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Archive for August, 2012

Curator/ Author: Aviral Vatsa, PhD, MBBS

In continuation with the previous posts that dealt with short history and chemistry of nitric oxide (NO), here I will try to highlight the pathways involved in NO chemical signalling.

NO is a very small molecule, with a short half life (<5 sec). It diffuses rapidly to its surroundings and is metabolised to nitrites and nitrates. It can travel short distances, a few micrometers, before it is oxidised. Although it was previously believed that NO can only exert its effect for a very short time as other nitrogen oxides were believed to be biologically inert. Recent data suggests that other NO containing compounds such as S- or N-nitrosoproteins and iron-nitrosyl complexes can be reduced back to produce NO. These NO containing compounds can serve as storage and can reach distant tissues via blood circulation, remote from their place of origin. Hence NO can have both paracrine and ‘endocrine’ effects.

Intracellularly the oxidants present in the cytosol determine the amount of bioacitivity that NO performs. NO can travel roughly 100 microns from NOS enzymes where it is produced. NOS enzymes on the other hand are localised to specific sub-cellular areas, which have relevant proteins in the vicinity as targets for signalling.

NO signalling occurs primarily via three mechanisms (according to Martínez-Ruiz et al):

  1. Classical: This occurs via soluble guanylyl cyclase (sGC). Once NO is produced by NOS it diffuses to sGC intracellularly or even in other cells. SGC is highly sensitive for NO, even nanomolar amounts of NO activates sGC, thus making it a potent target for NO in signalling pathways. sGC in turn increases the conversion of GTP to cGMP. cGMP further mediates the regulation of contractile proteins and gene expression pathways via cGMP-activated protein kinases (PKGs). cGMPs cause confirmational changes in PKGs. Signalling by cGMP is terminated by the action of phosphodiestrases (PDEs). PDEs have become major therapeutic targets in the upcoming exciting research projects.
  2. Less classical: Within the mitochondria NO can compete with O2 and inhibit cytochrome c oxidase (CcO) enzyme. This is a reversible inhibition that depends on O2and NO concentrations and can occur at physiological levels of NO. Various studies have demonstrated that endogenously generated NO can inhibit respiration or that NOS inhibitors can increase respiration at cellular, tissue or whole animal level. Although the exact mechanism of CcO inhibition of NO is still debated, NO-CcO interaction is considered important signalling step in a variety of functions such as inhibition of mitochondrial oxidative phosphorylation, apoptosis and reactive oxygen species (ROS) generation. Interestingly, at higher concentration (~1nM) NO can cause irreversible inhibition of cellular oxidation by reversible and/or irreversible damage to the mitochondrial iron–sulfur centers,In addition to the above mentioned pathways, NO (along with AMP, ROS and O2), can also activate AMP- activated protein kinase (AMPK), an enzyme that plays a central role in regulating intracellular energy metabolism. NO can also regulate hypoxia inducible factor (HIF), an O2-dependent transcription factor that plays a key role in cell adaptation to hypoxia .
  3. Non- classical: S-nitrosylation or S-nitrosation is the covalent insertion of NO into thiol groups such as of cysteine residues of proteins. It is precise, reversible, and spatiotemporally restricted post translational modification. This chemical activity is dependent upon the reactivity between nitrosylating agent (a small molecule) and the target (protein residue). It might appear that this generic interaction results in non-specific, wide spread chemical activity with various proteins. However, three factors might determine the regulation of specificity of s-nitrosylation for signalling purposes:
  • Subcellular compartmentalisation: high concentrations of nitrosylating agents are required in the vicinity of target residues, thus making it a specific activity.
  • Site specificity: certain cysteine residues are more reactive in specific protein microenvironments than others, thus favouring their modification. As a result under physiological conditions only a specific number of cysteine residues would be modified, but under higher NO levels even the slow reacting ones would be modified. Increased impetus in research in this area to determine protein specificity to s-nitrosylation provides huge potential in discovering new therapeutic targets.
  • Denitrosylation: different rates of denitrosylation result in s-nitrosylation specificity.

Other modifications in non classical NO mechanisms include S-glutathionylation and tyrosine nitration

Peroxynitrite: It is one of the important reactive nitrogen species that has immense biological relevance. NO reacts with superoxide to form peroxynitrite. Production of peroxynitrite depletes the bioactivty of NO in physiological systems. Peroxynitrite can diffuse through membranes and react with cellular components such as mitochondrial proteins, DNA, lipids, thiols, and amino acid residues. Peroxynitrite can modify proteins such as haemoglobin, myoglobin and cytochrome c. it can alter calcium homeostasis and promote mitochondrial signalling of cell death. However, NO itself in low concentrations have protective action on mitochondrial signalling of cell death.

More details about various aspects of NO signalling can be obtained from the following references.

The post is based on the following Sources:

  1. http://www.sciencedirect.com/science/article/pii/S089158491100236Xhttp://dx.doi.org/10.1016/j.freeradbiomed.2011.04.010
  2. http://content.karger.com/produktedb/produkte.asp?doi=338150Cardiology 2012;122:55-68 (DOI: 10.1159/000338150)
  3. http://content.onlinejacc.org/article.aspx?articleid=1137266 J Am Coll Cardiol. 2006;47(3):580-581. doi:10.1016/j.jacc.2005.11.016
  4. http://goo.gl/y6oY3

 

In addition, other aspects of NO involvement in biological systems in humans are covered in the following posts on this site:

  1. Nitric Oxide and Platelet Aggregation
  2. Inhaled NO in Pulmonary Artery Hypertension and Right Sided Heart Failure
  3. Cardiovascular Disease (CVD) and the Role of agent alternatives in endothelial Nitric Oxide Synthase (eNOS) Activation and Nitric Oxide Production
  4. Nitric Oxide in bone metabolism

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Reporter: Aviva Lev-Ari, PhD, RN

Covidien plc (COV) Conducts Voluntary Recall and Discontinues Duet TRS™ Reloa

8/22/2012 8:00:30 AM

 

MANSFIELD, Mass.–(BUSINESS WIRE)– Covidien today announced that it is conducting a voluntary recall of all production lots for the Duet TRS™ Universal Straight and Articulating Single-Use Loading Units (SULU). In addition, the Company has discontinued manufacturing the Duet TRS Universal Straight and Articulating SULU.

 

Covidien has received one report that links the Duet TRS tissue reinforcement material to a post-operative injury after abdominal surgery. The Company has concluded that Duet TRS may have the potential to injure adjacent anatomical structures, which may result in life threatening post-operative complications. This voluntary recall is in addition to the recall announced January 16, 2012, relating to the contraindication of the device in the thoracic cavity. At that time, Covidien received reports of 13 serious injuries and 3 fatalities following the application of Duet TRS in the thoracic cavity.

The affected product codes and descriptions are as follows:

DUET4535 Duet TRS 45 3.5MM STRAIGHT SULU

DUET4535A Duet TRS 45 3.5MM ARTICULATING

SULU DUET4548 Duet TRS 45 4.8MM STRAIGHT SULU

DUET4548A Duet TRS 45 4.8MM ARTICULATING

SULU DUET6035 Duet TRS 60 3.5MM STRAIGHT SULU

DUET6035A Duet TRS 60 3.5MM ARTICULATING

SULU DUET6048 Duet TRS 60 4.8MM STRAIGHT SULU

DUET6048A Duet TRS 60 4.8MM ARTICULATING SULU

Launched in 2009, the Duet TRS reload is a SULU with a fully integrated tissue reinforcement system to support staple lines in tissues. To date, the Company has sold more than 540,000 units worldwide.

http://www.devicespace.com/news_story.aspx?NewsEntityId=270735

 

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Reporter: Aviva Lev-Ari, PhD, RN

 
 
 
Fluidigm Corporation (NASDAQ: FLDM) develops, manufactures and markets microfluidic systems for growth markets in the life science and agricultural biotechnology, or Ag-Bio, industries. Fluidigm’s proprietary microfluidic systems consist of instruments and consumables, including chips, assays and other reagents. These systems are designed to significantly simplify experimental workflow, increase throughput and reduce costs, while providing the excellent data quality demanded by customers. Fluidigm actively markets four microfluidic systems, including nine different commercial chips, to leading academic institutions, diagnostic laboratories, and pharmaceutical, biotechnology and Ag-Bio companies. Fluidigm products are marketed for research purposes only (not for diagnostic use).
Fluidigm Announces Exercise of Underwriters’ Over-Allotment Option and Closing of $60 million Public Offering of Common Stock

SOUTH SAN FRANCISCO, CALIFORNIA – August 21, 2012 – Fluidigm Corporation (NASDAQ: FLDM), a supplier of microfluidic systems for growth markets in the life science and agricultural biotechnology industries, today announced that it has closed the previously announced underwritten public offering of 4,209,000 shares of its common stock at a price to the public of $14.25 per share for gross proceeds of approximately $60 million. The shares include 549,000 shares of common stock sold pursuant to the over-allotment option granted by Fluidigm to the underwriters, which option was exercised in full. The net proceeds from the sale of the shares, after deducting the underwriters’ discounts and commissions and other estimated offering expenses payable by Fluidigm, will be approximately $56.1 million.
Fluidigm currently plans to use the net proceeds from this offering for research and development, commercialization of its products, working capital and other general corporate purposes.
Piper Jaffray & Co. and Cowen and Company, LLC acted as the joint book-running managers for the offering.  Leerink Swann LLC, Oppenheimer & Co. Inc. and Cantor Fitzgerald & Co. acted as the co-managers for the offering.

A shelf registration statement (File No. 333-180550) relating to these securities was filed on April 4, 2012, as amended on May 7, 2012, and declared effective by the Securities and Exchange Commission on May 10, 2012.  A final prospectus supplement and accompanying prospectus describing the terms of the offering was filed with the SEC on August 16, 2012.  Copies of the prospectus supplement and accompanying prospectus relating to the offering may be obtained from Piper Jaffray & Co., Attention: Prospectus Department, 800 Nicollet Mall, J12S03, Minneapolis, MN 55402 or by telephone at 800-747-3924 or by email at prospectus@pjc.com, or from Cowen and Company, LLC (c/o Broadridge Financial Services, 1155 Long Island Avenue, Edgewood, NY, 11717, Attn: Prospectus Department, Phone: 631-274-2806, Fax: 631-254-7140). An electronic copy of the prospectus supplement and accompanying prospectus relating to the offering is available on the website of the Securities and Exchange Commission at http://www.sec.gov/.
This press release does not constitute an offer to sell or the solicitation of offers to buy any securities of Fluidigm, and shall not constitute an offer, solicitation or sale of any security in any state or jurisdiction in which such offer, solicitation or sale would be unlawful prior to registration or qualification under the securities laws of any such state or jurisdiction.

Forward-Looking Statements

In order to provide Fluidigm’s investors with an understanding of our current intentions and future prospects, this release may contain statements that are forward-looking.  Any statements contained in this press release that are not statements of historical fact may be deemed to be forward-looking statements. Words such as “believes,” “anticipates,” “plans,” “expects,” “will,” “intends,” “potential,” “possible” and similar expressions are intended to identify forward-looking statements. These forward-looking statements include our expectations regarding the offering and the use of proceeds from such offering.
Forward-looking statements involve risks and uncertainties related to our business and the general economic environment, many beyond our control. These risks, uncertainties and other factors could cause our actual results to differ materially from those projected in forward-looking statements, including market risk and the risks we identify in reports filed with the SEC.
Although we believe that the forward-looking statements contained herein are reasonable, we can give no assurance that our expectations are correct. All forward-looking statements are expressly qualified in their entirety by this cautionary statement. For a detailed description of our risks and uncertainties, you are encouraged to review the official corporate documents filed with the SEC. Fluidigm does not undertake any obligation to publicly update its forward-looking statements based on events or circumstances after the date hereof.

 
 

The C1™ Single-Cell Auto Prep System is a new approach to single-cell gene expression.

 
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Select from the Following Categories:

Gene Expression

Single-Cell Gene Expression

SNP Genotyping

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Single-Cell Gene Expression

 

SNP Genotyping

 

Targeted Resequencing

 

Copy Number Variation/Digital Quantification/Digital PCR

Protein Crystallization

 

Products

Fluidigm develops and distributes life science systems based on our proprietary Integrated Fluidic Circuits (IFCs).  We currently offer the following complete systems and products:

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Reproducible results down to
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Granicus_Right_315.jpgC1™ System
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b3.pngAccess Array™ System
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Accelerated workflow • Outstanding data Quality • Efficient high sample throughput SNP Genotyping
   
b2.pngDeltagene™ Assays
High quality—sensitivity and linearity
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b6.pngChips & Kits
192.24 – 192 samples x 24
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AA_TS_Primers_Image.jpgTarget-Specific Primers
Custom-designed primer sets •
multiplex capability allows up to 480 amplicons per sample • Amplicon tagging bypasses traditional library preparation
b1.pngSNPtype™ Assays 
Low start-up and running costs • Locus-specific primer sequences provided • Change targets on demand
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topazproduct.pngOther Products

 

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Author and Reporter: Anamika Sarkar, Ph.D and Ritu Saxena, Ph.D.

 Cartilage is the tissue lining of the joints and acts as a cushion between the joints. Osteoarthritis, a disease accompanied by severe pain and limitations of functions, is the result of degeneration of cartilage. Currently, such conditions of patients are considered irreversible and treatment options are mainly based on pain management and joint replacement therapy.

Some of these procedures are –  Autologous Chondrocyte Implantation (ACI), Osteochondral Allograft Transplantation, Meniscal Transplantation. In these procedures, healthy cartilage (or meniscus in case of Meniscal Transplantation) are taken either from the patients or deceased donors and transplanted in the damaged joints for cartilage repair. (Please see information regarding cartilage repair, cartilage supplement in sources below).

Harnessing use of regenerative powers of stem cells have been recognized as alternative methods of treatments. Stem cells are the cells that have the capacity to develop into different cell types. They can continue to renew themselves with cell division without being differentiated.  Moreover, with the right stimulus they can also be induced to differentiate into specialized cell types. Thus, with discovery and understanding of right stimuli and its signaling processes, stem cells can serve as a powerful candidate for repair of damaged tissues and organs.

