite prior to PCR and sequencing of the proviral DNA. The cells may also be analyzed for 5-hmC using 5-hmC monoclonal antibody (C15200200-200) or hMeDIP Kit (C02010031) to assess the level of hydroxymethylation. We may also consider using Diagenode’s MethylCap kit (C02020010) to fractionate the methylated DNA by CpG density.

For the chromatin modification analysis, the cells will be treated with trichostatin A (TSA) before chromatin immunoprecipitation (ChIP) analysis by chromatin IP – bisulfite – sequencing (ChIP-Bis-Seq) and as well Combining chromatin IP and DNA methylation profiles in one assay using the Premium Bisulfite kit, Diagenode. We may also perform pull-down methylated DNA analysis by using specific antibodies such as (1) H3K4 monoclonal antibody (C1541065) (2) H3K4 polyclonal antibody (C15410037) (3) H3K9 polyclonal antibody (C15410004). Beads only will be used as a control.

 

Epigenome-wide methylation pattern discovery for irradiated skin in radiotherapy

Maxwell Johnson, Ph.D.
Research Fellow, University of Southern California, Department of Plastic and Reconstructive Surgery

Radiotherapy is utilized in neoadjuvant, definitive, and palliative treatment of a wide variety of cancers. From a reconstructive perspective, however, irradiated fields pose significant challenges as the tissue is often stiff, brittle, and heals poorly. Little is known about the mechanism by which irradiation produces these changes. The objective of our research is to reveal the epigenetic changes that occur in irradiated skin in order to identify potential targets for therapy. We aim to translate our findings into interventional studies in both cell culture and a mouse model to assess their efficacy in vitro and in vivo.

We have access to a bank of paired samples of irradiated and non-irradiated tissues from patients who have undergone reconstructive procedures after cancer treatment. We have used the Illumina Infinium Human Methylation450 BeadChip array to assess epigenome-wide methylation status of eight paired samples, and have identified a signature methylation pattern for irradiated skin. We would like to utilize the Diagenode Premium WGBS Kit for bisulfite sequencing of additional paired samples for two purposes. First, we would like to confirm the findings of our BeadChip array utilizing a more robust method of assessing epigenome-wide methylation status. Second, we would like to assess methylation status at loci that are not evaluated by the BeadChip array. Using this information, we plan to identify loci with the greatest change in methylation status between irradiated and non-irradiated samples. By comparing these loci to literature, we intend to identify genes that are known to have an effect on wound healing. We then plan to design interventional studies to assess the effects of modulating the expression of these genes and/or supplementing gene products in cell culture and a mouse model. We would like to utilize the Diagenode Bisulfite Kit to confirm methylation status at target genes in these additional studies.

 

Next-generation sequencing based methylome study of primary breast tumours

Rajbir Batra, Ph.D. Researcher
Cancer Research UK Cambridge Institute, University of Cambridge

Breast cancer is one of the leading causes of cancer death in women, and is unanimously considered a heterogeneous disease displaying distinct therapeutic responses and outcomes. While recent advances have led to the refinement of the molecular classification of the disease, the epigenetic landscape has received less attention.

We are delighted to win the DNA methylation research grant award and intend to use it to conduct a next-generation sequencing based methylome study of primary breast tumours. DNA methylation markers will also be investigated in Patient Derived Tumour Xenografts (PDTXs) and in circulating tumour DNA (ctDNA) to identify potential prognostic and predictive methylation biomarkers in breast cancer.

 

 2015 Feb 1; 29(3): 238–249.
PMCID: PMC4318141
PMID: 25644600

Chromatin signatures of cancer

Abstract

Changes in the pattern of gene expression play an important role in allowing cancer cells to acquire their hallmark characteristics, while genomic instability enables cells to acquire genetic alterations that promote oncogenesis. Chromatin plays central roles in both transcriptional regulation and the maintenance of genomic stability. Studies by cancer genome consortiums have identified frequent mutations in genes encoding chromatin regulatory factors and histone proteins in human cancer, implicating them as major mediators in the pathogenesis of both hematological malignancies and solid tumors. Here, we review recent advances in our understanding of the role of chromatin in cancer, focusing on transcriptional regulatory complexes, enhancer-associated factors, histone point mutations, and alterations in heterochromatin-interacting factors.

Keywords: cancer, chromatin, histone proteins

Fifteen years ago, in their paper “The Hallmarks of Cancer,”  laid out a conceptual framework for the properties of cancer cells. Cancer development is a complex process involving diverse tissue types of distinct developmental origins, cell–cell interactions, and a myriad of signaling pathways. Digesting decades worth of research,  extracted fundamental properties common to many cancer types. Some aspects of their six hallmarks of cancer (resisting apoptosis, self-sufficiency in growth signals, insensitivity to anti-growth signals, invasive metastasis, unlimited cellular proliferation, and sustained angiogenesis) can be viewed in the light of deregulated gene expression at the level of transcription. Indeed, many signal transduction pathways perturbed in cancer ultimately modulate the activity of transcriptional regulators (). Moreover, genomic instability is recognized as an enabling characteristic of cancer (). Thus, transcriptional control and structural maintenance of the genome at the level of chromatin are likely suspects in the hunt for culprits underlying cancer development.

The eukaryotic genome is packaged into a structure called chromatin that, at its most basic level, comprises the four core histones H2A, H2B, H3, and H4 wrapped inside ∼147 base pairs (bp) of DNA to form the nucleosome core particle (). Additionally, histone H1 functions as an internucleosome linker and is involved in the compaction of chromatin (). The N-terminal tails of the core histones protrude out from the nucleosome and are subject to a diverse array of post-translational modifications that alter chromatin structure and dynamics (). Large families of proteins containing domains such as bromodomain, chromodomain, plant homeodomain (PHD) finger, Tudor domains, PWWP domains, and YEATS domains bind these modifications to effect diverse downstream chromatin-based processes (). Considering the importance of chromatin in regulating eukaryotic gene expression and maintaining genome stability, it is perhaps not wholly unexpected that recent genome-wide sequencing studies have uncovered cancer-associated mutations in genes encoding chromatin regulatory factors and enzymes (Fig. 1).

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Chromatin proteins mutated in cancer. A summary of cancer mutations that affect post-translational modifications of the histone H3 N-terminal tail. Protein classes are indicated by the fill color for the ovals ([red] methyltransferase; [green] demethylase; [orange] deacetylase; [blue] histone), whereas mutational status is indicated by the outline color ([gray] loss of function; [purple] overexpressed/hyperactive). Dashed lines indicate the residue of histone H3 that is expected to be modified due to the indicated cancer mutations.

The emerging picture of chromatin function in cancer is multifaceted and involves a complex interplay of chromatin-modifying enzymes. A recent review from  highlights the diverse mutations in genes involved in histone lysine methylation pathways associated with human cancer. In some instances, alterations in chromatin itself, such as histone H3.3 Lys27-to-methionine mutations in pediatric glioma, are highly context-specific to a single cancer type (). In other cases, mutations of related pathway component genes such as MLL3, MLL4, and UTX within the COMPASS (complex of proteins associated with Set1) family occur in a range of cancers, suggesting a broader tumor suppressor role (). As more cancer genomes are sequenced, perhaps one of the most stirring observations is co-occurrence as well as mutual exclusivity of mutations between related cancer types. These mutational signatures promise insight into not only cancer development but also the molecular signaling pathways underlying normal development. Paradoxically, whereas basic developmental biology research has supplied us with a rich understanding of the signal transduction pathways involved in cancer, the recent intense focus on cancer genomics may provide a better understanding of the interplay between cell signaling and chromatin during normal tissue development.

Mutations of Trithorax (Trx)/COMPASS and Polycomb-repressive complex 2 (PRC2) in cancer

The Trx and PCRC2 complexes were identified as factors controlling the developmentally regulated expression of the homeotic gene (Hox) clusters in Drosophila melanogaster (). Trx is essential for maintaining Hox gene activation, whereas PRC2 acts as a transcriptional repressor to prevent ectopic Hox expression. Genetically, these two complexes act in opposition to each other, suggesting that they converge on a common pathway (). Although the importance of Trx and PRC2 in developmental gene regulation has been established for some time (), the biochemical activity of these proteins remained elusive until ∼12 years ago. The first clues to the function of these complexes stemmed from the presence of a SET histone methyltransferase domain protein in both the Trx and PRC2 complexes. Studies in yeast revealed that Trx is a member of the COMPASS family of protein complexes that catalyzes methylation of histone H3 Lys4 (H3K4) (). Biochemical experiments and Drosophila genetics demonstrated that the Enhancer of Zeste [E(Z)] subunit of PRC2 is a histone methyltransferase specific for H3K27 (). Consistent with Trx’s and PRC2’s respective roles as activators and repressors of transcription, histone H3K4 trimethylation (H3K4me3) is associated with active promoters, whereas histone H3K27me3 is associated with transcriptional silencing ().

The first link between Trx function and cancer was made when it was observed that childhood mixed-lineage leukemias (MLLs) contain a translocation occurring at chromosome 11q23 involving the MLL1 gene, one of the two mammalian Trx homologs (). These translocations remove the C-terminal portion of MLL1, containing its catalytic SET histone methyltransferase domain, and create an in-frame fusion to generate gain-of-function chimeric proteins (). Recent work has elucidated the molecular mechanism underlying the oncogenic activity of these MLL1 fusions. A number of the most common MLL1 gene translocation partners, including AF4, AF9, ENL, and ELL, are components of the macromolecular complex called the super elongation complex (SEC) (). SEC associates with positive transcriptional elongation factor B (PTEF-b), a cyclin-dependent kinase (CDK) that promotes RNA polymerase II elongation by phosphorylating its C-terminal domain and other basal factors within the preinitiation complexes (). Thus, MLL1-SEC fusion proteins cause aberrant activation of MLL1 targets through misregulation of transcription elongation. MLL1 is required for normal hematopoietic stem cell function (), and MLL1 fusions likely result in altered stem cell properties that promote tumor formation.