Since, stem cells are precursor of many differentiated cell types, a lot of research is needed to determine the right conditions to direct the stem cell differentiation into the desired cell type for the purpose of treatment. Attempts have been made in the area of regenerative medicine for cartilage regeneration using stem cells. Kafienah et al (2007) bioengineered a three-dimensional cartilage using adult stem cells from the bone marrow of osteoarthritis patients. Although, this method could thus be used for repairing cartilage lesions, however, it needs to be implanted into the joint adding challenges to the development of therapy.

A very interesting study published in the recent issue of the journal Science (Johnson et. al., A Stem Cell-Based Approach to Cartilage Repair, Science, 336, p717,2012) described breakthrough discovery – a small molecule, Kartogenin (KGN), has the capability of promoting chondrocytes (cells which make healthy cartilage) differentiation.

The authors, Johnson et al. showed their finding of KGN as a stimulus for stem cell differentiation to chondrocytes in a systematic fashion. They used high throughput screening of images from 5 primary human stem cells derived from bone marrow in their in-vitro studies. Their results show when cells were treated with 100nM of KGN, they show regeneration of cartilage forming chondrocytes. They supported their finding in animal model using mice model by inducing Osteoarthritis and then treating them with KGN.

In order to make sure that KGN has a direct effect on the signaling of chondrocytes, Johnson et. al., showed activation of some of the key signaling components in the KGN stimulated chondrocytes pathway, using in-vitro studies. They showed that upon activation of cells with KGN, CBFb (core-binding factor β subunit)  translocates into the nucleus and activates signaling components of  RUNX (one of the runt-related transcription factor family member), leaving behind free cytoplasmic binding partner FLNA (Flaming A). They also show strong correlation between CBFb and regeneration of chrondocytes.

Stem cell therapy has uncounted potential for giving better life to patients with complex, chronic diseases.  Johnson et al’s, discovery of a small molecule, KGN, with further research in animal and human population, could lead to the development of an effective stem cell based treatment of Osteoarthritis. A possibility of such a drug can be seen as a lifestyle changing drug in patients who have very limited options of treatments today.

Sources:

Johnson et al article:  http://www.ncbi.nlm.nih.gov/pubmed/22491093

Arthritis information: http://orthopedics.about.com/cs/arthritis/a/arthritis.htm, h

http://www.cirm.ca.gov/node/2082

Stem cells: http://www.stemcellresources.org/pdf/uw_rm.pdf

http://stemcells.nih.gov/staticresources/info/scireport/PDFs/Regenerative_Medicine_2006.pdf

Kafienah et al article: http://www.ncbi.nlm.nih.gov/pubmed/17195220

Previous post in awesome capital on the paper by Johnson et. al. http://www.awesomecapital.com/1/post/2012/04/novartis-anti-arthritis-compound-spurs-cartilage-growth-from-stem-cells.html

Information about cartilage repair : http://www.jointpain.md/Procedures/CartilageTransplant.aspx

Cartilage Supplement in iHealth directory:http://www.ihealthdirectory.com/cartilage-regeneration-supplements/

Information about modern cartilage repair treatments offered at Brigham and Women Hospital: http://www.brighamandwomens.org/Departments_and_Services/orthopedics/services/CartilageRepair/default.aspx

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Reporter: Aviva Lev-Ari, PhD, RN

Will ‘gamifying’ drug R&D win more than Facebook fans for Boehringer?

By Tracy Staton, FiercePharma, August 22, 2012

Lots of computer games enlist players in quests to save the world. But how many would-be saviors are developing drugs? We can’t think of any–until now. Boehringer Ingelheim is on the verge of launching Syrum, a Facebook game of test tubes and titrations, not crossbows and assault rifles.

 “The health of the world is in your hands,” Boehringer’s director of digital, John Pugh, tells PSRK, in what could be a voice-over for a YouTube promo video for the game. “And you’re the only one who can save it.”

 Players have to solve a problem–e.g., a pandemic–via drug development, all the way from early discovery through clinical trials and launch. They can enlist help from Facebook friends, and advance in the game by checking into locations via the social network’s mobile app. “It wasn’t built with a view to being an educational platform,” Pugh says. “It’s very much a game which is meant to be engaging and entertaining … In the same way that Farmville doesn’t just appeal to people who like farms, Syrum isn’t just for people who like the pharmaceutical industry.”

But it was education that drew Pugh and his team into the project; as he points out for PSFK, the industry does a lot of it, whether that’s “educating” doctors about products, or teaching patients how to take their meds properly. Just because the game isn’t designed as an educational platform doesn’t mean it can’t educate, in a stealthy, backhanded way.

Syrum has been in development for two years. On Sept. 13, Boehringer will unveil a beta version at a London conference, aiming to get feedback from players for future iterations. “[T]he game will grow and evolve as more people play it,” Pugh says.

He also says Syrum is a “very unique offering from a highly regulated industry.” True. Whether it will remain unique depends, in part, on how Syrum actually fares. Will it attract a following? And if it does, will gamification of drug development actually benefit Boehringer’s business? Image? Relations with patients? Pharma’s social media advocates (and skeptics) will be watching.

John Pugh, Director of Digital for Boehringer Ingelheim, talks about driving innovation in his large organization with the forthcoming game Syrum – which he will launch at PSFK CONFERENCE LONDON on September 13.
 
 
 
 
By Tim Ryan on August 21, 2012.
  • John Pugh is the Director of Digital for Boehringer Ingelheim GmbH – a group of pharmaceutical companies that specialize in research and development for prescription medicine products. He spoke to PSFK recently about driving innovation in a large organization with his forthcoming game Syrum – which he will launch at PSFK CONFERENCE LONDON on September 13.

Your company has a new game, Syrum. What is it – and why is a pharmaceutical company like Boehringer Ingelheim involved in it?

What really sparked my interest in the potential of gaming is that a lot of what we do in pharma is around educating and teaching people; whether that’s teaching doctors about specific products, educating the general public and patients about diseases and healthy ways to live, or teaching people how to take their medication.

Gaming seems to be a useful way and effective way for us to do that. I basically began the journey to try and work out what I could do in gaming that wasn’t an arcade or platform based game — but was something a bit more immersive.

Syrum has been in development for at least two years. At the beginning, we called in lots of experts from different industries, different locations in countries, and with different skill sets. We had various leaders, from specialized futurologists to branding experts, from pharma people to gaming people, and even young entrepreneurs who’d made a million dollars by the age of 17.

We really worked together to create a vision of the future, and one of the strong things that came through was the influence of gaming and gamification.

After two years of hard work, the result is that we are about to launch Syrum, the pharmaceutical industry’s first social game.

syrum-boehringer-ingelheim

Can you tell us a little more about the gameplay in Syrum?

Syrum is a social game. The health of the world is in your hands, and you’re the only one who can save it. In each chapter, you have to solve a particular problem, which could be a disease or a pandemic that is sweeping the world. The player’s goal is to discover cures, create a stable drug, and then create a clinical trial so that you can launch the drug and cure the disease.

It’s a social game, because you can collaborate with friends or other people, and you can give them gifts, even headhunt their staff. As the game progresses, it gets more and more complicated.

syrum-boehringer-ingelheim-game

What do you think people will get out of it?

First, it’s a fun game. It wasn’t built with a view to being an educational platform or anything like that. It’s very much a game which is meant to be engaging and entertaining to play. In the same way that Farmville doesn’t just appeal to people who like farms, Syrum isn’t just for people who like the pharmaceutical industry. It’s for anyone to play.

It’s built on Facebook because that’s the world’s biggest gaming platform. What we really wanted to do was try to use a lot of the features of Facebook. For example we leverage Facebook Places, a service where people can check into locations. It’s really bridging that offline/online world. Places helps players market the products they make. Wherever the players check in through the Facebook mobile app, that data gets integrated into the game and you get rewarded accordingly.

syrum-boehringer-ingelheim-game

When will it be available?

September 13. We are taking a Silicon Valley approach, where we know we have got a really good game that’s stable but we’ll launch a beta version. We really want to make it so that we get lots of feedback from the people who are playing.

We’re offering rewards and prizes for people to give feedback so that we can really create the duration of the game, and develop it, and have more of a crowdsourced collaborative effort to develop the future stages of it, so the game will grow and evolve, as more people play it. This is a very unique offering from a highly regulated industry.

Can we finish by understanding your role within the organization – and how you drive change.

My job is anything which is connected to digital, so that includes apps, mobile, websites, gaming, crowdsourcing, and so forth. Our goal is to find applications for all of that. I bring to this company new ideas and I inspire them, educate them, cajole them, prod them to try new things, particularly in digital. I want BI to stretch out beyond the traditional marketing activities because in pharmaceuticals, and particularly at Boehringer, we’re still very traditional in what we do.

Thanks John!

Come see John talk about the launch of Syrum at PSFK CONFERENCE LONDON.

Syrum / @johnpugh / Boehringer Ingelheim

Click the banner below to purchase tickets and find additional information about this year’s event.

 

via PSFK: http://www.psfk.com/2012/08/pharma-social-game-psfk-london.html#ixzz24IgR5ZEm

http://www.psfk.com/2012/08/pharma-social-game-psfk-london.html

How Sanofi Is Writing The Social Media Rules For Big Pharma Without Running Afoul Of The FDA

BY BEN PAYNTER

 | 

AUGUST 20, 2012

After a Facebook PR meltdown two years ago, Sanofi has emerged as a social media leader with a robust community for diabetics. Here’s how they are writing #TheRules while the FDA catches up.

About This Series

#therules

Follow Fast Company’s roadmap to social media: surefire rules, data, and expert wisdom guaranteed to show why this market is completely unpredictable.READ MORE

The biggest challenge to treating patients with diabetes isn’t doling out medications, it’s making sure that people control their habits. Poor diet and lack of exercise generally create complications with the disease. To combat the problems, researchers in the diabetes division of Sanofi US took an unusual step for Big Pharma: they went social, jumping into online networking with a Facebook page, Twitter presence, and eventually three different engagement platforms.

“Treatment is an important aspect to blood sugar management, but it isn’t the only aspect,” says Laura Kolodjeski, Sanofi’s diabetes community manager, who has become the virtual face of the company. “There is a huge community of people already that live with diabetes and are connecting and sharing [online] to improve each other’s experience with the disease.”

 

Laura Kolodjeski

 

Sanofi now helps direct and police those interactions online. The company won’t release total visitor numbers, but it has about 4,000 followers on Facebook and another 4,000 on Twitter, all of whom are sharing links to broader content. And for better or worse that community is going to grow: About 8 percent of Americans or roughly 26 million people have diabetes, and the Centers for Disease Control predicts that as many as one third of us could have the disease by 2050.

But the social frontier is potentially prickly for Sanofi because the FDA has not yet written the rules about how pharmaceuticals are allowed to engage with potential customers and patients. The only guidelines came out in a December 2011 advisory statement declaring that while allowing virtual comments about things like off-label uses isn’t technically illegal, it’s shady territory; basically, pontificate at your own risk. “We are working on the area and it’s something we feel is important but we don’t have a specific timeline right now,” says Ernest Voyard, senior regulatory council at the FDA’s Office of Prescription Drug Promotion.

For Sanofi, drawing up their own social media strategy is also a defensive move: In 2010, the company’s cancer division suffered a PR nightmare after a patient, who claimed to have experienced permanent hair loss from one of their treatment drugs, posted complaints and photos on that group’s unmonitored Facebook page. John Mack, the editor of Pharma Marketing News, which tracks shifts in the pharmaceutical industry, says such hits are common anytime you try to pioneer a new space. “They’ve had some rough times, but they are learning a lot,” he adds.

Mack considers Sanofi a leader in the category, especially compared with the offerings from other companies. Diabetes juggernaut Novo Nordisk sponsors IndyCar driver Charlie Kimball to tweet @racewithinsulin, including when he injects with their products. And Pfizer’s ThinkScienceNow blog about developments and advances in research is wonky but not exactly customer friendly.

Sanofi has created a template they hope will eventually be deemed both acceptable to the FDA and cool for customers. The lessons they’ve learned in the last two years is a valuable addition to The Social Media Roadmap from our current issue.

Be Transparent

When she took over as social media director, one of the first things Kolodjeski did was post a bio with a photo of herself online at DiscussDiabetes to show who was moderating. She also disclosed that she wasn’t diabetic. Why? To build trust, the kind community members might not have for a faceless company run by mostly non-diabetics. The message: “If Laura is going to work every day to solve [issues] on our behalf, then others must be doing the same,” Kolodjeski says.

Rather than just explain the rules of their forums in a jargon-y “terms of use” agreement Kolodjeski also tapped Mark Gaydos, head of the company’s U.S. regulatory affairs for marketed products division, to do a Q&A about how the sites would function. For instance, anytime someone on the site mentions a product, they are technically promoting it, so there needs to be fair balance of potential benefits and risks explained alongside that per FDA guidelines. That means many posts get quarantined internally before posting, so the company can add additional links or annotations to more information. Sanofi only wants to allow discussion of FDA-approved uses for products–any mention of possible side-benefits or bonuses from tweaking the usual dose regimen is prohibited. To make sure everything meets these requirements, there is often a delay–sometimes up to 24 hours–between when users make comments and those comments become publicly visible.

To explain their business interest, Kolodjeski also interviewed Dennis Urbaniak, the head of the company’s U.S. diabetes business unit to explain what he calls the “360-degree partner” principle–an effort to inspire others to talk more and tap into that as a focus group for new ideas.

Let Users Shape Expansion

Sanofi launched their diabetes Facebook and Twitter handles in September 2010 mainly to offer news updates about the company and its offerings. On Facebook, any clinical questions were directed to a separate tab and often answered privately. On Twitter, medical concerns were covered via direct message. What was missing was a way to collect various poster’s lifestyle tips and inspirational messages all in one place. In January 2011, the company launched DiscussDiabetes to address that. They also run their own stories about successes, including highlights from A1C Champions, another company sponsored group of diabetics who have maintain the best or “A1C” target range of blood sugar levels.

By March of this year, the company took a look at the discussions that were being generated and realized that terms like A1C weren’t actually as universally understood as they once thought. To speed that learning curve, they launched Diabetepedia, which provides both simple definitions and links to other sites showing how terms are actually used in other online conversations.