Whereas MLL1 gene mutations involve a characteristic chromosomal translocation in a specific tumor type, PRC2 appears to a have a more complex role in cancer. Frequent point mutations of the EZH2 gene are observed in non-Hodgkin lymphoma (follicular and diffuse large B-cell lymphoma) (). These affect the EZH2 catalytic site and convert Tyr641 (Y641) to a variety of other amino acids, with asparagine being the most common substitution. In vitro, these mutants are unable to methylate an unmodified histone peptide (). However, subsequent studies revealed that these mutations are not inactive but rather possess an altered activity. Remarkably, EZH2 Y641 mutants show increased activity toward the di- and trimethylated states (). Thus, tumor cells with Y641 mutations in the EZH2 gene contain increased H3K27me3. This finding is intriguing because H3K27 monomethylation (H3K27me1), H3K27 dimethylation (H3K27me2), and H3K27me3 were recently shown to have distinct enrichment patterns across the genome, with H3K27me2 being implicated in the suppression of enhancer function (). In addition to Y641, the A677G EZH2 mutant exhibits a similar increase in H3K27me3 accompanied by a decrease in H3K27me2 (). In contrast, a recently characterized A687V mutant displayed both increased H3K27me3 and H3K27me2 (). Remarkably, a Drosophila mutation of E(Z) that mimics the Trx loss-of-function phenotype has also been shown to possess hyperactive methyltransferase activity (). The E(Z) Trx mimic mutation [E(z)(Trm)] converts Arg741 (Arg727 in human EZH2) to lysine (R741K), suggesting that this position may also be important for regulating PRC2 catalytic activity (). The activating nature of these mutations makes PRC2 an attractive target for therapeutic intervention. Recently, a small molecule inhibitor of EZH2, GSK126, was shown to specifically inhibit the growth of B-cell lymphomas containing activating EZH2 mutations, whereas tumor lines with wild-type EZH2 were largely unaffected ().

While EZH2 activating mutations are common in non-Hodgkin lymphoma, loss of PRC2 activity is associated with cancer development in other contexts. Inactivating mutations of the PRC2 components EZH2SUZ12, and EED are detected in T-cell acute lymphoblastic leukemia (T-ALL) (Fig. 2). Removal of the H3K27 methyl mark is catalyzed by the Jumonji domain containing demethylases UTX/KDM6A and JMJD3/KDM6B (). A recent study explored whether disruption of UTX and JMJD3 activity might provide a therapeutic benefit for T-ALL by increasing H3K27me3 levels (). Surprisingly, UTX and JMJD3 have strikingly distinct roles in T-ALL. UTX acts as a tumor suppressor, as mice with a NOTCH1-driven model of T-ALL succumb to disease more rapidly on a UTX mutant genetic background (). In contrast, JMJD3 is highly expressed in T-ALL versus normal T cells and is required for leukemogenesis, as mice with JMJD3 mutant T-ALL show improved survival rates. GSK-J4, an inhibitor of KDM6-type demethylases (), causes cell cycle arrest and apoptosis in T-ALL cells but not myeloid leukemia or normal hematopoietic progenitors (). Remarkably, GSK-J4 treatment results in gene expression changes that resemble knockdown of JMJD3 but are inversely correlated with the changes observed for UTX knockdown. Chromatin immunoprecipitation (ChIP) combined with sequencing (ChIP-seq) revealed a significant overlap between JMJD3 and NOTCH1 targets, including genes with known oncogenic function such as HEY1, NRARP, and HES1. Strikingly, these genes gain H3K27me3 and are repressed upon JMJD3 depletion or GSK-J4 treatment. It is unclear why GSK-J4 appears to inhibit JMJD3 but not UTX functional activity in T-ALL, but perhaps the molecule has a higher affinity for JMJD3 in vivo. Recent studies have also suggested that GSK-J4 may also target KDM5-type demethylases but with an affinity five to 10 times lower than JMJD3 and UTX (). Despite these caveats, GSK-J4 appears to be a promising drug for modulating chromatin modifications and perhaps a chemotherapeutic agent.

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Drugging the histone H3K27 methyl/acetyl switch in cancer. (A) Antagonism between H3K27 methylation and acetylation machinery. H3K27 methylation and acetylation are mutually exclusive, and the PRC2 and CBP/p300 complexes act in opposition to one another. In addition, deacetylation of H3K27ac by the HDAC1/2–NURD complex promotes PRC2-mediated repression, whereas demethylation of H3K27me3 by UTX within COMPASS or JMJD3 is required for acetylation to occur. (B) In NOTCH-driven T-ALL, the histone H3K27 demethylases UTX and JMJD3 have distinct functions. UTX acts as a tumor suppressor by activating genes such as FBXW7 that negatively regulate the NOTCH pathway. In contrast, JMJD3 exists in a complex with NOTCH and is responsible for activation of oncogenic NOTCH targets. Inhibition of JMJD3 with the small molecule GSK-J4 promotes PRC2-mediated H3K27me3 at NOTCH target genes, resulting in their silencing. (C) MPNSTs often carry mutations in the genes encoding the components of both the RAS pathway inhibitor NF1 and the PRC2 component SUZ12. In this cell type, PRC2 functions to suppress RAS target genes. Reduced H3K27 methylation by PRC2 results in increased H3K27ac, increased recruitment of BRD4, and amplification of the RAS transcriptional signature. Inhibition of BRD4 with JQ1 in combination with dampening of the RAS pathway with the MEK inhibitor PD-0325901 suppresses RAS targets, resulting in tumor regression.

Loss of PRC2 components EED and SUZ12 is often detected in combination with mutation of NF1 and CDKN2A genes in malignant peripheral nerve sheath tumors (MPNSTs) (Fig. 2). In addition to loss of H3K27me3, PRC2 mutant MPNSTs also display increased H3K27 acetylation (H3K27ac) levels, an effect observed for loss of PRC2 in multiple contexts (). Histone H3K27 methylation and acetylation are mutually exclusive modifications that correlate with gene silencing and activation, respectively. Strong evidence suggests that complexes responsible for implementing these modifications act in opposition to one another (). A recent study examined whether these increased acetylation levels in MPNSTs could serve as a therapeutic target. Bromodomain-containing protein 4 (BRD4) is a member of the bromodomain and extraterminal (BET) family of chromatin-associated proteins that bind to acetylated histone H3 and H4 via tandem bromodomains (). The small molecule JQ1 binds to the BRD4 bromodomains and evicts the protein from chromatin (). JQ1 has shown promise as a potential chemotherapeutic agent in a number of cancers in part due to regulation of the c-Myc oncogene by BRD4 (). BRD4 localizes to enhancers containing H3K27ac, and the effects of JQ1 may involve disruption of enhancer activity (). As PRC2 mutant MPNSTs display increased H3K27ac levels, BRD4 is an attractive target in this context. Indeed, loss of SUZ12 and NF1 (a negative regulator of the oncogenic RAS pathway) in MPNSTs renders them sensitive to treatment with JQ1 in combination with inhibition of the RAS pathway by the MEK inhibitor PD-0325901 (). Interestingly, the RAS pathway and PRC2 appear to synergize in MPNSTs, as SUZ12 loss promotes cell proliferation in NF1 mutant cells but not wild-type cells, and, moreover, SUZ12 loss enhances the RAS transcriptional signature (). MEK inhibition has been shown to inhibit PRC2 activity in embryonic stem cells, suggesting a potential negative feedback loop (). It will be important to determine the molecular details of the connection between RAS/MEK signaling and PRC2 activity and examine whether this link is conserved in multiple types of cancer.

PRC2 gene mutations in cancer highlight both the biochemical complexity of chromatin-modifying pathways and the rich potential for therapeutic intervention. In PRC2 loss-of-function cancer models, inhibition of BRD4, which binds to increased acetylated histones in PRC2 mutant cells, as well as inhibition of H3K27me3 demethylases show therapeutic effects. In contrast, drugs inhibiting EZH2 activity are more appropriate for non-Hodgkin lymphomas carrying hyperactive EZH2 mutations. Thus, the search for therapeutic targets should take into consideration cross-regulation between histone modification pathways (i.e., methylation and acetylation) as well as effectors of those pathways, such as bromodomain and chromodomain proteins that bind to modified histones. These studies also highlight the importance of determining the precise mutational status of individuals to determine what pathways should be targeted for treatment.

Misregulation of enhancer chromatin in cancer

Enhancers are noncoding DNA elements that play an essential role in transcriptional regulation by conferring tissue-specific gene expression patterns (). Although enhancers have been intensely studied for several decades, their precise mode of action is not fully understood. Enhancers can act across very long ranges of intervening DNA to activate a specific promoter (). Enhancer–promoter communication involves the formation of chromatin loops mediated by cohesin complexes and other trans-acting factors (). However, the mechanisms that restrict enhancer activity to a single promoter in the presence of multiple promoter choices are unclear.

Enhancers carry a unique chromatin structure characterized by the presence of 3K4me1 (). In addition, histone H3K27ac distinguishes active enhancers from poised enhancers (). Promoters typically contain H3K4me3 implemented by the Set1A/B and MLL1/2 COMPASS-like complexes, whereas MLL3/4 COMPASS catalyzes H3K4me1 at enhancers (). Acetylation of H3K27 is mediated by the acetyltransferases CREBBP (CBP) and EP300 (p300) (). Besides H3K4me1 methylase activity, MLL3/4 complexes also contain the H3K27 demethylase KDM6A (UTX), raising the possibility that removal of H3K27 methyl marks by the MLL3/4 complex facilitates acetylation by CBP and p300 ().

Recent genome-wide studies have identified mutations in genes for the regulators of enhancer chromatin in cancer (). Mutations of the H3K4 monomethylases MLL3 and MLL4 as well as their cofactor, UTX, within the COMPASS family have been identified in a range of malignancies, including the pediatric brain cancer medulloblastoma (), non-Hodgkin lymphoma (), and bladder cancer (). MLL4 is particularly frequently mutated in non-Hodgkin lymphomas and often co-occurs with mutations in the histone acetyltransferase gene CREBBP and activating mutations of EZH2 (). Mutations of EP300 and CREBBP have been found to co-occur with UTX in bladder cancer (). MEF2B, a transcription factor involved in recruiting CREBBP and EP300 to target sites in chromatin, is frequently mutated in non-Hodgkin lymphoma (). Intriguingly, the majority of these mutations result in single amino acid changes at one of four positions (K4, Y69, N81, and D83) (), and a subset of these mutations results in increased MEF2B transcriptional activation activity by loss of binding to the corepressor CABIN1 () Another enhancer-associated factor, LIM domain-binding protein 1 (LDB1), is mutated in medulloblastoma (). LDB1 is involved in the formation of chromatin loops in both Drosophila and mammalian cells and participates in enhancer–promoter communication ().

A large body of evidence implicates enhancer malfunction in cancer, and much remains to be learned about the molecular mechanisms of this process (). For instance, how does mutation in genes for factors such as EP300 and CREBBP that are thought to function globally at most enhancers play a role in cancer development? Inappropriate enhancer–promoter communication is known to play a role in the pathogenesis of some cancers. For instance, the classical chromosomal translocation found in Burkitt’s lymphoma places the c-Myc gene under the regulation of the immunoglobulin heavy chain enhancer, thus boosting its expression in B cells, resulting in lymphomagenesis. Recent studies of acute myeloid leukemia with a chromosomal translocation near the GATA2 and EVI1 genes revealed that this inversion allows a GATA2 enhancer to inappropriately activate EVI1 expression (). This raises the possibility that mutation in genes for enhancer-associated factors may lead to defective enhancer–promoter restriction, perhaps allowing for promiscuous activation of oncogenic gene products ().