The final step: After noticing how activity at Diabetepedia was spiking, Sanofi launched another site collecting lots of the content they were already linking to all in one place. The DX, which launched at the end of May, hosts daily dispatches by both Kolodjeski and stable of already popular bloggers (none of whom are paid directly) that include everything from a diabetes related comic strip to mommy blogs for parents with diabetic kids. “We really allowed the community to help identify what might be useful to them and where they might go next,” Kolodjeski says.

Give Users Even More Control

The medical glossary at Diabetepedia doesn’t just provide standard definitions to complex terminology, users are encouraged to submit their own entries, creating a sort of slang dictionary that makes complicated stuff more relatable to newcomers. For instance, glucoaster: that’s shorthand for “a rollercoaster of blood glucose levels, with blood sugar lows followed by blood sugar highs.” User contributions have helped the database grow by 30 percent to include more than 150 terms, all of which make it easier to users themselves to better convey thoughts in future postings.

The company also considers each media outpost an exclusive “channel,” which means there is lots of cross-posting of content from different platforms to make sure users who only tune into one place are being best served. “We certainly have people that overlap but for the most part people have selected which channel they feel represented by and communicate through,” Kolodjeski says. But at each stop, the company still tries to crowdsource bigger ideas.

This year, they asked users to help set priorities for the company’s annual Data Design Diabetes Innovation Challenge, which asks individuals, businesses and non-profits to create new initiatives for using big data to help others struggling with the disease. To help brainstorm for that, Sanofi’s social media troop was given the chance to visit a competition homepage and answer questions about what aspects of life with the disease might be consistently overlooked or ignored. Their answers were used to shape a final guideline for contestants that solutions must address the overall wellness and family life of patients, not just symptom mediation. The winner: a program created by the n4a Diabetes Care Center that matches people with certain cost or risk profiles directly to the services they might need to slow the progression or expense of the disease. Mood problems can be addressed by better disease management, hopefully cutting into the 18 percent of all diabetics who require hospitalization each year.

After realizing just how open users are to sharing and connecting, Sanofi also launched their own new product, the iBGStar, a personal blood glucose monitor that plugs directly into an iPhone or iPod Touch with an app that saves data and maps correlations between blood sugar levels and meal times, carb and sugar intake, and physical activity. Users can share results with their family or email them to health care providers. But the product, which hit the market in May 2012, wasn’t just inspired by early community actions; ensuing reviews and comments in their own forums will help refine future updates. “It’s a big hit with the online community,” Kolodjeski says. “It’s also given us a great opportunity to prove back to them that if we hear someone comment about something, we have the ability to engage in a public manner.”

Correction: An earlier version of this article said that iBGStar came on the market in 2011, it was released in May 2012.

http://www.fastcompany.com/3000457/how-sanofi-writing-social-media-rules-big-pharma-without-running-afoul-fda

Lilly to develop company-wide social media strategy

11 Jul 2012

 
Nearly two years after launching its first major foray into the world of social media in the shape of its LillyPad corporate blog, Eli Lilly is developing a company-wide social media strategy.

Lilly has so far had strict rules about who can use social media on behalf of the company, authorising just a handful of people in corporate communications and government affairs, but now wants to empower other departments to do so.

“There are a lot of parts of the company that are getting interested in social media so I’m working on a strategy that will keep these aligned with one another,” Lilly’s director of corporate communications Greg Kueterman told SMI’s Social Media in the Pharmaceutical Industry conference on Monday.

“We don’t want to have eight different social media platforms that all look and sound very different from one another. So we’re going to try and do something where they all have their own identity but are still consistent within the company.”

Kueterman acknowledged LillyPad, launched September 2010, and the company’s Campaign For Modern Medicines, a US health policy initiative Lilly founded last year that uses Twitter, Facebook and YouTube, were set up “before we had a full blown strategy”.

“But sometimes that is important,” he said. “Because you have to know what you have, before you can make it even bigger.”

The company’s Clinical Open Innovation team, a group working to improve the drug development process, also began using social media earlier this year, with a blog and Twitter account.

The next stage for Lilly will be to continue its expansion of LillyPad (as previewed herein March), following the launch in May of a Canadian version of the corporate blog.

“We’ve started to go global with LillyPad and we’re working with a number of our affiliates to do this. Lilly Canada has been the first one out of the box to do that and they’re off to a nice start,” Kueterman said.

Discussions are underway with the company’s European affiliates in the UK and Belgium along with its operations in Mexico. “Hopefully some of those are going to be launching this year, although we don’t have firm dates yet,” Kueterman said.

“We’re excited that this is a programme that’s going to start picking up momentum. Looking ahead there are still things that we can do much better. I’m never really satisfied with the way things are going with LillyPad – I’m happy, because I think we’re doing things the right way, but I also believe that we can be even more proactive than we are.”

• Links to Lilly’s social media presences can be found in the Pharma Social Media Directory‘s blogsTwitterFacebook and YouTube sections 

http://www.pmlive.com/digital_intelligence_blog/archive/2012/jul_2012/lilly_to_develop_company-wide_social_media_strategy

What Else Can We (Really) Do?

by Greg Kueterman 07/10/12 


On Monday, I had the pleasure of presenting Lilly’s social media history and strategy at a conference in London. The history part was easy: LillyPad — our first major platform — has been around for 22 months. We’re not experiencing the Terrible Twos just yet, but we’ve still got plenty to learn.

The London audience — consisting of European and U.S. communicators and marketing experts at the Social Media for Pharmaceutical Industry conference. — warmly embraced our strategy of addressing issues such as public policy and medical innovation. And the reception was not unusual. Over the last two years, we’ve talked LillyPad in live settings from London to New York to Indianapolis to San Francisco — and our peers typically offer two thumbs up for the good work.

For that, we are grateful. But it’s a good reminder about a couple questions we need to ask more often:

What else can we be doing? What else should we be doing?

As our loyal readers, you know what we offer — and you know what you need to become more informed. We would love to hear more from you: the good, the bad, and the ugly. We’re always looking to enhance LillyPad, and we’ve taken a lot of steps in recent months to do so (more video, more guest blogs, and — we think — clearer, more conversational writing). And while we will remain a non-product communications vehicle, we’re open to any and all ideas that make your LillyPad experience even better.

From London (where I’ve seen more rain in three days than my backyard has seen in two months) thanks for reading!

http://lillypad.lilly.com/entry.php?id=1736

 

 

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Reported by: Dr. V.S. Karra, Ph.D

Transcription is a cellular process by which genetic information from DNA is copied to messenger RNA for protein production. But anticancer drugs and environmental chemicals can sometimes interrupt this flow of genetic information by causing modifications in DNA.

Chemists at the University of California, Riverside have now developed a test in the lab to examine how such DNA modifications lead to aberrant transcription and ultimately a disruption in protein synthesis.

The chemists report that the method, called “competitive transcription and adduct bypass” or CTAB, can help explain how DNA damage arising from anticancer drugs and environmental chemicals leads to cancer development.

“Aberrant transcription induced by DNA modifications has been proposed as one of the principal inducers of cancer and many other human diseases,” said Yinsheng Wang, a professor of chemistry, whose lab led the research. “CTAB can help us quantitatively determine how a DNA modification diminishes the rate and fidelity of transcription in cells. These are useful to know because they affect how accurately protein is synthesized. In other words, CTAB allows us to assess how DNA damage ultimately impedes protein synthesis, how it induces mutant proteins.”

Study results appeared online in Nature Chemical Biology on Aug. 19.

Wang explained that the CTAB method can be used also to examine various proteins involved in the repair of DNA. One of his research group’s goals is to understand how DNA damage is repaired—knowledge that could result in the development of new and more effective drugs for cancer treatment.

“This, however, will take more years of research,” Wang cautioned.

His lab has a long-standing interest in understanding the biological and human health consequences of DNA damage. The current research was supported by the National Cancer Institute, the National Institute of Environmental Health Sciences and the National Institute of Diabetes and Digestive and Kidney Diseases of the National Institutes of Health.

Wang was joined in the research by UC Riverside’s Changjun You (a postdoctoral scholar and the research paper’s first author), Xiaoxia Dai, Bifeng Yuan, Jin Wang and Jianshuang Wang; Philip J. Brooks of the National Institute on Alcohol Abuse and Alcoholism, Md.; and Laura J. Niedernhofer of the University of Pittsburgh School of Medicine, Penn.

Next, the researchers plan to use CTAB to investigate how other types of DNA modifications compromise transcription and how they are repaired in human cells.

A quantitative assay for assessing the effects of DNA lesions on transcription

Source:

http://www.rdmag.com

University of California, Riverside

 

 

 

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New Drug-Eluting Stent Works Well in STEMI

Reporter: Aviva Lev-Ari, PhD, RN

UPDATED on 8/8/2013

Meta-analysis makes case for drug-eluting stents in STEMI

AUGUST 7, 2013 

New York, NY – Newer-generation drug-eluting stents, particularly the everolimus-eluting stent (Xience V, Abbot; Promus, Boston Scientific), significantly reduce the risk of target vessel revascularization (TVR) in patients with ST-segment-elevation MI (STEMI) without increasing the risk of adverse safety outcomes, including rates of stent thrombosis, when compared with bare-metal stents [1].

These are the principal findings of a new meta-analysis of 28 randomized, controlled clinical trials involving more than 34 000 patient-years of follow-up.

Published online August 6, 2013 in Circulation: Cardiovascular Interventions, the analysis showed that compared with the sirolimus-eluting stent (Cypher, Cordis), the paclitaxel-eluting stent (Taxus, Boston Scientific), and bare-metal stents, the use of an everolimus-eluting stent reduced the relative risk of stent thrombosis 62%, 61%, and 58%, respectively.

“I would make a strong argument to say that the current guidelines should change,” lead investigator Dr Sripal Bangalore (New York University School of Medicine) told heartwire. “The reduction in TVR is not surprising. We know that drug-eluting stents compared with bare-metal stents reduce TVR, but the biggest thing we were able show was that stent thrombosis is also reduced when compared with a bare-metal stent, as well as compared with first-generation drug-eluting stents.”

The current American College of Cardiology/American Heart Association (ACC/AHA) and European Society of Cardiology (ESC) clinical guidelines state that drug-eluting-stent implantation is a class IIa indication in STEMI patients. The recommendations are based on concerns about an increased risk of stent thrombosis with the drug-eluting stents compared with their bare-metal counterparts. Bangalore said concerns have also been raised about the risk of stent thrombosis beyond one year with the first-generation drug-eluting stents, a time point when dual antiplatelet therapy is stopped.

The newer-generation drug-eluting stents, however, have been shown in various studies to be as safe asbare-metal stents in the STEMI setting. For this reason, they conducted a meta-analysis of randomized, controlled trials comparing the sirolimus-, paclitaxel-, everolimus-, and zotarolimus-eluting stents against each other and against bare-metal stents.

When compared with bare-metal stents, the sirolimus-, paclitaxel-, and everolimus-eluting stent reduced the relative risk of TVR by 53%, 31%, and 57%, respectively. The sirolimus-eluting stent was significantly more effective than the paclitaxel-eluting stent at reducing TVR, as was the everolimus-eluting stent. Overall, there was a 67% probability that the Endeavor Resolute zotarolimus-eluting stent (Medtronic) had the lowest risk of TVR, although the data are based on just one trial with 281 patients, note the investigators.

Median rate of efficacy and definite/probable stent thrombosis

Stent type TVR rate (per 1000 patient-years of follow-up) Definite/probable stent thrombosis (per 1000 patient-years of follow-up)
Bare metal 64.00 16.60
Sirolimus 28.93 15.75
Paclitaxel 44.38 18.46
Everolimus 26.55 6.54
Zotarolimus 59.01 11.41
Zotarolimus (Resolute) 14.76 NA*

 

*For stent thrombosis, there were no available data on the Resolute stent

When compared with bare-metal stents, the everolimus-eluting stent reduced the risk of any stent thrombosis by 58%. The Xience stent was also associated with a statistically significant 62% and 61% reduction in the risk of stent thrombosis compared with the first-generation Cypher and Taxus stents.

Bangalore said that a previous patient-level analysis conducted by Dr Giuseppe De Luca (Ospedale Maggiore della Carità, Novara, Italy), reported by heartwire at that time, showed there was a significant 50% increase in the risk of late (more than one year) reinfarction with drug-eluting stents and an almost doubling of very late stent thrombosis with first-generation stents. In this newest meta-analysis, however, the researchers did not observe a similarly increased risk of very late stent thrombosis with the everolimus-eluting stent.

“Based on the totality of data, I would say that it’s time the guidelines make drug-eluting stents and especially the everolimus-eluting stent a class I indication in STEMI patients who can take dual antiplatelet therapy,” said Bangalore.

Source

  1. Bangalore S, Amoroso N, Fusaro M, Kumar S, Feit F. Outcomes with various drug-eluting or bare-metal stents in patients with ST-segment elevation myocardial infarctionCirc Cardiovasc Interv 2013; DOI:10.1161/CIRCINTERVENTIONS.113.000415. Available at: http://circinterventions.ahajournals.org.

 

New Drug-Eluting Stent Works Well in STEMI

By Michael Smith, North American Correspondent, MedPage Today

Published: August 21, 2012

Reviewed by Robert Jasmer, MD; Associate Clinical Professor of Medicine, University of California, San Francisco and Dorothy Caputo, MA, BSN, RN, Nurse Planner

 Watch Video

 A new-generation biodegradable drug-eluting stent had a lower rate of major cardiac events than similar bare-metal devices, researchers reported.

In a randomized trial, patients with ST-segment elevation myocardial infarction (STEMI) needed fewer revascularization procedures and had a lower risk of a new heart attack in the target blood vessel, according to Stephan Windecker, MD, of Bern University Hospital in Bern, Switzerland, and colleagues.

On the other hand, rates of cardiac death were not significantly different, Windecker and colleagues reported in the Aug. 22/29 issue of the Journal of the American Medical Association.

Drug-eluting stents have been shown to reduce the need for repeat revascularization, compared with bare-metal stents, but at the cost of delayed healing, chronic inflammation, and late stent thrombosis, the researchers noted.

The long-term effects result from the persistence of the polymer, Windecker and colleagues noted — something that might be avoided by using a biodegradable polymer.

The biodegradable BioMatrix Flex stent, which delivers the immunosuppressant drug biolimus, was non-inferior in a 4-year trial to the sirolimus-eluting Cypher stent, which does not break down over time.

But it had not been tested against bare-metal stents. To help fill the gap, Windecker and colleagues studied 1-year outcomes in 1,161 STEMI patients randomly assigned to get either the biolimus-eluting biodegradable stent or a similar bare-metal device.

The primary endpoint of the trial was the 1-year rate of major adverse cardiac events — a composite of cardiac death, target vessel-related re-infarction, and ischemia-driven target-lesion revascularization.

Windecker and colleagues found that 24 patients (4.3%) with biodegradable stents had a major adverse cardiac event at 1 year, compared with 49 (8.7%) who were given the bare-metal devices (HR 0.49, 95% CI 0.30 to 0.80, P=0.004).

The difference was driven by a lower risk of two of the elements of the combined endpoint: target vessel-related reinfarction and ischemia-driven target-lesion revascularization. Specifically:

  • Three patients getting the biodegradable stent (0.5%) had a re-infarction related to the target vessel, compared with 15 (2.7%) of those with bare-metal devices (HR 0.20, 95% CI 0.06 to 0.69, P=0.01).
  • Nine patients (1.6%) with biodegradable stents and 32 (5.7%) with bare-metal devices needed target-lesion revascularization (HR 0.28, 95% CI 0.13 to 0.59, P<0.001).
  • Rates of cardiac death were numerically lower, but not significantly so, in the biodegradable stent patients — 16 deaths, or 2.9%, versus 20, or 3.5%.

Definite stent thrombosis occurred in five patients treated with the drug-eluting stents and 12 patients with bare-metal stents, but the difference did not reach significance.

The findings should be “reassuring” to both doctors and patients, Windecker said in a video released by the journal.

The study is “a well-done trial with convincing results regarding its primary end point,” commented Salvatore Cassese, MD, and Adnan Kastrati, MD, both of the Technische Universitat in Munich, Germany.

But, in an accompanying editorial, they argued that it still may not settle the question of long-term complications.

Despite “positive signals,” they wrote, the study has “neither the required sample size nor the sufficient length of follow-up to provide the definitive answer about the long-term safety” of the new biodegradable drug-eluting stents.

The researchers cautioned that the biodegradable drug-eluting stent is not yet approved in the U.S., although European authorities have given it the nod.

They also noted that the study, while demonstrating superiority on the overall endpoint, did not have sufficient statistical power to address the individual components definitively.

The study had support from the Swiss National Science Foundation and Biosensors Europe SA. Windecker reported financial links through his institution with Abbott, Boston Scientific, Biosensors, Biotronik, Cordis, Medtronic, and St. Jude Medical.

The editorial authors reported support from the European Commission. Kastrati reported holding a patent related to polymer-free sirolimus and probucol coating, as well as financial links with Abbott, Biosensors, Cordis, and Medtronic.

From the American Heart Association:

Related Articles in Heart.org

Related links

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Reported by: Dr. V.S.Karra, ph.d

Researchers have created a new type of biosensor that can detect minute concentrations of glucose in saliva, tears, and urine, and might be manufactured at low cost because it does not require many processing steps to produce.

“It’s an inherently noninvasive way to estimate glucose content in the body,” says Jonathan Claussen, a former Purdue University doctoral student and now a research scientist at the U.S. Naval Research Laboratory. “Because it can detect glucose in the saliva and tears, it’s a platform that might eventually help to eliminate or reduce the frequency of using pinpricks for diabetes testing. We are proving its functionality.”

Claussen and Purdue doctoral student Anurag Kumar led the project, working with Timothy Fisher, a Purdue professor of mechanical engineering; D. Marshall Porterfield, a professor of agricultural and biological engineering; and other researchers at the university’s Birck Nanotechnology Center.

Findings are detailed in a research paper published in Advanced Functional Materials.

“Most sensors typically measure glucose in blood,” Claussen says. “Many in the literature aren’t able to detect glucose in tears and the saliva. What’s unique is that we can sense in all four different human serums: the saliva, blood, tears, and urine. And that hasn’t been shown before.”

The paper, featured on the journal’s cover, was written by Claussen, Kumar, Fisher, Porterfield, and Purdue researchers David B. Jaroch, M. Haseeb Khawaja, and Allison B. Hibbard.

The sensor has three main parts: layers of nanosheets resembling tiny rose petals made of a material called graphene, which is a single-atom-thick film of carbon; platinum nanoparticles; and the enzyme glucose oxidase.

Each petal contains a few layers of stacked graphene. The edges of the petals have dangling, incomplete chemical bonds, defects where platinum nanoparticles can attach. Electrodes are formed by combining the nanosheet petals and platinum nanoparticles. Then the glucose oxidase attaches to the platinum nanoparticles. The enzyme converts glucose to peroxide, which generates a signal on the electrode.

“Typically, when you want to make a nanostructured biosensor you have to use a lot of processing steps before you reach the final biosensor product,” Kumar says. “That involves lithography, chemical processing, etching, and other steps. The good thing about these petals is that they can be grown on just about any surface, and we don’t need to use any of these steps, so it could be ideal for commercialization.”

In addition to diabetes testing, the technology might be used for sensing a variety of chemical compounds to test for other medical conditions.

“Because we used the enzyme glucose oxidase in this work, it’s geared for diabetes,” Claussen says. “But we could just swap out that enzyme with, for example, glutemate oxidase, to measure the neurotransmitter glutamate to test for Parkinson’s and Alzheimer’s, or ethanol oxidase to monitor alcohol levels for a breathalyzer. It’s very versatile, fast, and portable.”

The technology is able to detect glucose in concentrations as low as 0.3 micromolar, far more sensitive than other electrochemical biosensors based on graphene or graphite, carbon nanotubes, and metallic nanoparticles, Claussen says.

“These are the first findings to report such a low sensing limit and, at the same time, such a wide sensing range,” he says.

The sensor is able to distinguish between glucose and signals from other compounds that often cause interference in sensors: uric acid, ascorbic acid and acetaminophen, which are commonly found in the blood. Unlike glucose, those compounds are said to be electroactive, which means they generate an electrical signal without the presence of an enzyme.

Glucose by itself doesn’t generate a signal but must first react with the enzyme glucose oxidase. Glucose oxidase is used in commercial diabetes test strips for conventional diabetes meters that measure glucose with a finger pinprick.

Source:

www.rdmag.com

Purdue University

 

 

 

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Guidelines for the welfare and use of animals in cancer research.

via Guidelines for the welfare and use of animals in cancer research.

 

Reported by: Dr. V. S. Karra, Ph.D.

We dedicate these Guidelines to Professor Lloyd Kelland and Dr Peter Twentyman, who made important contributions to these Guidelines and/or previous published versions, and who have now sadly passed away.

P Workman1, E O Aboagye2, F Balkwill3, A Balmain4, G Bruder5, D J Chaplin6, J A Double7, J Everitt8, D A H Farningham9,18, M J Glennie10, L R Kelland11, V Robinson12, I J Stratford13, G M Tozer14, S Watson15, S R Wedge16, S A Eccles1 and An ad hoc committee of the National Cancer Research Institute19

  1. 1Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, Cotswold Road, Sutton, Surrey SM2 5NG, UK
  2. 2Comprehensive Cancer Imaging Centre, Imperial College London Faculty of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 ONN, UK
  3. 3Centre for Cancer & Inflammation, Barts and The London School of Medicine and Dentistry, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
  4. 4Helen Diller Family Comprehensive Cancer Center, University of California San Francisco 1450 3rd Street, San Francisco, CA 94158, USA
  5. 5Paterson Institute for Cancer Research, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
  6. 6OXiGENE Inc., 701 Gateway Boulevard, San Francisco, CA 94080, USA
  7. 7University of Bradford, Richmond Road, Bradford BD7 1DP, UK
  8. 8GlaxoSmithkline Pharmaceutical R&D, PO Box 13398, Five Moore Drive, N2.2210.2B, Research Triangle Park, NC 27709-3398, USA
  9. 9Cancer Research UK, Clare Hall Laboratories, Blanche Lane, South Mimms, Herts EN6 3LD, UK
  10. 10Tenovus Laboratory, Cancer Sciences Division, Southampton University School of Medicine, General Hospital, Southampton SO16 6YD, UK
  11. 11Cancer Research Technology Development Laboratories, Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, UK
  12. 12National Centre for the Replacement, Refinement and Reduction of Animals in Research 20, Park Crescent, London W1B 1AL, UK
  13. 13School of Pharmacy and Pharmaceutical Sciences, University of Manchester, Stopford Building, Oxford Road, Manchester M13 9PT, UK
  14. 14Department of Oncology, K Floor, School of Medicine, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, UK
  15. 15Division of Pre-Clinical Oncology & PRECOS, D Floor West Block, Queen’s Medical Centre, University Hospital, Nottingham NG7 2UH, UK
  16. 16Cancer Bioscience, AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK
  17. 17The Home Office, ASPD (mail point 1B), 1st floor Seacole Building, 2 Marsham Street, London W1P 4DF, UK
  18. 18Current address: Medical Research Council, 20 Park Crescent London W1B 1AL, UK

Correspondence: Professor P Workman and Dr SA Eccles, E-mail: Paul.Workman@icr.ac.uk and Sue.Eccles@icr.ac.uk

19The National Cancer Research Institute (NCRI) is a partnership of 21 organisations from the government, charity and commercial sectors who support cancer research in the UK. Further information about NCRI can be found at http://www.ncri.org.uk

*Observers: V Navaratnam and S Ryder17

Received 5 March 2010; Accepted 15 March 2010.

Abstract

Animal experiments remain essential to understand the fundamental mechanisms underpinning malignancy and to discover improved methods to prevent, diagnose and treat cancer. Excellent standards of animal care are fully consistent with the conduct of high quality cancer research. Here we provide updated guidelines on the welfare and use of animals in cancer research. All experiments should incorporate the 3Rs: replacement, reduction and refinement. Focusing on animal welfare, we present recommendations on all aspects of cancer research, including: study design, statistics and pilot studies; choice of tumour models (e.g., genetically engineered, orthotopic and metastatic); therapy (including drugs and radiation); imaging (covering techniques, anaesthesia and restraint); humane endpoints (including tumour burden and site); and publication of best practice.

Unfortunately we are unable to provide accessible alternative text for this. If you require assistance to access this image, please contact help@nature.com or the author

Keywords:

animal welfare; cancer research; fundamental and translational research; replacement, reduction and refinement (3Rs); pilot studies; tumour models; genetically engineered mouse models; human tumour xenografts; orthotopic models; metastatic models; therapy; imaging; pharmocokinetic, pharmacodynamic and efficacy studies; drugs; radiation therapy; imaging techniques; anaesthesia; restraint; humane endpoints; tumour burden; clinical signs; publication; best practice

Background and scope

Over the last decade there has been an extraordinary increase in our knowledge of the fundamental molecular processes that are involved in the development of cancer and its response to treatment (Hanahan and Weinberg, 2000Vogelstein and Kinzler, 2004Stratton et al, 2009). The public rightfully expect this explosion in basic research understanding to be translated into rapid improvements in prevention, diagnosis and treatment, particularly for the more common cancers and indeed for any malignant disease where there is still clearly an unmet need for more effective therapies. In recent years the identification of the genes and pathways that give rise to cancer dependencies and vulnerabilities has taken us further towards the development of individualised, molecularly targeted therapies (Sawyers, 2004Collins and Workman, 2006;Workman and de Bono, 2008).

Along with growth in fundamental knowledge and greater translational insight has come the development of new in vitro and ex vivo methodologies and research techniques that should further extend our still incomplete genetic, molecular and holistic understanding of cancer, and in addition should help to ensure that improved methods for diagnosis, therapy and prevention will be developed more effectively for patient benefit. Nevertheless, we are still some way from the point where all of the necessary information that is required to introduce a new drug into the clinic in terms of safety and efficacy could be gained without the use of animals in research. Moreover, animals remain essential to extend our understanding of the mechanisms responsible for cancer and to identify, for example, new targets and biomarkers.

It is clearly important that the welfare of animals in cancer research is protected, both from an ethical point of view and also because it is widely acknowledged to be entirely consistent with good science (Osborne et al, 2009). Under the earlier sponsorship of the former United Kingdom Coordinating Committee for Cancer Research (UKCCCR), two sets of guidelines have been published previously (Workman, 1988Workman et al, 1998). Although these guidelines were well received, and are still widely used and cited, it is over 10 years since they were last revised, in which time the science has moved on appreciably. The main aim of this article is to provide new guidelines for the cancer research community concerning the use of experimental animals in oncology, with a major emphasis on their welfare. We focus on rodents as these are predominantly used for cancer research: in 2008, for example, the UK government Home Office statistics showed that 96.8% of animals used in cancer research were mice (http://scienceandresearch.homeoffice.gov.uk/animal-research/publications-and-reference/statistics/index.html). While development of medicines may require testing in other species, use of animals in regulatory toxicology is outside the scope of this review.

The present guidelines should be applied to studies focused on all aspects of cancer research, including experiments aimed at understanding fundamental cancer biology as well more translational work, and should be used in conjunction with more general guidelines for the care and welfare of animals (see examples below and Additional information). It is expected that animal housing will be maintained according to the highest standards, including environmental enrichment (Tsai et al, 2006), and that local ethical review will precede any experimental animal studies. In addition, these guidelines should be used in conjunction with appropriate national legislation: UK Animals (Scientific Procedures) Act 1986; USA Institute for Laboratory Animal Research (ILAR) Guide for the Care and Use of Laboratory Animals (http://dels.nas.edu/Laboratory); EU webpage on laboratory animals (http://ec.europa.eu/environment/chemicals/lab_animals/home_en.htm); Public Health Service Policy on Humane Care and Use of Laboratory Animals (Office of Laboratory Animal Welfare, National Institutes of Health, 2002); http://grants.nih.gov/grants/olaw/references/phspol.htm. A complementary key recent publication, coordinated by the UK’s National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3R), is also recommended (Biotechnology and Biological Sciences Research Council; Department for Environment, Food and Rural Affairs; Medical Research Council; Natural Centre for the Replacement, Refinement and Reduction of Animals in Research; Natural Environment Research Council; Wellcome Trust, 2008). We also feel it is important that the public is made fully aware of the current justification for the use of animals in cancer research and the genuine concern for their welfare by researchers involved with their use. To help with this, a lay summary of the guidelines is also provided on page 1555. A glossary of terms can be found at the end of this article. Finally, it is important to emphasise that high standards of animal care and welfare should be fully consistent with, and helpful to, the conduct of high-quality cancer research (Osborne et al, 2009).