Histone gene mutations in cancer

Mutations and translocations in genes encoding chromatin regulatory proteins such as the MLL family within COMPASS have been linked with oncogenesis for many years (); however, cancer-associated mutations of histone genes themselves were only recently identified. Genome sequencing studies of aggressive pediatric brainstem glioma uncovered point mutations in histone H3 (). These mutations convert Lys27 to methionine (H3K27M) or Gly34 to arginine or valine (H3G34R/V), occurring primarily in the replication-independent histone H3.3 (H3F3A) and, to lesser extent, the replication-dependent histone H3.1 (HIST1H3B) (). Strikingly, these mutations occur in only a single copy of the multiple histone H3 genes, suggesting that they have gain-of-function activity. Mutations of H3K27M and H3G34R/V define distinct subtypes of glioma, as they occur in distinct regions of the brain and display unique molecular characteristics ().

Histological examination of tumors harboring the H3K27M mutation revealed a dramatic reduction in the levels of H3K27me3 (). Further molecular studies revealed that H3K27M as well as other histone lysine-to-methionine mutants act as dominant inhibitors of histone lysine methylation pathways in tissue culture (). Histone H3K27M expression in Drosophila recapitulates the phenotype observed for depletion of the PRC2 component E(Z) and mirrors the phenotype of replacing all histone H3s with a H3K27R mutant (). In contrast, the H3K34R/V mutations do not dominantly inhibit bulk H3K27me3 or H3K36me3 in trans but do block methylation of H3K36 in cis ().

The precise mechanism of H3K27M action is still unclear. In vitro methyltransferase assays and immunoprecipitation followed by Western blotting suggest that H3K27M interacts strongly with EZH2 (). However, using an unbiased proteomic approach, we failed to detect increased enrichment of PRC2 subunits relative to wild-type H3.3 control (). In contrast, we found increased association of the bromodomain protein BRD4, which is consistent with increased histone acetylation levels observed in H3K27M mutant cells (). It is also intriguing that mutations in genes encoding for the PRC2 components do not appear to be prevalent in these pediatric gliomas.

Recent studies of chondroblastoma and giant cell tumors of bone revealed additional histone H3.3 gene mutations associated with distinct disease phenotypes (). Remarkably, 95% of chondroblastoma samples analyzed carried a mutation of the H3.3 gene at Lys36 to methionine (H3.3K36M) in the H3F3B gene, whereas 92% of giant cell tumors of bone harbored mutations of H3.3 Gly34 to tryptophan or leucine (). Similar to H3.3K27M, H3.3K36M can dominantly inhibit methylation of H3K36 ().

Histone gene mutations in cancer are not restricted to histone H3. Recent work in follicular lymphoma identified mutations in a number of histone H1 genes (). Whereas histone H2A, H2B, H3, and H4 constitute the nucleosome core, histone H1 acts as a linker histone and is involved in chromatin compaction. Like H3 gene mutations, H1 gene mutations are primarily single amino acid substitutions; however, instead of occurring at a few specific positions, the H1 gene mutations are scattered throughout the H1 globular domain (). Molecular analysis of one of these mutants, H1S102F, revealed that it has a reduced capacity to associate with chromatin () and binding to DNA methyltransferase 3B (DNMT3B) (). This suggests that histone H1 may lead to defective chromatin compaction and cause transcriptional misregulation or result in genomic instability. It will be important to examine the molecular function of histone H1 gene mutations in B-cell lymphoma in more detail.

Analysis of mutations that co-occur or are mutually exclusive to histone H3 gene mutations have been insightful. For instance, in pediatric glioblastoma, mutations of histone H3K27M, H3G34R/V, and isocitrate dehydrogenase 1 (IDH1) are mutually exclusive and occur in tumors with different molecular signatures, neuroanatomic locations, and prognostic outcome (). H3K27M mutants lose H3K27 methylation, whereas H3G34V/R mutants display DNA CpG hypomethylation, and IDH1 mutants have a CpG hypermethylation phenotype (). Mutations of the IDH1 gene are particularly prevalent in glioma but are also detected in leukemias (). IDH1 alterations occur in the substrate-binding site at position Arg132, and most mutations convert this residue to histidine (IDH1 R132H), although other substitutions have also been detected (). Under normal circumstances, IDH1 converts isocitrate to α-ketoglutarate and nicotinamide adenine dinucleotide phosphate (NADP+) to NADPH. However, the mutant IDH1 R132H enzyme generates the 2-hydroxyglutarate in place of α-ketoglutarate (). This metabolite inhibits α-ketoglutarate-dependent enzymes (including Jumonji-containing histone demethylases) as well as TET family methylcytosine dioxygenases thought to be involved in the process of DNA demethylation by converting 5-methylcytosine to 5-hydroxy-methylcytosine (). Thus, cells with the mutant IDH1 gene display CpG hypermethylation as well as increased histone lysine methylation. Interestingly, histone H3G34R/V gene mutations show an opposite effect on CpG methylation (). It is also notable that H3G34R/V gene mutations tend to co-occur with mutations of the histone H3.3 chaperone genes ATRX and DAXX, suggesting that altered histone incorporation into chromatin may play a role in these cancers ().

Recently, mutations in the gene for BMP receptor ACVR1/ALK2 were detected in pediatric glioma with H3K27M mutations (). These point mutations convert ACVR1 into a constitutively active form, and several cancer-associated mutations are identical to those found in the rare but devastating bone formation disorder fibrodysplasia ossificans progressiva (FOP) (). Interestingly, ACVR1 mutations tend to overlap with H3.1K27M mutations. Mutations of H3.3K27M are more prevalent than H3.1K27M in pediatric gliomas (), and these mutational types have distinct properties, as patients with H3.1K27M show an early disease onset with tumors located in the pons, whereas H3.3K27M tumors are located at multiple brain regions along the midline (). Determining the biological significance of these mutational signatures will be important to understanding pediatric glioma and may shed light onto other developmental disorders, such as FOP.

Maintenance of genome stability through heterochromatin

In eukaryotic cells, chromosomal structures such as pericentromeric regions and telomeres are associated with blocks of condensed heterochromatin (). Heterochromatin is characterized by histone hypoacetylation and methylation of histone H3 at Lys9, which serves as a binding substrate for the chromodomain protein heterochromatin protein-1 (HP-1) (Fig. 3). These features are essential for normal chromosome function and establish a transcriptionally repressed state (). Maintenance of heterochromatic silencing is dependent on both histone H3K9 methyltransferases and HP-1 proteins (Fig. 3). Moreover, heterochromatin is epigenetically stable through a self-reinforcing circuit by which HP-1 associates with the DNA replication machinery and recruits H3K9 histone methyltransferase complexes ().

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Maintenance of genome stability through the heterochromatin pathway. Centromeric heterochromain is essential for normal segregation of chromosomes during mitosis, and defects in this pathway result in aneuploidy. H3K9me3 and binding of HP-1 are hallmarks of heterochromatin. At pericentromeric heterochromatin, SETDB1 monomethylates H3K9, whereas Suv39 converts H3K9me1 to H3K8me2/3. Disruption of Suv39 function results in aneuploidy and lymphoma development in mice. Active deacetylation is also important for centromeric heterochromatin. Treatment of cells with the class I and II histone deacetylase inhibitor TSA results in abnormal mitosis. Similarly, Suv39 and SETDB1 are essential for telomeric heterochromatin. At telomeres, disruption of Suv39 results in loss of H3K9me2/3 and a depletion of HP-1 recruitment. However, Suv39 mutant telomeres contain increased H3K9me1 mediated by SETDB1 and exhibit abnormal telomere lengthening. Overexpression of SETDB1 has been reported in some cancers. Whereas centromeres depend on type I and II HDACs, the sirtuin deacetylase SIRT6 is essential at telomeres. Lack of SIRT6 in mice results in telomere fusions and premature senescence. In other contexts, SIRT6 functions as a tumor suppressor.

Heterochromatin plays an essential role in genomic stability at multiple levels. Mice doubly mutant for the H3K9 methyltransferases Suv39h1 and Suv39h2 lack H3K9 methylation at pericentric heterochromatin, exhibit aneuploidy and male germline meiosis defects, and develop B-cell lymphomas (). Mutations in the gene for the H3K9 methyl-binding protein HP1 also disrupt genomic stability through both aberrant centromere and telomere function. HP1 mutant flies display defective chromosome segregation as well as telomere fusions (). Interestingly, cells mutant for Suv39h1 and Suv39h2 exhibit abnormally elongated telomeres (). These mutant telomeres have reduced H3K9me2/3 and loss of HP-1 binding but display increased H3K9me1 (). This is consistent with the function of SETDB1 as a H3K9 monomethyltransferase, whereas Suv39h1/2 act as H3K9 di- and trimethylases (). Intriguingly, studies suggest that amplification of SETDB1 may play a role in development of human cancer as well as in a zebrafish model of melanoma (). It remains to be examined whether these oncogenic effects may be mediated through abnormal telomere lengthening.

Maintenance of histone hypoacetylation is also important for heterochromatin function. Treatment of cells with the class I and II histone deacetylase inhibitor trichostatin A (TSA) results in loss of HP1 binding to pericentric regions and relocalization of these domains to the nuclear periphery (). TSA also causes abnormal mitotic structures consistent with a defect in centromere function (). SIRT6, a histone deacetylase specific for histone H3K9, is essential for maintenance of telomeric heterochromatin (). SIRT6 mutant mice display genomic instability and exhibit a premature aging phenotype (). Human cells depleted for SIRT6 display telomere hyperacetylation, chromosome end-to-end fusions, and premature senescence that can be rescued by overexpression of telomerase (). While Sirt6-null mice exhibit premature aging and early death, they do not develop spontaneous tumors (). However, immortalized Sirt6-null mouse embryonic fibroblasts (MEFs) are able to form tumors in immunocompromised mice even in the absence of transformation with an activated oncogene (). Moreover, SIRT6 is frequently deleted in human cancer, and a conditional mutant mouse model revealed it to act as a tumor suppressor in an intestinal cancer model in vivo ().