General recommendations

The use of animals raises scientific and ethical challenges. In 1959, Russell and Burch published The Principles of Humane Experimental Technique in which they stated that all animal experiments should incorporate, as far as possible, the 3Rs: replacement (of animals with alternative methods), reduction (in the numbers of animals used to achieve scientific objectives) and refinement (of methods to minimise animal suffering) (Russell and Burch, 1959). These principles underpin the legislation, guidelines and working practices concerning the use of animals in scientific procedures. Consideration of the 3Rs must be an integral part of planning cancer research using animals and the 3Rs need to be implemented throughout the lifetime of the study. Funding bodies and scientific journals (Osborne et al, 2009) should encourage scientists to use humane methods, to supply information on how the principles of the 3Rs are implemented and to publish improvements in experimental design and animal models for the benefit of the research community (www.nc3rs.org.uk/reportingguidelines). Details on the application of the 3Rs in cancer research are provided in Box 1 for ease of reference, together with information on implementation and monitoring in Box 2. Examples of tumour models, experimental design and procedures are provided throughout these guidelines. However, it is emphasised that these are intended to act as a guide only, and each study should be tailored to the specific experimental objectives.

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Tumour models

Preclinical cancer studies fall into two broad categories: those using tumour cell transplantation (Tables 1Aand B), and those in which tumours arise or are induced in the host (Tables 2A and B). The choice of animal model depends on the scientific question being investigated, but the mildest possible procedure should always be used. An example of the type of illustrative aid that can be used to facilitate the rational choice of appropriate models is shown in Figure 1. Cellular interactions and immune responses require immunocompetent animals and syngeneic systems, whereas cancer development or chemoprevention studies may use transgenic models or chemically induced tumours. In the case of translational studies designed, for example, to discover and develop therapies to exploit oncogenic abnormalities, the tumours should have the appropriate molecular genetic defect. Furthermore, real-time optical imaging will require engineered bioluminescent/fluorescent tumour models.

Figure 1.

Figure 1 - Unfortunately we are unable to provide accessible alternative text for this. If you require assistance to access this image, please contact help@nature.com or the authorAn illustrative process for tumour model selection and use. This representative schema provides an illustration of factors to be considered when designing an animal study. In this particular example, all the factors listed at a given stage (and potentially others) should be considered before moving down, stepwise, to the next stage. Here, an initial consideration is that the choice of model may be based on the relevant molecular status, clinical tumour type or in vitro studies. At the next stage, the animal host will be dictated by the need for, say, a human tumour xenograft versus a genetically engineered mouse model, which have advantages discussed in the text. Considerations of tumour environment and site then follow, after which, in therapy studies, are dosing and endpoint aspects. Note that this schema is illustrative and not prescriptive and that each study must be tailored to the specific scientific question and experimental objectives, with appropriate humane endpoints always applied and pilot studies carried out as needed.

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Transplantation tumour models

These normally involve the transplantation of mouse or rat tumour cells into a host of the same (syngeneic) species and strain. Growth of human (xenogeneic) tumour cells can be achieved using immunodeficient (e.g., nude or SCID) mice to prevent rejection (Table 1A). Most transplantable tumours are established subcutaneously. These subcutaneous (s.c.) tumours are simple to initiate but may lack relevance in terms of stromal/vascular interactions and metastasis. More complex models may involve orthotopic transplantation at appropriate primary sites, or inoculation of tumour cells through routes which maximise the chance of metastatic spread (Table 1B). There is an increasing trend to establish xenograft tumours directly from human cancers, to avoid artificial selection of cells in tissue culture and changes in gene expression and phenotype, which this may induce. Such transplants may better model the principal facets of clinical cancer, for example, maintenance of tumour architecture, heterogeneity, expression of certain targets and response to therapy (Dong et al, 2010), but can be less reproducible (especially as primary grafts) and slower growing than well-established models (Neale et al, 2008Rubio-Viqueira and Hidalgo, 2009). Detailed molecular and genetic characterisation, facilitated by modern high-throughput technologies (e.g., seehttp://www.sanger.ac.uk/genetics/CGP), is now available for human cancer cell lines used for xenografts (Masters et al, 2001Park et al, 2010) and is important to understand the biology of these models and to select the most appropriate for each study.

Autochthonous tumour models

There are two broad categories: those arising in outbred or inbred rodents (Table 2A), or those from animals harbouring genetic changes that alter tumour susceptibility (Table 2B). Certain mouse or rat strains are susceptible to spontaneous development of tumours. More commonly, tumours are induced by chemical carcinogens, radiation, viruses or bacteria. Such models may mimic some of the aetiological events in human cancer development; exposure to such agents may induce systemic effects that are difficult to replicate in genetically engineered models.

Major advances have been made in the development of sophisticated mouse models of cancer that mimic many of the genetic and biological characteristics of human malignancies, although the host genetic background may affect tumour incidence and/or malignant potential (Lifsted et al, 1998Winter and Hunter, 2008). A range of technologies now allows the inducible expression of oncogenes or inactivation of tumour-suppressor genes in vivo in a precisely controlled manner in virtually any tissue or cell type. (Chen et al, 2004Christophorou et al, 2006Sharpless and DePinho, 2006). Such genetically engineered mouse models (GEMMs) provide excellent experimental systems to develop a deeper understanding of cancer biology in vivoand are increasingly being used for preclinical testing of molecularly targeted therapies, as they depend on or are ‘addicted’ to the specific molecular abnormalities and biochemical pathways engineered to drive the malignant process.

Routine use of GEMMs for preclinical testing of anticancer therapies can be hampered by variable tumour latency, incomplete penetrance and complicated breeding schemes. The full potential of such mouse models is yet to be realised and further work is required to derive maximum benefit for cancer patients from these initiatives (Frese and Tuveson, 2007). Newer models (e.g., exploiting double or multiple genetic abnormalities) have resulted in enhanced tumorigenicity and metastatic capacity, and some studies have shown that mouse cancer models with relevant human gene mutations respond to appropriate targeted therapies (Politi et al, 2006), and also may develop common secondary mutations associated with acquired resistance (Politi et al, 2010). As an example of target validation, reversible, systemic expression of a dominant-negative mutant Myc oncogene in transgenic Ras-induced lung carcinoma model caused the tumours to regress, whereas effects on normal regenerating tissue were well tolerated and reversible (Soucek et al, 2008). To overcome heterogeneity issues, transplantation of transgenic tumours can provide higher throughput models, for example, for testing therapeutics (Varticovski et al, 2007). Commonly used GEMMs include mammary carcinomas induced by the viral oncogene polyoma virus middle T (Guy et al, 1992Fluck and Haslam, 1996;Marcotte and Muller, 2008) or by the human or rat Her2/neu oncogene (Chan et al, 1999Quaglino et al, 2008), or colon adenomas and carcinomas induced by inactivation of the adenomatous polyposis coli (APC) tumour-suppressor gene (Taketo, 2006). Space constraint does not allow a full description or listing of the many more sophisticated, patient-like models now available, examples of which are shown in Table 2B. The reader is referred to the more complete information available at http://emice.nci.nih.gov/mouse_models.

A key question that continues to be debated is whether human cancer xenografts or murine transgenic models best reflect the human disease in terms of biology and predictions of efficacy of therapeutic agents (Becher et al, 2006Dennis, 2006Garber, 2006Sausville et al, 2006Sharpless and DePinho, 2006). Some GEMMs have shown patterns of sensitivity to chemotherapeutic agents and development of resistance that are similar to their human tumour counterparts (Rottenberg and Jonkers, 2008). The predictive value of neither type of model has been fully established; however, there is agreement that molecular characterisation of all tumours is required to underpin the choice of model.

Selection and optimisation of experimental systems

As mentioned, selection of tumour models should be based on both molecular characteristics, for example, expression or mutation of a target of interest or other relevant molecular pathology, either endogenously or through transfection/transgenic technology, together with desired properties such as the rate and reproducibility of growth, metastatic potential and chemosensitivity.

Cell line verification and molecular characterisation

Given the frequency of misidentification and cross-contamination (Nardone, 2007Lacroix, 2008) it is essential that all cell lines are rigorously checked for their provenance and genetic identity (Parodi et al, 2002Yoshino et al, 2006). It is also important that cell lines are free from contamination with infectious agents such as mycoplasma, which can influence their biological behaviour and present a risk to handlers and animals (Ishikawa et al, 2006Sung et al, 2006Harlin and Gajewski, 2008). Regardless of origin, detailed characterisation of tumours should be performed and checked periodically to ensure that desired properties are maintained and are commensurate with the molecular pathology of the corresponding human malignancy (Santarius et al, 2010). A thorough literature review should establish their reported tumorigenic and immunogenic properties, with special attention paid to the selection of the correct host animal strain and sub-strain. Residual immune responses to xenografted tumours in nude/SCID mice may occur and the sex of the host should be considered, particularly for hormone-responsive tumours such as breast and prostate.

Pilot studies and optimisation

Pilot tumour growth studies using small numbers of animals (5–10) are recommended to establish that patterns of local and metastatic growth are reproducible. They also show any adverse effects associated with tumour progression and enable humane endpoints to be identified. The data derived should feed into group numbers used for definitive studies (e.g., therapy experiments) in order for experimental time frames and statistically significant endpoints to be established. Use of a relevant positive control treatment may be useful at this stage to ensure that tumour growth/responsiveness is as expected. This can be dictated by a variety of factors, including the site of growth. Subcutaneous tumours may grow rapidly and some are prone to developing haemorrhagic areas, which can cause rapid expansion and ulceration (e.g., human A2780 ovarian carcinoma and AR42J pancreatic carcinoma xenografts).

For tumours growing as a suspension in the peritoneal cavity, it is important to establish clear criteria to ensure that studies are terminated before animal welfare is compromised. This site is only appropriate for models where ascites is a feature of the natural progression of the human cancer (e.g., ovarian carcinoma, peritoneal mesothelioma, gastrointestinaI tumour carcinomatosis). Similar criteria apply to other sensitive specialised sites such as muscle or brain. For metastatic models, pilot experiments should define the extent and time course of dissemination to internal organs.

Pilot studies should include sequential analysis of animals to determine the time course required to achieve scientific goals. Termination of studies at the earliest possible point will minimise adverse effects on the animal. Where possible, use of biomarkers (e.g., serum levels of prostate-specific antigen, PSA) and real-time imaging are highly recommended. It is also possible to measure circulating tumour cells using fluorescence and PCR-based techniques (Glinskii et al, 2003Komatsubara et al, 2005). For spontaneously arising tumours, including those in transgenic animals, particular attention should be paid to the time course of tumour development and issues relating to the development of multiple tumours. Progression may be unpredictable and involve rapid dissemination and subsequent deterioration in clinical condition, in which case careful and frequent monitoring is required.

Refinement and welfare issues

Subcutaneous implantation of tumour material should use a trochar or surgical formation of a small s.c. pocket. Appropriate anaesthetics must be used and post-implantation analgesia is also strongly recommended. Veterinary advice should be sought to ensure that the agents selected reflect contemporary best practice. Anaesthesia/analgesia is also required for implantation of ‘hollow fibres’ or slow release devices such as osmotic mini-pumps. Hormone pellets (oestrogen/testosterone) may be required to support hormone-dependent tumours, but first-time use in a particular strain will require pilot experiments with different doses/exposures to assess tolerance, especially with oestrogen pellets where urinary tract side effects may be encountered (Pearse et al, 2009).

For injection of cell suspensions, the minimum number of cells in the smallest volume should be used, consistent with the properties of the tumour. For s.c. sites, 1–5 million cells in 100 μl is typical. For orthotopic sites, this should be reduced to avoid excessive tissue damage or leakage (e.g., 50 000 cells in 30 μl into the prostate, or 10–50 000 cells in 5 μl into the brain). Intramuscular tumours in the leg can affect mobility, and this site should only be used if there is special justification (e.g., for tumours which naturally develop in this tissue). Similarly, footpad injection, which has been traditionally used to potentiate lymphatic dissemination, is unacceptable without exceptional scientific justification and should then only involve a single paw.

Surgical removal of a primary tumour may be justified, for example, from s.c. sites, mammary fat pad or removal of the spleen following intrasplenic injection, to allow time for outgrowth of any secondary deposits. Surgery must be performed using sterile techniques with appropriate post-operative monitoring and control of any pain and inflammation/infection.

Cell lines should be checked regularly for contaminating microorganisms to avoid infection of host animals. This is especially important if tumours are routinely passaged between animals, which may be justified for those that are difficult to establish from cell cultures. Asymptomatic infection of experimental animals may affect tumour properties, for example, metastasis (Rodriguez-Cuesta et al, 2005). Procedures can be used to improve tumour take rate. For example, moderate doses of whole-body irradiation may further enhance engraftment of tumour cells in athymic mice (Baersch et al, 1997Nijmeijer et al, 2001Li et al, 2006), although the added stress and risk to the animal must be considered. Co-administration of human tumour cells with allogeneic bone marrow transplantation may reduce graft-vs-host activity but preserve graft-vs-tumour effects in allogeneic leukaemia models (Prigozhina et al, 2002Giver et al, 2004).

Transplanted tumours (especially xenografts) may not develop with an incidence, growth rate or malignant potential required; however this can often be enhanced by selection of tumorigenic/metastatic variants (Bruns et al, 1999Nguyen et al, 2009a). In addition, co-injection of tumour cells with extracellular matrix proteins and/or angiogenic factors (Collado et al, 2007), cancer-associated fibroblasts (Noel et al, 1993;Orimo et al, 2005) or mesenchymal stem cells (Karnoub et al, 2007Spaeth et al, 2009) can increase tumorigenicity, better recapitulate the human tumour microenvironment and enhance metastatic potential. Cells may be transfected with fluorescent or bioluminescent markers allowing serial imaging of internal tumours/metastatic spread. However, such tagged cell lines should be profiled to establish that their biological characteristics are unchanged and consideration should be given to the dependence of luminescence/fluorescence on factors in the tumour microenvironment, for example. molecular oxygenation, necrosis, or ascites fluid from peritoneal tumours (Condeelis and Segall, 2003).