Recent work has linked heterochromatin function to the regulation of DNA replication. Methylation of histone H3K9 and K36 have been linked to DNA replication in fission yeast (). The mammalian Jumonji domain protein KDM4A/JMJD2A is a histone lysine demethylase specific for methylated H3K9 and K36 (). Studies in Caenorhabditis elegans and mammalian cells revealed that KDM4A overexpression positively regulates S-phase progression, whereas depletion slowed DNA replication and induced cell death (). Moreover these effects were dependent on HP1 levels, implying that KDM4A influences cell cycle in part by removing H3K9me3 and evicting HP1. A follow-up study revealed that KDM4A is amplified in human cancers, and overexpression in tissue culture results in focal copy number gains during DNA replication (). However, these copy number gains are transient and become resolved during entry into G2/M through an as-yet-undetermined mechanism (). These copy gains are suppressed by increasing the cellular concentration of the H3K9 methyltransferase Suv39h1 or HP1-γ. Interestingly, expression of the mutant histones H3.3K9M or H3.3K36M, which inhibit bulk methylation of H3K9 and H3K36, respectively, also results in copy number gains. Recent work has shown that H3.3K9M disrupts heterochromatic transcriptional silencing in D. melanogaster (). Whereas the function of H3K9 methylation in heterochromatin is well established, studies by Whetstine and colleagues () implicate H3K36 methylation in a pathway involving heterochromatin machinery that controls mammalian DNA replication. In yeast, H3K36 methylation restricts nucleosome dynamics over transcribed regions and prevents “cryptic” transcription (). Perhaps a similar mechanism is involved in restricting access of DNA replication machinery.

Concluding remarks

The role of chromatin proteins in cancer is complex and highly context-specific. Relatively few chromatin modifiers seem capable of independently causing cancer development; they are typically mutated in combination with essential tumor suppressors and cell cycle regulators such as p53 and CDKN2A. Although some chromatin regulators, such as the MLL3/4-UTX of the COMPASS family, may play a broad tumor suppressor role in various cancers, many mutant chromatin proteins are highly tissue-specific. Moreover, in the case of PRC2, both hyperactivating and loss-of-function mutations are found in cancers of distinct origins. Whereas B-cell lymphomas tend to acquire hyperactivating mutations of the EZH2 gene in combination with loss of MLL4, other cancer types, such as T-ALL and MPNST, harbor inactivating mutations in genes encoding for PRC2 components EZH2, EED, and SUZ12. These differences likely reflect tissue-specific functions for PRC2. Thus, it is important to determine the precise molecular consequence of altered chromatin proteins, particularly in the case of point mutations that may cause either loss of function or gain of function. As the majority of cancer-associated mutations in chromatin protein-encoding genes have yet to be functionally characterized, biochemical analysis of these mutants may lead to exciting new avenues of research.

The rapid proliferation of next-generation genome sequencing promises to reveal not only novel mutations involved in cancer but also co-occurring and mutually exclusive mutations. These will likely connect developmental signaling pathways to their downstream chromatin effector proteins. In the instance of the NF1 mutant MPNST, PRC2 appears to dampen the RAS signaling pathway. Similarly, in T-ALL, PRC2 antagonizes the NOTCH1 signal transduction pathway, whereas the H3K27 demethylase JMJD3 directly associates with NOTCH1 to remove PRC2-deposited H3K27me3. Interestingly, recent studies have identified activating mutations in the gene for the BMP receptor ACVR1/ALK2 in combination with histone H3.1K27M gene mutations, suggesting a potential connection between BMP–SMAD1/5/8 signaling and PRC2-mediated repression. Thus, future collaborative efforts between clinicians, geneticists, biochemists, and developmental biologists may shed light onto both the mechanisms underlying cancer development and the connection between cell signaling pathways and the chromatin signatures of cancer.

Acknowledgments

We are grateful to the members of the Shilatifard laboratory for conversation and discussion during the writing of this review. Studies in A.S.’s laboratory are supported by grants R01CA150265, R01GM069905, and R01CA89455 to A.S.

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Live Notes from @AACR’s #cbi16 Meeting on Precision Medicine: 5:10PM Big Idea A survivor’s Story

Tom Whitehead, father of Emily, CHOP’S first CAR-T success story

Reporter: Stephen J. Williams, Ph.D.

  • Emily Whitehead was 5 years old when came to UPENN and CHOP (2010) with unresponsive leukemia
  • she was healthy up to day she was diagnosed and went to Hershey Medical Center and recieved diagnosis of CLL (came in with 21 bruises, symptom of leukemia)
  • parents told her that it would be the roughest time of her life but they would always tell her the truth about what would happen
  • she started to have relapsed disease
  • Dr. Sue Reingold at CHOP said to get transplant but could do at Hershey
  • Feb. 2012 thought got a matching donor but up to May did not find one, they wanted to do new rounds of chemo but Emily did not want that and CHOP suggested a new drug but they felt it was not right for her

 

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Is the Warburg effect an effect of deregulated space occupancy of methylome?

Larry H. Bernstein and Radoslov Rosov, co-curation

LPBI

UPDATED

8/20/2024

Editor Correction:  One of the co-curators names on this article was misspelled. The co-curators should be Larry H. Bernstein and  Radislov Rosov.

Therefore the correction version of the article title and authors should read

Is the Warburg effect an effect of deregulated space occupancy of methylome?

Larry H. Bernstein and Radoslov Rosov, co-curation

The editors of LPBI Group apologize for the confusion.

 

It would appear that pyruvate is directly used by cancer cell machinery for sustaining genome independence, and that CRISP-Cas9 system is essentially a modified CAD protein for making small bases.

13C-labeled biochemical probes for the study of cancer metabolism with dynamic nuclear polarization-enhanced magnetic resonance imaging

Lucia Salamanca-Cardona and Kayvan R. Keshari

Cancer & Metabolism 2015; 3:9          http://dx.doi.org:/10.1186/s40170-015-0136-2

In recent years, advances in metabolic imaging have become dependable tools for the diagnosis and treatment assessment in cancer. Dynamic nuclear polarization (DNP) has recently emerged as a promising technology in hyperpolarized (HP) magnetic resonance imaging (MRI) and has reached clinical relevance with the successful visualization of [1-13C] pyruvate as a molecular imaging probe in human prostate cancer. This review focuses on introducing representative compounds relevant to metabolism that are characteristic of cancer tissue: aerobic glycolysis and pyruvate metabolism, glutamine addiction and glutamine/glutamate metabolism, and the redox state and ascorbate/dehydroascorbate metabolism. In addition, a brief introduction of probes that can be used to trace necrosis, pH changes, and other pathways relevant to cancer is presented to demonstrate the potential that HP MRI has to revolutionize the use of molecular imaging for diagnosis and assessment of treatments in cancer.

 

Since the hallmark discovery of the Warburg effect in cancer cells in the 1920s, it has been widely accepted that the metabolic properties of cancer cells are vastly different from those of normal cells [1]. Starting from the observation that many cancerous (neoplastic) cells have higher rates of glucose utilization and lactate production, the development of tools and methods to correlate specific cellular metabolic processes to different types of cancer cells has received increased research focus [2, 3]. Several imaging techniques are currently in use for this purpose, including radiography, scintigraphy, positron emission tomography (PET), single-photon emission computed tomography (SPECT), and magnetic resonance (MR) [4, 5].

For more than 30 years, MR has been a revolutionary diagnostic tool, used in a wide range of settings from the central nervous system to cardiomyopathies and cancers. MR imaging (MRI) can outline molecular and cellular processes with high spatial resolution. Typically, MRI of body tissues is achieved via contrast visualization of the protons (1H) of water, which are present in high abundance in living systems. This can be extended to MR spectroscopy (MRS), which can further differentiate between less abundant, carbon-bearing, biological metabolites in vivo utilizing 1Hs of these compounds [6, 7]. However, despite its usefulness in imaging whole body tissues, 1H MRS has low spectral resolution and poor sensitivity for these less abundant metabolites. In addition,13C MRS is increasingly difficult, in comparison to 1H MRS, in that both the gyromagnetic ratio (approximately 25 % of 1H) and natural abundance (1.1 % of 1H) are significantly lower, making the detection of carbon-bearing compounds difficult [8, 9]. The low spectral resolution of 1H MRS for metabolites can be addressed by using 13C-enriched compounds, and with this direct 13C MRS, metabolic processes can be traced, utilizing enriched tags on specific carbons in a given metabolite [10]. While enrichment of molecules in 13C can also moderately address the sensitivity limitation of MRS, recent work in hyperpolarization (HP) provides a means of dramatically increasing sensitivity and enhancing signals, well beyond that of the equilibrium state obtained via MRS. [11, 12]. The focus of this review will be the introduction of this approach in the setting of cancer metabolism, delineating probes of interest, which have been applied to study metabolic processes in vivo.

Obtaining a hyperpolarized probe

In MR, a desired target is placed in a magnetic field where the nuclear spins of molecules are aligned with or against the direction of the magnetic field. The nuclear spins have thus different energies, and an MR signal is detected upon relaxation of nuclear spins of higher energy. At thermal equilibrium, the number of spins aligned with the magnetic field nearly equals the number of spins opposing the direction of the magnetic field. Thus, at thermal equilibrium, spin polarization is in the order of >0.0005 % resulting in a limited signal. Signal increases on the order of 100,000-fold can be achieved by hyperpolarizing the system via the redistribution of the spin population levels found at equilibrium [10, 13]. There are several techniques that have been used to achieve hyperpolarization of various nuclei: spin-exchange optical pumping of 3He and 129Xe, parahydrogen-induced polarization (PHIP), and dissolution dynamic nuclear polarization (DNP) [11,14, 15]. Both PHIP and DNP techniques can polarize biologically relevant nuclei like 13C and 15N, although there is a wider range of molecules that can be targeted for hyperpolarization using dissolution DNP [14, 1618].

The goal of DNP is the transfer of polarization from highly polarized unpaired electron spins to the nuclear spins of a desired target compound. This is achieved by applying an external magnetic field to a free-radical agent in order to polarize electron spins, followed by saturating the electron spin resonance via microwave irradiation in order to obtain polarization transfer. The free-radical agent is generally a stable organic compound that is compatible with aqueous buffers, which are used as solvent in order to obtain a homogeneous distribution of the radical [13]. Nearly 100 % of the electrons on the free-radical agent are polarized when the free-radical/solvent mixture is subjected to high magnetic fields (≥3.3 T) followed by rapid freezing to 1 K using liquid helium in order to obtain a sample frozen to an amorphous state, which is necessary for retention and transfer of polarization [18]. For biological applications, after transfer of electron spin polarization to the nuclei of interest has occurred, the preparation must exist in solution, which can be achieved utilizing a dissolution process in which the solid sample is rapidly melted via injection of a hot solvent, typically a biologically compatible buffer, into the frozen sample [13]. The dissolution process results in a liquid sample at room temperature, while still preserving the enhanced polarization obtained by the microwave irradiation of the frozen sample [8]. Additionally, the use of chelating agents (e.g., EDTA) with the solvent to eliminate trace metals and more recently the use of gadolinium (Gd) chelates with the DNP sample have been used to further enhance and retain polarization in the liquid sample, albeit with caution over potential toxic effects when applied in vivo and the potential for loss of hyperpolarization due to T 1 shortening [11, 19, 20]. More in-depth exploration of the technical aspects of probe development has been previously reviewed [8, 11].

Considerations in probe selection and current research

The usefulness of a molecule for hyperpolarized MRS is dependent on the polarization lifetime of the nucleus of interest, and this property is determined by the spin-lattice relaxation constant (T1) [21]. Dipolar coupling, the magnetic field range, and molecular size can also affect the T1 of a given nucleus. In general, high magnetic fields and large molecular weights decrease the T1. Dipole-dipole coupling of 13C with 1H is common in biologically relevant molecules, and it shortens relaxation times; therefore, carbon atoms directly bound to 1H are generally not useful as probes for HP. For example, all carbons present in glucose (an important substrate in cancer cells) have relaxation times shorter than 2 s [22]. On the other hand, carbonyl carbons of biologically relevant molecules generally have T1’s above 20 s even at high magnetic fields like [1-13C] pyruvic acid, which has relaxation times of 67, 48, and 44 s at 3, 11.7, and 14.1 T, respectively [2325]. Even carbons that are less oxidized than carbonyls, like the hemi-ketal in [2-13C] fructose have T1’s one order of magnitude higher than glucose carbons. Short spin-lattice relaxation times can sometimes be increased by deuterium enrichment of the sample. With this technique, protons that are directly bound to carbons are exchanged for deuterium atoms which results in the reduction of dipole-dipole relaxation, further preserving the hyperpolarized state [26]. This has resulted in increased T1’s of 13C nuclei in molecules such as glucose (T1 increased from 2 s to 10–14 s), providing the possibility of utilizing them in future metabolic studies [2729]. Despite the effect of deuterium enrichment, research efforts have largely focused on developing carbonyl-bearing molecules as molecular imaging probes. The focus of this review is to introduce representative compounds relevant to metabolism that are characteristic of cancer tissue and have been applied in the work of multiple groups: aerobic glycolysis, glutamine addiction, and the redox state.

Pyruvate and aerobic glycolysis

Of particular interest to cancer metabolism is the increased conversion of glucose to lactate as a result of modulated aerobic glycolysis. This process, also known as the Warburg effect, is characteristic of many tumors with altered metabolism where pyruvate generated from glucose metabolism via glycolysis is preferentially converted to lactate by lactate dehydrogenase (LDH) as opposed to entering the tricarboxylic acid cycle [1]. With this phenotype, cancer cells show a preference for lactate fermentation even in the presence of oxygen, thus bypassing oxidative respiration for ATP generation. Because of this, pyruvate has been the preferred probe for HP MRS research since it is an intermediate metabolite in pathways characteristic of aberrant metabolism in cancer cells, including increased lactate production as a result of aerobic glycolysis where detection of HP pyruvate-derived lactate can be used as a marker for cancer and response to treatment [30, 31] as well as an intermediate in amino acid metabolism (e.g., interconversion to alanine via transamination with glutamate) (Fig. 1). In addition, as mentioned before, carbonyl carbons in pyruvate have long relaxation times where even the methyl carbon can have T1’s above 50 s after deuterium enrichment [32]. The interconversion of pyruvate to lactate has been exploited for MRI by using [1-13C] pyruvate and detecting the accumulation of increased lactate in cancerous tissue as compared to surrounding benign tissue. Increased conversion of pyruvate to lactate and alanine has been demonstrated to precede MYC-driven tumorigenesis by using HP [1-13C] pyruvate in murine models [33]. Furthermore, in the same study, a decrease in the flux of alanine was observed at the tumor stage while a decrease in lactate conversion was indicative of tumor regression [33]. In transgenic adenocarcinoma of mouse prostate (TRAMP) models, in vivo studies using HP [1-13C] pyruvate demonstrated that hyperpolarized pyruvate and its metabolic products can be used non-invasively and with high specificity to obtain a profile of the histologic grade of prostate cancers [34]. In vivo imaging following hyperpolarized pyruvate has also been used to evaluate the role of glutaminase and LDH in human lymphoma models [35] as well as to elucidate metabolism of pyruvate in breast cancer [36] and renal cell carcinoma with treatment [30, 37].
http://static-content.springer.com/image/art%3A10.1186%2Fs40170-015-0136-2/MediaObjects/40170_2015_136_Fig1_HTML.gif
Flux of hyperpolarized [1-13C] pyruvate to [1-13C] lactate in prostate regions. a MR image from patient with prostate cancer showing regions of cancerous tissue and surrounding normal tissue. bd Localized dynamic hyperpolarized [1-13C]pyruvate and [1-13C]lactate spectral from voxels overlapping the contralateral region of prostate (turquoise), a region of prostate cancer (yellow), and a vessel outside the prostate (green). Adapted with permission from ref. [43]

Early work that utilized HP pyruvate to assess the response of tumors to treatment was conducted in mice xenografted with EL-4 lymphoma cells and treated with etoposide, a topoisomerase inhibitor that causes rapid cell death [38, 39]. In this study, tumor necrosis was correlated to a decrease in the flux of hyperpolarized lactate which was suggested to be due to a decrease in NAD+ and NADH in the intracellular pool as well as loss of LDH function. More recently, HP [1-13C] pyruvate has been used as a biomarker to evaluate early response to radiation therapy in glioma tumors by observing a decrease in hyperpolarized lactate suggested to be a result of changes in tumor perfusion which can be detected between 24 and 96 h following treatment [40, 41]. HP [1-13C] pyruvate has also been used to detect early response to temozolomide (TMZ) treatment on human glioblastoma rat models [42]. The study successfully showed for the first time detection of response to TMZ therapy 1 day after TMZ administration. The continued reports on using HP pyruvate as an imaging probe for assessing treatment response indicate the potential of the compound to become a standard in the field. Moreover, these studies demonstrate the usefulness of HP [1-13C] pyruvate as a tool for early assessment of therapy response, which can improve treatment selection at the clinical level. Pyruvate has also been validated as a metabolic imaging marker for use in humans [43]. In a two-phase study, patients with biopsy-proven prostate cancer of various histological grades were injected with HP [1-13C] pyruvate. In the first phase, a maximum dose level was determined to establish pharmacological safety of the HP probe while still injecting enough pyruvate to allow visualization. This addressed one of the major challenges faced in translating HP MRI to clinical applications: the potential toxicity of compounds that must be injected into patients. In the second phase, metabolism of pyruvate was visualized in real time and differences in the ratio of [1-13C] lactate to [1-13C] pyruvate between identified cancerous regions and normal tissue regions were successfully observed (Fig. 1ad). [1-13C] lactate in regions that did not contain tumor was not detected, confirming previous biopsy and preclinical studies that demonstrated low flux of [1-13C] pyruvate to lactate and low concentrations of lactate in benign prostate tissues [44, 45]. Preliminary results indicated the possibility of detecting previously unobserved cancerous regions by HP [1-13C] pyruvate, later confirmed to be Gleason 4+3 cancer by biopsy, though further investigation into the relationship between grade and metabolism in prostate cancer patients is needed. While there are challenges associated with translation to clinical use for HP [1-13C] pyruvate, the first in human study demonstrated the feasibility of hyperpolarization technology as a safe diagnostic tool and provides the potential for utilizing this approach in preclinical models with direct translation to the clinic.

Glutamine metabolism

Glutamine is an amino acid that plays an important cellular role as nitrogen donor in the form of an amide group for purine and pyrimidine biosynthesis, leaving a glutamate molecule in the process although glutamine can also be converted to glutamate by glutaminase in a reaction independent of nucleotide biosynthesis. Glutamate is the primary nitrogen donor for the biosynthesis of non-essential amino acids. Transaminases catalyze the transfer of the amine group from glutamate to α-ketoacids to synthesize alanine, aspartate (precursor for asparagine), serine (precursor for glycine and cysteine), ornithine (precursor for arginine), and proline which is derived from the glutamate carbon backbone. Glutamine is considered a non-essential amino acid as it can be recycled from glutamate and ammonia in a reaction catalyzed by glutamine synthetase; however, some cancer cells show increase consumption of glutamine and are unable to grow in the absence of exogenous glutamine [46, 47]. This metabolic characteristic of cells to require exogenous glutamine for growth has been termed “glutamine addiction” and has generated extensive research interest as an indicator of development of cancerous tissues [48]. In particular to the field of HP MRI, the conversion rate of glutamine to glutamate (Fig. 2) was explored in hepatocellular carcinoma (HCC) using a [5-13C] glutamine probe (Fig. 2) [49]. Using the ratio between [5-13C] glutamine and [5-13C] glutamate, it was demonstrated that HCC cells convert glutamine at a higher rate than normal cells supporting the notion of glutamine addiction. One important aspect of this study was the choice of [5-13C] glutamine as a probe as opposed to [1-13C] glutamine, which has a longer T1 (16.1 vs. 24.6 s at 9.4 T) [49, 50]. [5-13C] glutamine was selected because the chemical shift change obtained from [1-13C] in glutamine and glutamate is far too small, which could prevent proper identification and quantification of the peaks. This highlights the importance of understanding not only the target compound to be hyperpolarized but also the metabolic products to be detected and their resulting spectra in MR. This is further emphasized with studies that demonstrate the usefulness of [1-13C] glutamine as a source for [1-13C] glutamate in order to follow the metabolism of α-ketoglutarate to observe the metabolic state of the TCA cycle in transformed cells [51]. Furthermore, [1-13C] α-ketoglutarate has been hyperpolarized and used to visualize other metabolic events involving [1-13C] glutamate such as mutations in IDH1 expression in glioma tumors and pathways dependent on hypoxia-inducible factor (HIF) [5153]. More recently, [5-13C] glutamine has been used to visualize the metabolism of liver cancer in vivo and in vitro, as well as the treatment response of prostate cancer cells in vitro [54]. Based on the promise of glutamine as a biomarker for cancer diagnosis and treatment response, extending the spin-lattice relaxation time of the [5-13C] glutamine has been researched and successfully accomplished. The facile synthesis of [5-13C-4-2H2] glutamine has been reported, and its study showed that by relying on the effect of deuterium enrichment to lessen dipolar coupling effects, the T1 of [5-13C] glutamine could be increased from approximately 15 to 30 s [55]. Visualization of real-time conversion of glutamine to glutamate in SF188 cells was achieved using this probe, demonstrating the promise of [5-13C-4-2H2] glutamine as a probe for molecular imaging of metabolic events in real time. Further investigation of this probe applied to in vivo preclinical models will lay the foundation for its clinical translational potential in the future.
http://static-content.springer.com/image/art%3A10.1186%2Fs40170-015-0136-2/MediaObjects/40170_2015_136_Fig2_HTML.gif
Metabolism of [5-13C] glutamine to [5-13C] glutamate. a Time-dependent spectral data following conversion of [5-13C] glutamine to [5-13C] glutamate. The signals are from 13C-enriched [5-13C]glutamate at 181.5 ppm and [5-13C]glutamine at 178.5 ppm and from natural abundance 13C label in [1-13C]glutamate at 175.2 ppm and [1-13C]glutamine at 174.7 ppm. b Plot of the ratio of the signal intensities of [5-13C]glutamate/[5-13C]glutamine showing the ratio in hepatoma cells (shaded circle), cell lysate (square), and control (triangle). These results demonstrated that hepatoma cancer cells convert glutamine to glutamine at a higher rate than normal cells. Adapted with permission from ref. [49]