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Therapy

Preclinical discovery and development of therapeutics

There is a concerted effort to identify and develop small-molecule drugs or biopharmaceuticals (e.g., antibodies, protein therapeutics, vaccines, gene therapy) targeted against cancer cells or associated host cells (Sawyers, 2004Collins and Workman, 2006Workman and de Bono, 2008). A representative ‘test cascade’ for discovering new small-molecule inhibitors of cancer targets is shown in Figure 2. As a consequence of extensive in vitro testing, comparatively small numbers of prioritised compounds progress to examination in vivo (Collins and Workman, 2006). In vivo studies use sequential, discriminatory tests to prioritise compounds at each stage. Different tests may need to be applied to biopharmaceuticals, such as antibodies and vaccines, as they may work by recruiting host effectors (e.g., cytotoxic leukocytes). Epitope specificity can also require the development of an antibody or vaccine initially using anti-rodent reagents (before switching to the clinical form) or use of a genetically modified mouse model. In addition, agents directed against the tumour microenvironment (e.g., angiogenesis, tumour-promoting stromal or inflammatory cells) will require appropriate specialised assays. A range of technical platforms are used preclinically to define responses to therapy, the most informative of which are adopted for use in patients (Figure 3). Careful assessment of a therapy’s safety profile (outside the scope of this review) is also required for regulatory submission.

Figure 2.

Figure 2 - Unfortunately we are unable to provide accessible alternative text for this. If you require assistance to access this image, please contact help@nature.com or the authorExample of a drug discovery test cascade for identifying small-molecule antitumour drugs. A representative test cascade for identifying a potential small-molecule drug against a given target is shown. A subset of a compound library is initially screened vsthe target in vitro, in recombinant protein or cellular assays, using high-throughput automation to identify ‘hits’. Subsequent leads are examined in more detail by assessing their effect on downstream molecular events in cells and their selectivity vsother proteins. A battery of additional in vitro tests is also used for measurement or prediction of physical properties and pharmacokinetic parameters. Only compounds with a promising balance of features are progressed to in vivo testing, usually in mice. Pharmacokinetic (PK) studies, used to understand drug exposure, may initially involve co-inoculation of low doses of compounds (‘cassette dosing’) to minimise animal usage. The tolerability of leads with favourable PK is then assessed at higher doses, before evaluating their pharmacodynamic (PD) effect on tumour and normal tissues at well-tolerated doses. Compounds that do not meet the anticipated level of performance at any stage may result in subsequent rounds of iterative medicinal chemistry to generate improved leads. Selected leads are progressed to efficacy testing to determine the link between target inhibition and the effect on tumour growth or spread (metastasis). Safety studies on late-stage leads are also required before a candidate drug can be selected for examination in cancer patients (not covered here). The application of the test cascade means that compounds are filtered by the earlier stage assays so that a smaller number of compounds, and only those of higher quality, are taken into later stage in vivo assays in animals.

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Figure 3.

Figure 3 - Unfortunately we are unable to provide accessible alternative text for this. If you require assistance to access this image, please contact help@nature.com or the authorExamples of technologies used in animals for therapeutic cancer research. In vivotumour models have an essential role in the development of new cancer medicines, enabling the temporal and quantitative effects of treatment to be examined on tumour and normal tissues in the intact organism. Methods used include those to examine (clockwise from far left) molecular determinants of sensitivity to treatment (initially in vitro, corroborated in vivo) such as (a) gene mutations by sequencing, or (b) gene amplification by fluorescent in situ hybridisation; detection of target phospho-epitopes and their inhibition in tumour tissue as determined by: (c) immunohistochemistry or (d) western blotting of cell lysates; (e) tumour vascular density and maturation by fluorescent immunohistochemistry; (f) tumour mRNA expression by gene array analysis with hierarchical clustering of information; (g) imaging techniques such as dynamic contrast-enhanced MRI to measure tumour haemodynamics; and (h) pharmacokinetic analysis of drug concentrations in plasma by mass spectrometry.

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Defining tolerable doses for efficacy studies

An investigational treatment should be examined at a potential therapeutic dose level and using a relevant dosing regimen that covers the longest duration anticipated. These parameters can, for example, be estimated from consideration of mechanism of action, in vitro potency, pharmacokinetics, protein binding and pharmacodynamic biomarker data. Studies typically use two mice per dose level with a doubling dose-escalation or dose-halving de-escalation design. For studies involving a single dosing event, an interval of 24 h should be used before an alternative dose level is examined, to allow any acute adverse effects to be seen. For more chronic administration schedules (e.g., daily for 21–28 days) this interval should be at least 5 days. Animals should be examined at least twice daily (see humane endpoints below). Note that presence of a tumour may reduce host tolerance to therapy. Studies of mice may be used to predict dose requirements in other species through allometric scaling of pharmacokinetic parameters (Freireich et al, 1966).

Combination studies

There is a strong rationale to study combinations of agents in vivo to guide clinical studies. Relevant prior in vitro studies such as Combination Index or isobologram analyses to discriminate additive, synergistic or antagonistic interactions should be completed to guide the selection of combinations and schedules. Compounds are added to tumour cells in culture over a range of concentrations, alone or in combination, and the changes in sensitivity are observed. Compounds may also be added sequentially as the order of administration may significantly influence responses (Chou, 2006). Care needs to be taken with in vivo studies in addressing the choice of individual drug doses and scheduling, particularly if overlapping toxicities are likely. Pilot experiments must assess tolerability (see above), and pharmacokinetic data (see below) should also be generated to determine whether interpretation of efficacy data is affected by pharmacokinetic interactions (Siim et al, 2003).

Pharmacokinetic studies

In vitro and in silico methods are useful to predict absorption, distribution, metabolism and elimination (ADME) properties and to help prioritise compounds for evaluation in animals (Table 3Singh, 2006). However, at present such methods are unable to predict accurately the full pharmacokinetic profile of an agent. Pharmacokinetic studies should use a validated and sufficiently sensitive detection method, ideally avoiding the need to pool separate blood samples, thereby minimising animal usage. Typical experiments on mice use a single dose and 5–8 time points (2–3 mice per point) over 24–48 h with small molecules (usually administered p.o., i.v. or i.p. at doses of 0.5–100 mg kg−1) and over 1–21 days with biopharmaceuticals (administered i.v., i.p. or s.c. at doses ranging from 10 to 1000 μg per mouse).

More recently, repeat sampling of small volumes of blood from a superficial vein in mice over a series of time points has been established to reduce animal numbers. This can be employed either for isolation of plasma and analysis by sensitive liquid chromatography–mass spectrometry/mass spectrometry (LC/MS-MS or tandem MS) instrumentation (Abatan et al, 2008), or by spotting microlitre volumes of whole blood onto specialised paper cards, which are then dried and extracted before analysis (Barfield et al, 2008). In rats, a 5–8 time-point pharmacokinetic profile may be generated using 2–6 animals in total, through repeated blood sampling. ‘Cassette dosing’, which involves administration of low doses of compound mixtures, should also be considered initially as this can reduce animal usage (Watanabe et al, 2006Smith et al, 2007). Wherever possible, computational compartmental kinetic modelling should be used to predict optimal doses or multiple dosing protocols, to facilitate more limited sampling (Rowland and Tozer, 1995). It is noteworthy that the plasma half-life of monoclonal antibodies is frequently extended in immunocompromised mice, which are deficient in IgG production (Bazin et al, 1994).

Pharmacodynamic biomarkers

Initial studies of investigational therapies using tumour-bearing animals should aim to determine whether the target, or an appropriate downstream pathway or phenotype, is modulated by using suitably validated pharmacodynamic biomarkers (Collins and Workman, 2006). Typically, animals are humanely killed at intervals to determine the extent and duration of pharmacodynamic changes and to investigate biomarkers in tumour and normal tissues (e.g., blood or skin) that may be relevant to clinical development (Banerji et al, 2005). In vaccine studies, responses are assessed by changes in immune status, including evidence of tumour-infiltrating leukocytes by immunohistochemistry, and specific cellular or humoral immunity (Gajewski, 2000). It should be possible to use much smaller group sizes of 3–5 in pharmacodynamic studies in comparison to those in efficacy studies (see below). Simultaneous measurement of drug concentrations and mechanistic biomarkers is recommended to reduce animal numbers and establish a pharmacokinetic–pharmacodynamic relationship. Judicious application of such studies in a drug discovery test cascade should be used to prioritise agents before entry into efficacy studies.

Efficacy determinations

All relevant information should be used to guide the design of tumour efficacy studies. Such studies generally involve examination of treatment effects over a 2- to 4-week period and establish how the therapeutic response relates to pharmacokinetic and pharmacodynamic parameters. Typically, with treatments delivered by an appropriate route of administration (Table 4), response is determined in 6–10 animals per study group (vs a control group) either by direct twice-weekly calliper measurement of superficial tumours (Kelland, 2004), counting lung or liver metastases ex vivo, or using imaging methodologies (Edinger et al, 2002Hoffman and Yang, 2005Brindle, 2008McCann et al, 2009Yang et al, 2009). Alternatively, post-treatment excision of tumours for in vitro determination of clonogenic survival, or determination of the dose required to inhibit tumour growth by 50% (tumour control dose-TCD50) may be appropriate (see Radiation therapy section below). Methods are available to determine sample sizes for single- and combination-agent studies and to allow for incomplete data sets (Tan et al, 2005). For certain targets, alternative, surrogate in vivo efficacy models in non-tumour-bearing animals may be used, such as assessment of anti-oestrogenic activity by determining the effect on hypothalamic function (Kato et al, 1968).

Administration of experimental agents

Various sources are available for advice on well-tolerated injection volumes and recommended administration schedules. It is important to note that, from an animal welfare point of view, frequency and duration of dosing are as important as the volume and composition of the injected solution. Some commonly used examples are given in Table 4 and the following references: Diehl et al (2001)Morton et al (2001). More frequent dosing would need to be justified by pharmacokinetic or pharmacodynamic data. As an illustration of standard procedures, for oral/i.p. or i.v. dosing in mice, volumes of 10 and 5 ml kg−1, respectively (equating to 200 and 100 μl for a 20 g mouse), are widely accepted. However, the smallest volume that can be accurately and safely administered must always be used.

Where possible, compounds should be administered in an aqueous solution (sterile water for injections, 0.9%saline or 5% dextrose/saline) that is as close to physiological pH as possible, as highly acidic or basic solutions can be an irritant. If organic solvents (like dimethylsulphoxide, DMSO) are necessary, these should not exceed 5 ml kg−1 or 10% of the injected volume. Detergents (such as Tween), solubilisers or emulsifiers should not exceed 20% of the injected volume. Cyclodextrins should not exceed 2 ml kg−1 or 45% of the injected volume, and where used at >20% of the injected volume, animals need to be rehydrated within 2–4 h.

Experimental design including statistics

To maximise the scientific integrity of data generated while at the same time using the minimum number of animals, statistical expertise should be applied to all experimental design and analyses (Festing, 2002Festing and Altman, 2002Festing et al, 2002; see Boxes 3 and 4).

Chemoprevention

These studies routinely use either carcinogen-induced rat tumours (e.g., azoxymethane-induced colorectal cancer) or mouse genetic models of carcinogenesis (e.g., ApcMin colorectal; Corpet and Pierre, 2003Cai et al, 2009). Generally, animals receive the putative chemopreventive agent in the diet or drinking water over an extended period at innocuous doses. Tumour development is measured at the end of the study and compared with animals on a relevant control diet. Relatively large numbers of rodents (e.g.; greater than or equal to14 per group; Cai et al, 2009) may be required for the observed differences between the intervention and control groups to be robust. Mechanistic and pharmacodynamic endpoints should also be included (Yang et al, 2001Corpet and Pierre, 2003).

Radiation therapy

External beam radiotherapy is primarily used for local tumour irradiation, which requires lead shielding to minimise normal tissue exposure. Typically, s.c. tumours are used and combination treatment with a novel therapy is tested. Endpoints include local control, growth delay and in vivo–in vitro clonogenic survival (TCD50). Time to re-growth is preferred to a single time point analysis. Local tissue toxicity is usually manifest as skin erythema but should be minimised by restricting localised doses to less than 30 Gy (single dose). Exploration of better tolerated, clinically relevant fractionated doses (e.g., 2–5 Gy per fraction over 1–2 weeks) is encouraged. Should moist desquamation occur, this should not be allowed to persist for more than 24 h. Irradiated s.c. tumours can show ulceration, which may reflect tumour response. However, if there is evidence of infection and/or no signs of tissue repair the animal should be humanely killed. The acute and late effects of radiation treatment may also be examined in a relevant organ, particularly when studying new combination paradigms. A common endpoint has been the development of fibrosis in lung tissue, although more recently measurement of breathing rate has been implemented to detect symptoms before they become distressful to the animal (Jackson et al, 2010).

Radiotherapy can also be delivered in the form of targeted radionuclides (normally attached to antibodies; e.g., Martensson et al, 2005). Normal tissue toxicity will depend on antigen expression on tissues relative to the tumour and the nature of the emitter. Whole-body irradiation can also be used to suppress the immune response of an animal, for example, or to treat disseminated disease. Selected doses should not manifest toxicity over the duration of the experiment, for example, gut toxicity within 5 days or haematological toxicity within 30 days.

UV radiation (UVR)

The response of mouse skin to UVR may be used, for example, to study the aetiology of non-melanoma skin cancer (van Kranen and de Gruijl, 1999Hedelund et al, 2006). Generally, experiments are performed with hairless (Skh-hr2) mice. As mouse skin does not show signs of burning, it is important to use a biologically relevant, non-burning dose of 0.2–0.3 MED (minimal erythema dose; 50% skin thickening=0.5 MED). Skin thickness should be measured 2–3 times weekly after increasing the dose of UVR until 20–30% thickening has occurred. If hyperplasia is maintained over 12–15 weeks skin tumours may form. A protective mouse restrainer should be used as UV radiation is damaging to eyes and ears.