Dehydroascorbate as a redox sensor

Reactive oxygen species (ROS) like the hydroxyl radical, superoxide, and hydrogen peroxide have been shown to cause DNA damage and can lead to mutations that transform normal cells into cancerous cells [56]. The reduction/oxidation (redox) state, which is dependent on the balance between oxidizing equivalents like ROS and reducing cofactors, can provide insight into the physiological condition of the cell with respect to potential cancer transformations. Furthermore, the presence of ROS in tissue has been implicated to be a factor in developing resistance to radiation therapies [57]. During oxidative stress (i.e., when there is an increase in ROS), redox homeostasis is maintained by the action of antioxidant compounds, such as ascorbate (or vitamin C, VitC), which can scavenge for ROS and reduce the compounds to rid the cells of damaging agents [58]. In this process, ascorbate that is available to cells in high concentrations can be oxidized to dehydroascorbate (DHA) while reducing ROS. DHA can then be transported into the cell where DHA is reduced back to ascorbate resulting in a process of recycling ascorbate and DHA (Fig. 3) [59]. In this sense, the ratio of DHA to ascorbate can be used as a molecular marker to investigate the redox state and thus the physiological state of tissues. Additionally, conversion of DHA to ascorbate can be enzymatically catalyzed in an NADPH-dependent manner or via oxidation of glutathione (GSH) to glutathione sulfide (GSSG); thus, visualization of ascorbate/DHA metabolism offers a method for probing in vivo metabolism of NADPH as well as determination of GSSG to GSH ratio, both of which have been implicated to be indicators of oxidative stress in the cells, particularly for neurodegenerative, cardiovascular, and cancer diseases [6062]. Hyperpolarized [1-13C] DHA was successfully used in murine models to detect increased reducing capacity in prostate cancer with the purpose of developing a non-invasive, early diagnostic tool for improving selection of treatment therapies [62, 63]. DHA demonstrates a relatively long T1 at clinically relevant field strengths (>50 s at 3 T) and adequate chemical shift separation between it and its metabolic product ascorbate (δ = 3.8 ppm). Increased reduction of HP [1-13C] DHA to ascorbate was observed in tumor tissue compared to normal tissue as well as other metabolic organs (Fig. 3). This was additionally demonstrated in lymphoma cells, further supporting the potential for using DHA as a probe in living systems [64]. A following study validated these results, and the correlation between increased DHA reduction and glutathione was established in vivo, thus showing the utility of [1-13C] DHA as a molecular imaging probe to detect events that go beyond the direct metabolism of DHA [63]. Notwithstanding the potential of HP DHA as a diagnostic probe, the toxicity of DHA remains to be validated. Earlier studies on mammalian cells showed DHA toxicity starting at 10 mM, while a study carried on rats demonstrated neurological effects of DHA starting at injections of 50 mg/kg [65, 66]. However, as outlined above, successful use of DHA injections in rats and mice for hyperpolarization has been demonstrated without reported side effects on the animals. More research is needed to determine the parameters regarding the toxicity of DHA in larger animal models using pure formulations to assess its potential for clinical trials. Further work in DHA could demonstrate its applicability for the study of ROS and redox changes in model systems.
http://static-content.springer.com/image/art%3A10.1186%2Fs40170-015-0136-2/MediaObjects/40170_2015_136_Fig3_HTML.gif
Determination of redox state by imaging of HP [1-13C] ascorbate (VitC) and [1-13C] dehydroascorbate (DHA). Oxidative stress caused by ROS (1.) can be alleviated by oxidation of ascorbate to DHA (2.), and recycling of DHA to ascorbate can occur indirectly with oxidation of glutathione (3.) or directly with oxidation of NADH (4.). The ratio of [ascorbate] to [DHA] has been successfully used in mice models as a biomarker to determine pH in vivo. Adapted with permission from ref. [62]

Other metabolic imaging probes

While the three probes discussed earlier are the most well studied in metabolic events that are characteristic of cancer cells in general, other molecules have been evaluated in their potential to be used as biomarkers. Hyperpolarized bicarbonate (H13CO3) has been successfully used to determine the pH in extracellular matrix of lymphoma tumors in mice, and a correlation between acidic environments and cancer was established [67]. The relaxation times for bicarbonate compounds at 3 T are between 34 and 50 s, which is enough time to detect the rapid conversion of H13CO3 and 13CO2 catalyzed by carbonic anhydrase [23]. The attractive feature of this probe is based on how ubiquitous acidic extracellular environments are to a wide variety of diseases; thus, HP bicarbonate has the potential for clinical translation beyond cancer research, though extensive work will be necessary to generate a preparation which will result in an adequate dose for the clinic [68, 69]. More recently, the potential of α-ketoisocaproate (KIC) as a molecular probe for in vivo detection of branched chain amino acid transaminase (BCAT) has been explored. BCAT catalyzes the conversion of KIC to leucine, and its expression has been suggested to correlate to genetic characterization of certain tumors. In a pilot study, HP α-keto-[1-13C]-isocaproate was shown to have a T1 of 100 s so its metabolism can be sensitively traced for over a minute after injection [70]. In the same study, metabolism of HP [1-13C] KIC to [1-13C] leucine by BCAT was observed in murine lymphoma tumor tissue but was absent in rat mammary adenocarcinoma with a correlation between BCAT expression and [1-13C] leucine signal detection [70]. Additionally, in the same models, [1-13C] pyruvate conversion to [1-13C] lactate and [1-13C] alanine was detected in both types of tumors. These findings show the promise of using [1-13C] KIC as a discriminative probe in addition to pyruvate in order to diagnose different types of cancer [71, 72]. Furthermore, the correlation between BCAT expression and [1-13C] leucine detection was also shown in rat brain tissue, confirming the usefulness of HP [1-13C] KIC in assessing BCAT activity in vivo [73]. Choline is another compound that has been evaluated as a molecular imaging probe since elevated choline and choline-derived metabolites have been correlated by 1H-MRS imaging to cancer in the brain, breast, colon, cervix, and prostate [7476]. Despite its potential as a global marker for cancer because of the long T1 relaxation times that can be achieved with deuterium and 15N enrichment [77, 78], HP applications of 13C enriched choline are limited due to the small change in chemical shifts of choline and choline-derived metabolites as well as its potential toxicity [16, 79, 80]. It has been shown that choline toxicity occurs at doses of 53 mg/kg in mice, although a recent study successfully detected HP 13C choline in vivo without adverse effects in rats at doses of 50 mg/kg by using atropine to prevent cholinergic intoxication [81, 82] though metabolic products have been difficult to visualize in vivo. As mentioned earlier, the usefulness of glucose as a probe is limited due to the short relaxation times of all the carbons present in the molecule and although the T1’s can be increased through deuterium enrichment, the lifetime of the probe remains a hurdle for clinical applications [27, 28]. Thus, fructose (a pentose analog of glucose) has been successfully used as an alternative to probe glycolytic pathways [83] in TRAMP models where differences in HP [2-13C] fructose uptake and metabolism was visualized in tumor regions compared to surrounding normal tissues. Like choline, the limiting factor in the usefulness of [2-13C] fructose for in vivo studies is in small chemical shifts between the metabolite and its phosphorylated product. Finally, tumor necrosis can be used as a measure of treatment response, particularly early necrosis. HP [1,4-,13C] malate has been visualized in lymphoma mice models after injection of HP [1,4-13C] fumarate [84]. In normal cells, fumarate has a slow rate of transport into the mitochondria; however, in necrotic cells where the mitochondrial membrane is degraded, fumarase has access to the HP fumarate and its ubiquitous cofactor, water, thus facilitating rapid conversion to malate. Preliminary studies have shown the potential for its use in animal models though further work is required to determine the necessary density of necrotic cells for detection and the timings required for adequate visualization in patients.

Conclusions

The application of hyperpolarized 13C imaging has been extensively investigated in preclinical models, and the successful demonstration of HP [1-13C] pyruvate in patients with prostate cancer has validated the potential of HP MRI as a safe diagnostic and treatment assessment tool. Application of other probes beyond pyruvate is still in its infancy, particularly because of the need to further study the currently developed models under conditions that are relevant to a clinical setting (i.e., lower magnetic fields) as well as to study the necessary parameters (probe toxicity dose limits, safety limits for rapid injection) to withstand the necessary hurdles to translation. Nevertheless, these vast research findings are promising and indicate an eventual translation to humans. Furthermore, there is a large variety of biologically relevant molecules that have the potential to be hyperpolarized (Fig. 4), and molecular imaging of metabolic events in real time using not only one single probe but a combination of relevant probes could become an invaluable tool in elucidating so far undiscovered metabolic and proteomic interactions that play a role in cancer development and treatment. This gives HP MRI the great potential to revolutionize current molecular imaging technologies.
http://static-content.springer.com/image/art%3A10.1186%2Fs40170-015-0136-2/MediaObjects/40170_2015_136_Fig4_HTML.gif
Metabolic pathways with compounds that can be used as molecular imaging probes for HP MRI. A wide variety of metabolic pathways have already been visualized or have the potential to be visualized using hyperpolarization technology that can be applied to different pathological states of the cell including cardiovascular disease and a large variety of cancers. 1. Metabolism of C1 (red dots) in pyruvate. Theasterisks on selected compounds represent enrichment of 13C in the second pass of pyruvate in TCA cycle. 2. Metabolism of C1 (brown dots) in DHA using a pool of NADPH derived from the pentose phosphate pathway. 3. Metabolism of C1 (blue dots) and C5 (green dots) of glutamine. 4. Metabolism of C1 and C4 (purple dots) of fumarate unrelated to TCA metabolites. 5. Metabolism of extracellular bicarbonate (gray dots). MTC1 monocarboxylate transporter 1, MTC4 monocarboxylate transporter 4,System ASC amino acid transporter, GLUTs glucose transporters, DCT dicarboxylate transporter, DHARdehydroascorbate reductase, GR glutathione reductase, GSH glutathione, GSSG glutathione disulfide,LDH lactate dehydrogenase, ALT alanine transaminase, CA carbonic anhydrase, PC pyruvate carboxylase,PDH pyruvate dehydrogenase, CS citrate synthase, GLS glutaminase, GLDH glutamate dehydrogenase,IDH isocitrate dehydrogenase, OGDC oxoglutarate dehydrogenase complex, SCS succinyl CoA synthetase, SQR succinate dehydrogenase, FH fumarate hydratase, MDH malate dehydrogenase, FUMfumarase. Cofactors have been omitted for brevity

Abbreviations

ALT:   alanine transaminase;   BCAT:  branched chain amino acid transaminase;   DHA:  dehydroascorbate;   DNP:  dynamic nuclear polarization;   EDTA:  ethylenediaminetetraacetic acid;   GSH:  glutathione;   GSSG:   glutathione sulfide;   HCC:  hepatocellular carcinoma;   HIF:  hypoxia-inducible factor;   HP:  hyperpolarized/hyperpolarization;   IDH:  isocitrate dehydrogenase;   KIC:  ketoisocaproate;   LDH:  lactate dehydrogenase;   MR: magnetic resonance;   MRI:  Magnetic resonance imaging;   MRS:  magnetic resonance spectroscopy;   NAD(H):  nicotinamide adenine dinucleotide;   NADP(H):  nicotinamide adenine dinucleotide phosphate;   PET:  positron emission tomography;   ROS:  reactive oxygen species;   SPECT:  single-photon emission computed tomography;   TRAMP:  transgenic adenocarcinoma of mouse prostate

References

  1. Warburg O. On the origin of cancer cells. Science. 1956;123:309–14.View ArticlePubMed
  2. Gatenby RA, Gillies RJ. Why do cancers have high aerobic glycolysis? Nat Rev Cancer. 2004;4(11):891–9.View ArticlePubMed
  3. Vander Heiden MG, Cantley LC, Thompson CB. Understanding the Warburg effect: the metabolic requirements of cell proliferation. Science. 2009;324:1029–33.View ArticlePubMed CentralPubMed
  4. Shie P, Cardarelli R, Brandon D, Erdman W, AbdulRahim N. Meta-analysis: comparison of F-18 fluorodeoxyglucose-positron emission tomography and bone scintigraphy in the detection of bone metastases in patients with breast cancer. Clin Nucl Med. 2008;33:97–101.View ArticlePubMed
  5. Frangioni JV. New technologies for human cancer imaging. J Clin Oncol. 2008;26:4012–21.View ArticlePubMed CentralPubMed
  6. Castillo M, Kwock L, Mukherji SK. Clinical applications of proton MR spectroscopy. Am J Neuroradiol. 1996;17:1–16.PubMed
  7. Barker PB, Bizzi A, De Stefano N, Gullapalli R, Lin DD. Clinical MR spectroscopy: techniques and applications. Cambridge University Press; 2009.
  8. Comment A, Merritt ME. Hyperpolarized magnetic resonance as a sensitive detector of metabolic function. Biochemistry. 2014;53:7333–57.View ArticlePubMed
  9. Rider OJ, Tyler DJ. Clinical implications of cardiac hyperpolarized magnetic resonance imaging. J Cardiov Magn Reson. 2013;15:93.View Article
  10. Golman K, Olsson LE, Axelsson O, Månsson S, Karlsson M, Petersson JS. Molecular imaging using hyperpolarized 13C. Br J Radiol. 2003;76 Suppl 2:S118–S27.View ArticlePubMed

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sjwilliamspa commented on Is the Warburg effect an effect of deregulated space occupancy of methylome?

Is the Warburg effect an effect of deregulated space occupancy of methylome? Larry H. Bernstein and Radoslav Bozov, …

It would be an interesting figure, although I am not sure anyone has been able to measure it, is the spatial distribution of lactate and pyruvate over the tumor as a function of diffusion distance such as a heat map to see if pyruvate and lactate levels have a gradiant over a solid tumor. I am not sure it would but interesting to see where tumor cells, which undergo Warburg type metabolic phenotype actually exist, if it is a function of angiogenesis or a function of the proliferative capacity of cells in situ.

Response by LHB…

Radoslav Bozov has repeatedly referred to the real problem of space/time in the required experimental view that is intractable, as seen by Erwin Schroedinger.  It is confounded by
the restrictions imposed by research, and to an extent also the dilemma of location and velocity.

I think it is to an extent also inherent in the modern revelations of autophagy and apoptosis that were not part of the view in the mid 20th century.  However, the work of B. Chance led to a substantially better understanding of the hydride transfer in the NAD/NADH.  What is overlooked is the important role cited by NO Kaplan of NADPH/NADP vs NADH/NAD associated with synthetic and, alternatively, catabolic processes in the cell. What role the pyridine nucleotide transhydrogenase would play is anyones guess.   In any case the proliferation of malignant cells is dependent on NADPH.  This would limit the NAD/NADH related reactions. The effect in the cytoplasm is PYR –> LAC, with generation of NAD from NADH.  In addition, the type of isoenzyme favored should be consequential.  For instance, the M-type LDH does not form an abortive ternary complex LDH*NAD+*PYR. In addition, Bernstein, Everse and Grisham showed that in cancer there is an aberrant cytoplasmic MDH.

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3 Dimensional Ex vivo Technique for In situ Tumor Growth

Reporter: Stephen J. Williams, Ph.D.

3D Brain Culture, Ex vivo Brain, Vascular Glioma Chemotherapy

Brain tumors are both difficult to treat and hard to study because of the organ they affect. The structure of the brain is extremely sensitive to alterations. Until recently the study of architectural alterations and their effects was mostly restricted to in vivo experiments. Typical culturing of brain tissue requires disaggregation and manipulation into a 2-dimensional format, losing any anatomically relevant structure. To study the in situbrain structure, a new technique has been described by researchers from the University of Erlangen-Nürnberg. By carefully sectioning the brains of 4 day-old mice and placing them on a 0.4 uM pore-size transwell membrane 6 well plate insert within required culture medium, they were able to study the endogenous structure under varying conditions. They injected astrocytes or glioma cells with a micropipette into the slices, and investigated the structural changes brain tumors effect in their environment. Termed the Vascular Organotypic Glioma Impact Model (VOGIM), it revealed all the characteristic pathological alterations normally associated with the disease in vivo such as tumor size and borders, vessel length, vessel junctions, and vessel branches, microglia, cell survival, and neuronal modifications. As this method allows for live cell fluorescent observation, they employed the technique to observe cultures treated with the chemotherapeutic Temozolamide (TMZ, Temodal/Temcad®). Indeed they found reduced tumor growth in treatment groups vs controls, but also revealed surprising reduction in microglial cells in the peritumoral region. Additionally, they were able to observe the lack of response TMZ elicited from microglial in healthy regions of the tissue, despite its overall reduction in vascularization towards normal levels. The VOGIM technique allows for ex vivo study of brain tissue requiring three dimensional measurements, but may also be extended to other tissues with unique morphology such as kidney, liver, and intestine.

antibody news book Ghoochani, et al. (December, 2015) A versatile ex vivo technique for assaying tumor angiogenesis and microglia in the brainONCOTARGET

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Controlling CAR-T cells

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

New discovery – Remote control of CAR-T cells

T cells, Cancer immune therapy, autoimmune

CAR-T cells have been emerging as an effective approach to treat cancer and autoimmune diseases. A problem with CAR-T cells is that once they are infused, they are on their own exerting autonomous activities, which can lead to severe side effects due to the extensive lysis of tumor cells. Researchers have been seeking ways to control CAR-T cells after they are infused to balance the desired therapeutic effect and the side effect. Recently, a group of researchers at UCSF found a way to control CAR-T cells after they are put into patients, through a rapamycine analogue gated chimeric receptor.

CAR-T cell system has two components: one is the recognition domain that binds to CD19 to target B cells; the other is the functional domain to activate cellular pathways to killing the targeted cells. Those two domains are typically preassembled. What this group of researchers did is to separate those two domains and make them come together only in the presence of the activating molecule, a rapamycine analogue. They showed that in the absence of the activating molecule, CAR-T cells still bound to CD19. But, they didn’t kill the targeted cells unless the activating molecule was present. In addition, by adjusting the dose of the activating molecule, the strength of CAR-T cells activities can be titrated as well.

Chia-Yung Wu, etc. (October 2015) Remote control of therapeutic T cells through a small molecule–gated chimeric receptor.Science

 

Remote control of therapeutic T cells through a small molecule–gated chimeric receptor

 

 

http://pharmaceuticalintelligence.com/2016/02/06/reengineering-therapeutics/

Reengineering Therapeutics

Larry H. Bernstein, MD, FCAP, Curator

LPBI

The synNotch solution: UCSF scientists engineer a next-gen T-cell immunotherapy

Sunday, January 31, 2016 | By John Carroll

CAR-T has been all the rage in cancer R&D for several years now as a slate of biotech upstarts pursue highly promising work reengineering T cells into attack weapons by adding a chimeric antigen receptor that can zero in on particular cancer cells. The approach has been highly effective in acute lymphoblastic leukemia, triggering an attack on B cells by homing in on the CD19 antigen, a breakthrough that has inspired a race to the regulatory finish line with the first CAR-Ts.

 

http://pharmaceuticalintelligence.com/2016/02/11/regulatory-dna-engineered/

Regulatory DNA engineered

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

New Type of CRISPR Screen Probes the Regulatory Genome

Aaron Krol    http://www.bio-itworld.com/2016/2/8/new-type-crispr-screen-probes-regulatory-genome.html

February 8, 2016 | When a geneticist stares down the 3 billion DNA base pairs of the human genome, searching for a clue to what’s gone awry in a single patient, it helps to narrow the field. One of the most popular places to look is the exome, the tiny fraction of our DNA―less than 2%―that actually codes for proteins. For patients with rare genetic diseases, which might be fully explained by one key mutation, many studies sequence the whole exome and leave all the noncoding DNA out. Similarly, personalized cancer tests, which can help bring to light unexpected treatment options, often sequence the tumor exome, or a smaller panel of protein-coding genes.

 

sjwilliamspa commented on Controlling CAR-T cells

Controlling CAR-T cells Larry H. Bernstein, MD, FCAP, Curator LPBI New discovery – Remote control of CAR-T cells CAR-T …

Interesting method to use a chimeric heterodimer receptor to control CD19 activity however it would be ineresting to see if cancer replapses occur more frequently. Originally it was thought the CART would act, after initial treatment, eventually to patrol the body for any recurring tumor cells. Using rapamycin would be interesting although there had been some immunotoxic concerns with chronic use (although long term use of rapamycin and other mtor inhibitors seemed to prolong lifespan in immunodeficient animals)

Temsirolimus, an Inhibitor of Mammalian Target of Rapamycin athttp://clincancerres.aacrjournals.org/content/14/5/1286.short

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Intratumor heterogeneity challenge

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

Intratumor Heterogeneity Poses Challenge for Cancer “Moonshot” Program

Intratumor Heterogeneity Poses Challenge for Cancer “Moonshot” Program

The tiny fraction of cells in a biopsy of a heterogeneous cancer may not be representative of the entire tumor mass, which means important disease features might be missed. [istock/Vitanovski]

  • Vice President Joe Biden, in describing the cancer research initiative President Obama asked him to lead, said “the goal of this initiative—this ‘moonshot’—is to seize this moment…to accelerate our efforts to progress toward a cure, and to unleash new discoveries and breakthroughs for other deadly diseases.”