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Imaging

General considerations

Imaging techniques now have a principal role in translational cancer research, enabling sequential analysis of biological endpoints in the same animal, with obvious welfare benefits. The main utility of small-animal imaging is for monitoring deep-seated tumours and metastases with or without treatment. Applications include studies of basic biological processes and of tissue pharmacokinetics and pharmacodynamic responses to treatment (Paulmurugan et al, 2002Galbraith et al, 2003Pillai et al, 2008Tennant et al, 2009Nguyen et al, 2009b). However, animal numbers may not be reduced if, for example, full endpoint analysis requires surgical intervention such as cannulation of blood vessels or when contrast agents have a long half-life. Here, sequential imaging may not be possible and alternative techniques involving tissue excision may provide more information (usually at higher spatial resolution) from the same number of animals.

There is an increasing clinical need for pharmacodynamic imaging with molecularly targeted cancer therapeutics. However, interpretation of imaging signals is often difficult and animal models have an important role in rigorous validation of new techniques. This needs to be accompanied by consideration of unique animal welfare issues. Use of external imaging techniques on small animals is not completely non-invasive as some form of anaesthesia or physical restraint is necessary and surgery or administration of contrast agents may be required.

Imaging techniques

The applications, advantages and disadvantages of commonly used imaging technologies are summarised inTable 5 and have also been reviewed recently (Workman et al, 2006Brindle, 2008Weissleder and Pittet, 2008). Whole-body optical imaging is relatively simple and cost-effective (Edinger et al, 2002). Tumour cells are genetically modified to constitutively or inducibly express a fluorescent protein (e.g., eGFP, dsRed) or an enzyme that activates an exogenously administered substrate to a bioluminescent molecule (usually luciferase for activation of a luciferin). The whole animal is imaged using sensitive optical detectors, which may or may not incorporate a tomographic facility (Figure 4). The potential influences of genetic modification and/or substrate administration on immunogenicity and response to treatment, as well as animal welfare, must be considered (Tuchin, 1993Dennis, 2002Condeelis and Segall, 2003Wells et al, 2006).

Figure 4.

Figure 4 - Unfortunately we are unable to provide accessible alternative text for this. If you require assistance to access this image, please contact help@nature.com or the authorExamples of in vivo imaging in pre-clinical cancer research. (A) Optical surface bioluminescence imaging of orthotopically xenografted human PC3 prostate carcinoma cells transfected with luciferase (PC3luc2a). Mice were imaged using a Charged Coupled Device (CCD) camera, which is super-cooled to enhance detection sensitivity and image resolution. The images shown were taken after systemic administration of luciferin, with ‘intensity of luminescence’ shown as ‘heat’ maps and red as maximum intensity. The scale shows the number of photons detected. Top panel: Untreated mice at day 8–41 after transplantation; bottom panel: before and after treatment with 5 mg kg−1 taxotere on day 10. This technique is useful for monitoring treatment effects in deep-seated tumour sites. Light scattering through tissues makes precise quantitation difficult. (B) PET imaging of tumour cell proliferation using 18F-3′-fluoro-3′-deoxy-l-thymidine (FLT). Transverse and coronal (0.5 mm) images of HCT116 tumour-bearing mice 24 h before treatment and after 4 daily treatments with the histone deacetylase inhibitor LAQ842 at 25 mg kg−1. 30- to 60-min summed images from a dynamic scan are presented. Numerous radiotracers are available for investigating specific biochemical pathways in vivo, if specialised facilities are available. The scale shows the intensity of radiotracer uptake. (C) Intravital imaging of tumour vasculature of the P22 rat sarcoma growing in a dorsal skin flap window chamber. The image was obtained by multi-photon fluorescence microscopy after i.v. administration of 70 kDa FITC–dextran. High spatial resolution is obtained but surgical intervention is required.

Full figure and legend (276K)

Intravital microscopy uses a wide variety of optical imaging techniques, often incorporating fluorescent or bioluminescent genetic reporters or markers, including nano-particles (Hoffman, 2005). It has particular animal welfare issues because it involves surgery to provide optical clarity and visualisation on a microscope stage or using fibre-optic light guides (Weissleder and Pittet, 2008). Some intravital microscopy techniques (e.g., tumours growing in the intestinal mesentery) require laparotomy with deep anaesthesia, so that imaging is only possible for a few hours under terminal anaesthesia. Surgical implantation of ‘window’ chambers for tumour implantation enables imaging to be performed over days to weeks (Dewhirst et al, 1987Lehr et al, 1993Brown et al, 2001Reyes-Aldasoro et al, 2008). Here, general anaesthesia is only essential for the initial surgery and imaging may be performed with restrained animals. Strict aseptic technique and good post-operative care and analgesia are essential (Richardson and Flecknell, 2005Flecknell, 2008).

Most physical imaging techniques require use of exogenous contrast agents and only positron emission tomography (PET) and single photon emission computed tomography (SPECT) are sufficiently sensitive to allow use at true tracer levels; so possible pharmacological effects of contrast agents need to be carefully considered. The same procedures for tolerability testing should apply to imaging agents as for new drugs. Some magnetic resonance imaging (MRI) techniques use inherent properties of tissues to provide endogenous imaging contrast. For instance, BOLD (blood-oxygen-level-dependent) MRI allows assessment of tissue oxygenation. These techniques avoid the use of pharmacological agents but results may be difficult to interpret.

Contrast-enhanced CT has the highest spatial resolution of all clinically applicable imaging techniques and is amenable to rapid kinetics. However, depending on the operating parameters and scan length, this may involve considerable ionising radiation dose per scan (0.02–0.6 Gy; typically 0.1–0.3 Gy) (Boone et al, 2004;Carlson et al, 2007Brindle, 2008). Doses should be minimised to avoid compromising experimental results through interaction of ionising events with the biological processes of interest, as well as welfare issues; as a guide, total radiation dose >1 Gy can affect tumour growth and whole-body doses >6 Gy are generally lethal to small rodents. Users of fused PET–CT or SPECT–CT systems should note that the radiation dose from the PET or SPECT can be as large as the CT dose. In addition, iodine-based contrast agents are nephrotoxic and, if required for repeat studies, well-tolerated doses should be established.

Anaesthesia and restraint for imaging

Physical restraint and/or general anaesthesia are required for small-animal imaging. Both procedures can affect animal well-being and introduce experimental artefacts. Body temperature must be maintained and monitored during general anaesthesia using thermostatically controlled heating pads, microwaveable gels or warm air blowers. Light general anaesthesia using an inhalational anaesthetic such as isofluorane or a short-lived i.v. injectable such as propafol should be used for pharmacological restraint, wherever possible. Deleterious effects of physical restraint can be minimised by appropriate design of restrainers, provision of black-outs and acclimatisation (Warden et al, 2000Narciso et al, 2003King et al, 2005). Preferred methods will depend on the species, imaging modality and device used. Where general anaesthesia is not appropriate, sedation with use of gentle physical restraint is encouraged, taking account of veterinary advice. Acclimatisation needs to be thorough, as a short period of training can induce more stress (Warden et al, 2000Narciso et al, 2003).

Length of imaging sessions

If applicable, animals should be transported to imaging facilities in suitable transport boxes, with food and water provided before imaging. The length, total number of imaging sessions and intervals between them depend on factors such as time required to acquire images, tolerance to restraint or general anaesthesia, half-life of the contrast agent and whether cannulation is required. Consideration also needs to be given to exposure of immune-deprived animals to a non-pathogen-free environment, as well as monitoring and control of animal physiology during imaging. If animals have no access to water, an imaging session should typically last no more than 2 h and total imaging time should not exceed 2–3 h in a 24-h period. Use of un-anaesthetised animals restrained for more than 2 h must be avoided except where there is exceptional justification, for example, for animals recovering from general anaesthesia after cannulation of superficial vessels before imaging. In this case, use of local analgesia around the cannulation site is essential. Animals anaesthetised for more than 2 h should be rehydrated if recovery is prolonged, for example, by injection of dextrose/saline. If animals need to be anaesthetised more than once per day, they must be fully recovered, eating and drinking before being re-anaesthetised. On completion of a session, animals should either be killed or kept warm until full recovery from anaesthesia or until the next analysis session. Analysis may be repeated on the same animal but typically this should not exceed five sessions within a 1- to 2-week period and typically no more than one imaging session per day.

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Humane endpoints

There are ethical, scientific and legal reasons for ensuring that adverse effects are minimised. Choice of appropriate humane endpoints provides significant opportunities for refinement, and should be developed in tandem with the requirements for a valid scientific outcome. Early endpoints reduce non-specific systemic effects and so may increase the precision of the results obtained. Pilot studies, including autopsy to determine the full extent of tumour growth, will facilitate the definition of robust and refined endpoints. Endpoints for particular models must also take account of the known pathogenesis of the particular tumour model in question and should be regularly reviewed in the light of experience.

The endpoints proposed are based on animal models in widespread use (for examples see Tables 1 and 2); however, each study should be considered on its own merits. For example, tumorigenicity studies can be terminated as soon as progressive tumour growth is evident. By contrast, carcinogen-induced skin papillomas, for example, undergo malignant transformation late in their development and may require later endpoints. Imaging techniques facilitate the development of more defined endpoints for some tumour models. Every effort should be made to identify factors allowing scientific decisions to be made at the earliest stage possible, while taking into account the total burden of procedures on animal welfare. The intentional use of death as an endpoint is unacceptable and animals should not be allowed to become moribund.

The choice of site for solid tumours will influence the maximum acceptable tumour load and the appropriate humane endpoints. Sites such as the footpad, tail, eye or bone are likely to be painful or distressing and require special justification and earlier endpoints. Similarly, tumours that metastasise to sensitive sites need great care. If brain tumours can be justified (e.g., to increase understanding of their biology and to develop therapies for this area of unmet clinical need), body weight loss is reportedly a sensitive endpoint (Redgate et al, 1991) and MRI or bioluminescent imaging (BLI) techniques can be very useful (van Furth et al, 2003Ragelet al, 2008McCann et al, 2009). Intramuscular tumours are painful and only justified where there is a strong case for orthotopic studies, for example, for sarcomas.

In genetically modified animals, particular care is needed to ensure detection of unexpected sites of tumour development. As with all internal tumour sites, this includes clinical examination, measurement of body weight, abdominal palpation and loss of condition. Humane endpoints, specialist care and interventions should reflect best practice and be discussed and agreed between researchers, veterinarians and animal care staff before commencement of the experiment. Development and publication of appropriate experimental analyses (e.g., pharmacodynamic determinations, functional imaging) to capture detailed phenotypic information assists rational determination of endpoints.

Tumour burden

Tumour burden should always be limited to the minimum required for a valid scientific outcome. For example, efficacy studies should be terminated once durable, statistically significant therapeutic effects can be shown. Therapeutic studies should be designed to avoid the need for control tumours to become excessively large. The size of any tumours should be limited when they are used simply for routine transplantation or as a source of tumour tissue. In all cases the general health and condition of an animal remains the overriding determinant. Adverse effects on the animal will depend on the biology, site, mode of growth of the tumour and any additional procedures or treatments. Despite the caveats, estimation of tumour size and burden is an important consideration in determining endpoints.

Assessment of the size of superficial tumours using callipers (usually of two diameters at right angles) is an easy and definable method. Measurement variations can be minimised by ensuring that the same well-trained technician is involved for the duration of the study. Response to therapy may be measured by changes in tumour growth rate, re-growth delay, cell survival (measured by clonogenic assay) or an appropriate surrogate marker. Excising and weighing tumours at the end of a study can provide an additional objective endpoint, which avoids errors due to variations in tumour shapes and estimations of volume or mass. For an animal carrying a single tumour, the mean diameter should not normally exceed 1.2 cm in mice or 2.5 cm in rats, or 1.5 and 2.8 cm, respectively, for therapeutic studies. Where two tumours per animal are grown, for example, in contralateral flanks, the size should be correspondingly less and should not exceed the maximum burden of a single tumour. Multiple tumours may develop in genetically modified animals (e.g., mammary tumours in polyoma virus middle T transgenic mice; Guy et al, 1992) or in the skin of animals subjected to UVR (El-Abaseri and Hansen, 2007) or chemical carcinogens (Johansen et al, 2009), for which similar limits should be observed. Exceptions to these advised size limits would require rigorous scientific justification.

Determining the tumour burden of internal orthotopic cancers, systemic lymphoreticular tumours or metastatic disease is challenging. Pilot experiments using small numbers of animals are important to allow characterisation of the kinetics and patterns of spread, to predict clinical signs and to define humane endpoints. Biomarkers or circulating cancer cells may be used as surrogates for assessing the burden of lymphomas and leukaemias, and real-time imaging is a valuable adjunct. Appropriate biochemical and pathological indicators or use of engineered reporter systems or imaging techniques should be used to determine the onset of disease. Reliance must also be placed on the general condition of the animal, together with assessment of palpable tumours and specific signs such as hind-limb weakness or paralysis.

Clinical signs

In general the clinical signs shown in Box 5 are principal indicators of rare but severe symptoms of potential adverse effects, which should be avoided. Where any one sign is present the animal should immediately be humanely culled and vigilance increased for the remainder of the cohort.

With solid tumours, scoring of ulceration, distension of covering tissues and cachexia (severe body weight loss) should be incorporated into the endpoints. Ulceration is a lesion typified by necrosis of superficial tissues, which may be dry, suppurating or exudative. Necrosis resulting in skin breakdown or exudation persisting beyond 48 h is grounds for termination. Some tumours, such as those grown in sensitive sites or that develop extensive necrosis, may be painful, although objective criteria are lacking for mice. Further research is required to enable better assessment of pain and to assist in formulating the most appropriate endpoints.

In all cases endpoints must provide for action to be taken to terminate animals humanely when the degree of suffering cannot be justified by the scientific objective, when the objective has been achieved or cannot be realised, or when the quality of the results has been compromised.