    As he noted during his recent visit to the University of Pennsylvania’s Abramson Cancer Center to officially launch the initiative, however, he was “not naive about the likelihood of soon curing an entire group of diseases that have bedeviled humanity for centuries.” Rather, he said, the intention of the initiative is to accelerate progress already underway.

    Biden personally lobbied for a major increase in cancer research funding in the government spending bill that Congress passed in December, pledging to pursue an initiative to end cancer for the rest of his term and beyond. The bill will raise funding for the NIH by $2 billion, including a $264 million boost specifically for the NCI, the biggest increase for the institute in more than a decade. Scientists concur with the VP’s lack of naiveté.

    As Jose Baselga, M.D., Ph.D., the president of the American Association for Cancer Research and physician-in-chief and chief medical officer at Memorial Sloan Kettering Cancer Center (MSKCC), told The New York Times, “Cancer is way more complex than anyone had imagined in 1970,” reflecting many scientists’ sentiments that this kind of approach won’t succeed quickly or easily.

    Rebecca A. Burrell and colleagues, writing in the September 19, 2013, issue of Nature noted that the recently revealed genetic diversity both between and within tumors affecting key cancer pathways and driving phenotypic variation poses a significant challenge to personalized cancer medicine.

    Among the researchers focused on tumor heterogeneity is MSKCC biologist Scott W. Lowe, Ph.D., chair of the Cancer Biology and Genetics Program and the Geoffrey Beene Cancer Research Center, who commented in a MSKCC blog that “We are increasingly becoming aware of the problem of intra-tumor heterogeneity, the fact that one person’s tumor cells can vary depending on where in the body they are located. Even within the same tumor from the same patient, tumor cells might be subtly or even dramatically different. And there can be very important implications of this type of heterogeneity.”

    If doctors are dealing with a highly heterogeneous cancer, the tiny fraction of cells in the biopsy may not be representative of the entire tumor mass, which means important disease features could be missed. What this means in practical terms, said Dr. Lowe, is that “A potentially effective therapy could be overlooked because the indicator for that drug, such as a specific gene mutation, wasn’t found in the biopsy. Conversely, the wrong drug might be chosen if a biopsy reveals the presence of an indicator that isn’t actually that prevalent in the tumor.”

  • Cancer Therapeutic Challenges

    Recent investigations of tumor heterogeneity provide ample evidence of the challenges for cancer therapy and the scope of the problem. Particularly worrisome is the recent finding that post-treatment relapse among acute myelogenous leukemia (AML) patients is associated with the addition of new mutations and clonal evolution.

    Li Ding, Ph.D., and colleagues reported in the January 11, 2012 issue of Nature that they had sequenced the primary tumor and relapse genomes from eight AML patients and validated hundreds of somatic mutations using deep sequencing, allowing precise definition of clonality and clonal evolution patterns at relapse.

    The scientists pointed out the occurrence of novel, recurrently mutated genes (WAC, SMC3, DIS3, DDX41, and DAXX) in AML, as well as two major clonal evolution patterns during AML relapse. They discovered that the founding clone in the primary tumor gained mutations and evolved into the relapse clone, or that a subclone of the founding clone survived initial therapy, gained additional mutations, and expanded at relapse. In all cases, chemotherapy failed to eradicate the founding clone.

    The researchers concluded that comparison of relapse-specific vs. primary tumor mutations in all eight cases revealed an increase in transversions, probably due to DNA damage caused by cytotoxic chemotherapy. These data demonstrate, the authors said, that AML relapse is associated with the addition of new mutations and clonal evolution, shaped in part by the chemotherapy that the patients receive to establish and maintain remissions.

    A team working at Harvard and the Broad Institute sought to estimate the extent of clonal heterogeneity in multiple myeloma in a large-scale MM genome sequencing dataset that included untreated and previously treated patients. Jens G. Lohr, M.D., Ph.D., and colleagues, reporting results in the January 13, 2014 issue of Cancer Cell, performed a massive parallel sequencing of paired tumor/normal samples from 203 MM patients.

    Commenting on the study, co-senior author Todd Golub, M.D., founding core member of the Broad Institute, director of its cancer program, and professor of pediatrics at Harvard Medical School, said “What this new work shows us is that when we treat an individual patient with multiple myeloma, it’s possible that we’re not just looking at one disease, but at many. In the same person, there could be cancer cells with different genetic makeups. These findings indicate a need to identify the extent of genetic diversity within a tumor as we move toward precision cancer medicine and genome-based diagnostics.”

    The Cancer Cell authors identified significantly mutated genes and copy number alterations and discovered putative tumor suppressor genes by determining homozygous deletions and loss of heterozygosity. They reported their observation of frequent mutations in KRAS (particularly in previously treated patients), NRAS, BRAF, FAM46C, TP53, and DIS3 (particularly in nonhyperdiploid MM). Mutations were often present in subclonal populations, and multiple mutations within the same pathway (e.g., KRAS, NRAS, and BRAF) were observed in the same patient.

    These studies demonstrate how acquisition of genetic alterations over time leads to clonal evolution. Systemic treatment with chemotherapy may affect the fitness of some subclones more than others, and thus may alter the tumor composition by promoting particular subclones.

  • Understanding Glioblastoma

    Noting that accumulating evidence suggests that intratumor heterogeneity likely is the key to understanding Glioblastoma (GB) treatment failure, Andrea Sottoriva, Ph.D., and colleagues in the department of oncology at University of Cambridge developed a surgical multisampling scheme to collect spatially distinct tumor fragments from 11 GB patients.

    The authors reported their findings in the March 5, 2013 issue of PNAS. Their integrated genomic analysis, they said, uncovers extensive intratumor heterogeneity, with most patients displaying different GB subtypes within the same tumor. They also reconstructed the phylogeny of the fragments for each patient, identifying copy number alterations in EGFR and CDKN2A/B/p14ARF as early events, and aberrations in PDGFRA and PTEN as later events during cancer progression. Their clonal characterization of each tumor fragment at the single-molecule level detected multiple coexisting cell lineages.

    Taken together, the researchers concluded, their results reveal the genome-wide architecture of intratumor variability in GB across multiple spatial scales and patient-specific patterns of cancer evolution, with consequences for treatment design.

    Asked how his findings in MM and those of others with different tumors might immediately translate into practice for oncologists, Dr. Golub said that the notion of a yes or no answer, that is, whether or not a given mutation is present in a tumor, is too simplistic, particularly in interpreting clinical trial results testing targeted agents.

    “It is unreasonable to expect that an entire tumor would respond to a drug if the target of the drug is only present in a minority of the tumor cells,” he explained. “If the mutation, for example, is sub-clonal and the patient doesn’t respond clinically, it would be the wrong conclusion to say the drug is ineffective.”

    He added that what is needed is a quantitative approach to know in what proportion of the tumor the mutation is found.

    “For example, if a mutation is only present in a minority of the tumor cells, the drug might not be so good for the patient. But if the mutation were present in 100 percent of the cells, it’s a better choice,” he said. “Targeted agents that go after the least-heterogeneous aspect of the tumor might be a better choice.”

    The same goes for clinical trials as you might come to different results, continued Dr. Golub. In the MM study, for example, “we found that in some patients the BRAF mutation was clonal (present in all of the cells), but in some patients present only in a minority.” If you did a clinical trial of a BRAF inhibitor and you only enrolled sub-clonal patients, you might conclude that BRAF is not a good target in MM, “whereas, if you enroll only patients with clonal mutations in clinical trials, you might come to a completely different conclusion.”

    With respect to drug discovery, Dr. Golub is more optimistic about developing drugs that go after the founding mutations that will be present in all of a tumor’s cells. “Those will make the best therapeutic targets,” he said. “I am less optimistic about trying to pick off five sub-clones with a five-drug combination.”

    Beverly Mitchell, M.D., director of the Stanford Cancer Institute, David Rubenson, associate director for administration and strategic planning, and Daniel S. Kapp, M.D., professor emeritus of radiation oncology, posed some tough questions about the meaning of these findings for cancer therapeutics in the April 11, 2015 edition of The Scientist. These include whether intra-tumor heterogeneity implies that a single targeted therapeutic, while producing short-term responses, brings us any closer to enduring disease control. Or, they ask, do we simply need a better, or a second or third, targeted therapeutic?

    While uncertainties remain, they said, there is sufficient data for every major cancer research and treatment center to assess how intra-patient heterogeneity will affect research priorities, clinical trial design, and the patient’s choice of treatment.

sjwilliamspa commented on Intratumor heterogeneity challenge

Intratumor heterogeneity challenge Larry H. Bernstein, MD, FCAP, Curator LPBI Intratumor Heterogeneity Poses …

There are a few very important points here, and one commentary in which I would like to point to another post on this Open Access Journal in the Related section :
http://pharmaceuticalintelligence.com/2016/01/18/will-president-obama-s-cancer-immunotherapy-colloquium-dubbed-moonshot-mean-government-is-fully-behind-the-war-on-cancer-or-have-we-heard-this-before/

where my feeling was the most likely revolutionary achievement from Moonshot will be the closer collaboration of government, academia, industry, patient advocacy AND the PAYERS. This would be a goal I feel is much needed and one where VP Biden can make the greatest effect.

As to the points I was very interested in Dr, Golub’s remarks concerning shifting focus more on driver mutations than “end-stage” kinase mutations and relying on combination therapy. An initial hope of the personalized target medicine era was to remove the need for combination therapy as concerns over limiting toxicities and development of resistance is always a concern with more traditional chemotherapy, whether mono or combination therapy. However it is becoming clear, even with immune modulators and checkpoint inhibitors, that monotherapy may have limited efficacy.

That being said it appears that the VP and the Moonshot program is focusing on the new T cell engineered therapies (CAR-T and TCR) which have had much success with certain childhood lleukemia and just now adult leukemias. CAR-T are showing some promise with pancreatic which sees to be the first data out there with regard to solid tumors (although I feel pancreatic is a more “immune system available” tumor. And as CAR-T are engineered to a specific epitope expressed on tumor cells intratunoral heterogeneity will complicate the therapy. Indeed (as posted in this Online Journal) intra-tumoral heterogeneity is felt as another mechanism of resistance,

However the increased visibility to the cancer problem within government is a much needed boost and funds, hands, minds, and support can join together to at least address some of these issues which stymie the oncology field.

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