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Summary and concluding remarks

This set of guidelines is designed to update and enhance the second edition (Workman et al, 1998). Information is provided on the more complex, molecularly defined and biologically relevant models now available, including genetically engineered, orthotopic and metastatic tumour systems. These more ‘patient-like’ models require sophisticated methods of evaluation; hence a detailed section on the different imaging modalities that are now used has been added. Tables 1 and 2 provide examples of some widely used experimental models. Figure 1 offers an example of the type of illustrative aid that can be used to facilitate the rational choice of appropriate models in a given study. Examples of tumour models, experimental design and procedures are provided throughout. However, it is emphasised that these are intended to act as a guide only, and each study should be tailored to the specific experimental objectives. There is renewed emphasis on continuing applications of the 3Rs – replacement (of animals with alternative methods), reduction (in the numbers of animals used to achieve scientific objectives) and refinement (in experimental design, techniques and husbandry to minimise adverse effects and improve welfare). There is an expectation that the highest animal welfare standards will be demanded from grant-awarding bodies and scientific journals. It is also emphasised that there is a responsibility for researchers to publish improved models and methodology for the benefit of the research community worldwide. A comprehensive bibliography is included to cover all of the principal topics and links to other, online resources are also provided. It is to be stressed that animal welfare considerations are not only important for ethical and legal reasons, but also should be fully consistent with the highest standards of scientific investigation. It is anticipated that the appropriate use of animal models will make an important contribution to increasing further our fundamental understanding of cancer and will enhance our growing ability to diagnose, treat and prevent it.

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Notes

Additional information

Committee to Update Science, Medicine, and Animals, National Research Council (2004) Sciences, Medicine, and Animals: National Research Council of The National Academies. The National Academies Press: Washington, DC, USA

Dennis C (2006) Cancer: off by a whisker. Nature 17: 739–741

Garber K (2006) Realistic rodents? Debate grows over new mouse models of cancer. J Natl Cancer Inst 98:1176–1178

Guidelines for the Care and Use of Mammals in Neuroscience and Behavioural Research. Committee on Guidelines for the Use of Animals in Neuroscience and Behavioural Research, (Institute for Laboratory Animal Research, Washington, D.C. 2003). National Research Council

Flecknell P (2008) Analgesia from a veterinary perspective. Br J Anaesth 101: 121–124

Richardson CA, Flecknell PA (2005) Anaesthesia and post-operative analgesia following experimental surgery in laboratory rodents: are we making progress? Altern Lab Anim 33: 119–127

Roughan JV, Flecknell PA, Davies BR (2004) Behavioural assessment of the effects of tumour growth in rats and the influence of the analgesics carprofen and meloxicam. Lab Anim 38: 286–296

The Royal Society (2004) The Use of Non-human Animals in Research: a Guide for Scientists. Science Advice Section, The Royal Society: London, UK

Useful weblinks

http://scienceandresearch.homeoffice.gov.uk/animal-research/publications-and-reference/statistics/

http://www.sanger.ac.uk/genetics/CGP

http://emice.nci.nih.gov/mouse_models

http://dels.nas.edu/ilar_n/ilarhome/reports.shtml

http://ec.europa.eu/environment/chemicals/lab_animals/home_en.htm

http://www.iasp-pain.org/AM/Template.cfm?Section=Animal_Research

http://ec.europa.eu/european_group_ethics/docs/opinion7_en.pdf

http://conventions.coe.int/treaty/en/treaties/html/123.htm

http://www.ecopa.eu/

http://caat.jhsph.edu/

http://www.imm.ki.se/sft/pdf/OECD19.pdf

http://oacu.od.nih.gov/ARAC/index.htm

http://www.research.psu.edu/arp/health/endpoints.html

http://www.nc3rs.org.uk/news.asp?id=759

http://ddgs.utu.fi/request.php?4

http://www.lal.org.uk/index.php?option=com_content&view=article&id=56&Itemid

http://www.nc3rs.org.uk

GLOSSARY

Allometric scaling: Calculation of doses of drugs to be administered to animals according to their relative sizes where the relationship of a biological variable to body mass is non-linear. For example, drug dosage can be linearly related to body surface area rather than to body weight.

Ascites: Cells/fluid in the peritoneal cavity.

Autochthonous tumours: Tumours originating within the host animal, either spontaneously, or due to genetic or pharmacological intervention.

Cachexia: Severe loss of weight and muscle mass that cannot be reversed nutritionally. Can be caused by release of biologically active molecules (cytokines) from certain tumours.

Cassette dosing: Administration of multiple compounds to an individual animal followed by individual measurements in the same blood sample.

Clinically equivalent dose: A dose of a drug, which results in blood/tissue levels that reflect those that are achieved in patients.

Clonogenic assay: Measuring the effect of treatments on the ability of tumour cells to proliferate expansively. Treatment may be in vitro or initiated in vivo and the clonogenic ability of explanted cells testedin vitro.

Desquamation: Loss of skin integrity. Moist desquamation can be a consequence of exposure to ionising radiation (UV or X-rays) where the skin thins and then begins to weep tissue fluid as the epithelial cells lose their barrier function.

Distension: Stretched beyond normal dimensions.

Ectopic: Site of growth different from the tissue of origin, for example, s.c. transplantation of tumours derived from internal organs.

Erythema: Skin reddening and thickening in response to UV irradiation, as in mild sunburn.

Factorial design: Involves the inclusion of two or more variables and measuring the response to each variable and interactions between variables.

Genetically engineered mouse models (GEMMs): Animals in which the genetic material has been altered. For example, introduction of a mutation in cells of a particular organ may result in the development of benign or malignant tumours.

Hyperplasia: Refers to the proliferation of cells within an organ or tissue beyond that which is ordinarily seen. Microscopically cells resemble normal cells but are increased in numbers. It is a benign condition, unlike neoplasia, which is malignant.

Intravital microscopy: A technique, which allows direct observation of small blood vessels within the organs of anesthetised animals.

Maximum Tolerated Dose (MTD): The highest dose of a drug in which the clinical condition of the experimental animal is maintained.

Metastasis: The spread of tumour cells from a primary site to distant sites in the body, usually through the blood or lymph. The term ‘experimental metastasis’ is sometimes used to describe the colonisation of organs after injection of cells directly into the peripheral circulation.

Oncogenesis: The process of malignant transformation resulting in tumour development.

Orthotopic: Anatomically correct site (opposite of ectopic), for example, transplantation of renal tumour cells into the kidney or mammary carcinoma cells into the mammary fat pad.

Pharmacodynamics: The study of the action of and the duration of effects of agents in the body, including confirmation of mechanism of action through identification of relevant biomarkers of activity.

Pharmacokinetics: The study of the process by which agents are absorbed, distributed, metabolized and eliminated by the body, including measurement of the rate of excretion, metabolism, blood and tissue concentrations.

Syngeneic tumour models: Cells transplanted between animals of the same inbred strain.

Ulceration: An inflamed lesion on the skin or internal surface involving tissue destruction.

Xenogeneic tumour models: Cells transplanted between species (e.g., human to mouse). Requires recipients that cannot mount an immune response and reject the foreign tissue graft such as athymic mice which lack T-lymphocytes, or severe combined immunodeficient (SCID) mice.

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SDS-PAGE with Taq DNA Polymerase. SDS-PAGE is ...

SDS-PAGE with Taq DNA Polymerase. SDS-PAGE is an useful technique to separate proteins according to their electrophoretic mobility. (Photo credit: Wikipedia)

Proteomics and Biomarker Discovery

Reporter: Larry H. Bernstein, MD, FCAP

 

 

Advanced Proteomic Technologies for Cancer Biomarker Discovery

Sze Chuen Cesar Wong; Charles Ming Lok Chan; Brigette Buig Yue Ma; Money Yan Yee Lam; Gigi Ching Gee Choi; Thomas Chi Chuen Au; Andrew Sai Kit Chan; Anthony Tak Cheung Chan

Published: 06/10/2009

This report is extracted from the article above with editing and shortening as much as possible for the reader, and updated from LCGCNA Aug 12,  2012; 8
www.chromatographyonline.com

Part I

Abstract

This review will focus on four state-of-the-art proteomic technologies, namely 2D difference gel electrophoresis, MALDI imaging mass spectrometry, electron transfer dissociation mass spectrometry and reverse-phase protein array. The major advancements these techniques have brought about biomarker discovery will be presented in this review. The wide dynamic range of protein abundance, standardization of protocols and validation of cancer biomarkers, and a 5-year view of potential solutions to such problems is discussed.

English: Public domain image from cancer.gov h...

English: Public domain image from cancer.gov http://visualsonline.cancer.gov/details.cf?imageid=3483. TECAN Genesis 2000 robot preparing Ciphergen SELDI-TOF protein chips for proteomic  analysis. (Photo credit: Wikipedia)

Introduction

A common method used for isolating and identifying cancer biomarkers involves the use of serum or tissue protein identification. Unfortunately, currently used tumor markers have low sensitivities and specificities.[2] Therefore, the development of novel tumor markers might be helpful in improving cancer diagnosis, prognosis and treatment.

The rapid development of proteomic technologies during the past 10 years has brought about a massive increase in the discovery of novel cancer biomarkers. Such biomarkers may have broad applications, such as for the detection of the presence of a disease, monitoring of disease clearance and/or progression, monitoring of treatment response and demonstration of drug targeting of a particular pathway and/or target. In general, proteomic approaches begin with the collection of biological specimens representing two different physiological conditions, cancer patients and reference subjects. Proteins or peptides are extracted and separated, and the protein or peptide profiles are compared against each other in order to detect differentially expressed proteins. Commonly, quantitative proteomics is mainly performed by protein separation using either 2DE- or liquid chromatography (LC)-based methods coupled with protein identification using mass spectrometry (MS). Limitations include inability to obtain protein profiles directly from tissue sections for correlation with tissue morphology, limited ability to analyze post-translational modifications (PTMs) and low capacity for high-throughput validation of identified markers. Progress in proteomic technologies has led to the development of 2D DIGE, MALDI imaging MS (IMS), electron transfer dissociation (ETD) MS, and reverse-phase protein array (RPA).

2D Difference Gel Electrophoresis

The 2DE method has been one of the mainstream technologies used for proteomic investigations.[3,4] In this method, proteins are separated in the first dimension according to charge by isoelectric focusing, followed by separation in the second dimension according to molecular weight, using polyacrylamide gel electrophoresis. The gels are then stained to visualize separated protein spots,[5] separating up to 1000 protein spots in a single experiment and  protein spots are then excised and identified using mass spectrometry (MS).[6,7]

We previously used a 2DE approach to compare the proteomic profiles to identify differentially expressed proteins that may be involved in the development of nasopharyngeal cancer, [8]   as well as proteins that were responsive to treatment with the chemotherapeutic agent 5-fluorouracil (5FU) in the colorectal cancer SW480 cell line. Briefly, cell lysates from SW480 cells that were either treated with 5FU or were controls were separated using 2DE. After staining and analysis of the gels, differentially expressed protein spots were excised and identified using MS. The upregulation of heat-shock protein (Hsp)-27 and peroxiredoxin 6 and the downregulation of Hsp-70 were successfully validated by immunohistochemical (IHC) staining of SW480 cells.[9]

The 2D DIGE method improved the 2DE technique. Figure 1 shows how two different protein samples (e.g., control and disease) and, optionally, one reference sample (e.g., control and disease pooled together) are labeled with one of three spectrally different fluorophores: cyanine (Cy)2, 3 or 5. They have the same charge, similar molecular weight and distinct fluorescent properties, allowing their discrimination during fluorometric scanning.[10-12]  The minimal dye causes minimal change in the electrophoretic mobility pattern of the protein, whereas the saturation dye labels all available cysteine residues but causes a shift in electrophoretic mobility labeled proteins.[13]  The same pooled reference sample used for all gels within an experiment is an internal reference for normalization and spot matching.[12] The gel is scanned at three different wavelengths yielding images for each of the different samples, and variation between gels is minimized and difficulties are reduced in correctly matching of protein spots across different gels.[10,11]  Significant advantages of the DIGE technology includes a dynamic range of over four orders of magnitude and full compatibility with MS.  However, careful validations of identified markers using alternative techniques are still needed.

In a study that compared three commonly used DIGE analysis software packages, Kang et al. concluded that although the three softwares performed satisfactorily with minimal user intervention, significant improvements in the accuracy of analysis could be achieved .[14] Moreover, it was suggested that results concerning the magnitude of differential expression between protein spots after statistical analysis by such softwares must be examined with care.[14]

Figure 1.  Procedures for performing a 2D DIGE experiment. CY: Cyanine; DIGE: Differential in gel electrophoresis.

The choice of appropriate statistical methods for the analysis of DIGE data has to be considered. Statistical methodological error can be addressed by the use of statistical methods that apply a false-discovery rate (FDR) for the determination of significance. In this method, q-values are calculated for all protein spots. The q-value of each spot corresponds to the expected proportion of false-positives incurred by a change in expression level of that protein spot found to be significant.

Despite the ease of use and enabling the researcher to select an appropriate FDR according to study requirements, this approach was found to be only applicable to DIGE experiments using a two-dye labeling scheme, as a three-dye labeling approach violated the assumption of data independence required for statistical analysis.[16] Other statistical tests that have been applied for the analysis of DIGE results include significance analysis of microarrays,[7] principal components analysis[17,18] and partial least squares discriminant analysis.[18,19] Detailed discussions of the different statistical approaches applicable to proteomic research are beyond the scope of this review and readers may refer to[18,20] for further reading.

Using 2D DIGE, Yu et al. successfully identified biomarkers that were associated with pancreatic cancer.[21] In the study, 24 upregulated and 17 downregulated proteins were identified by MS. Among those proteins, upregulation of apolipoprotein E, α-1-antichymotrypsin and inter-α-trypsin inhibitor were confirmed by western blot analysis. Furthermore, the association of those three proteins with pancreatic cancer was successfully validated in another series of 20 serum samples from pancreatic cancer patients. Using a similar approach, Huang et al. identified and confirmed the upregulation of transferrin in the sera of patients with breast cancer.[22] When Sun et al. compared the proteomic profiles between malignant and adjacent benign tissue samples from patients with hepatocellular carcinoma, they proved 2D DIGE is not limited to serum or plasma samples.[23] In their study, overexpression of Hsp70/Hsp90-organizing protein and heterogenous nuclear ribonucleoproteins C1 and C2 were identified by 2D DIGE coupled with MS analysis, and the findings were successfully validated by both western blotting and IHC staining. Next, Kondo et al. applied 2D DIGE to laser-microdissected cells from fresh patient tissues.[13] Using this protocol, a 1-mm area of an 8-12-µm-thick tissue section was shown to be sufficient. These examples demonstrate the high sensitivity and broad applicability of 2D DIGE for proteomic investigations using various types of patient samples and provide evidence that 2D DIGE is a powerful technique for biomarker discovery.

MALDI Imaging Mass Spectrometry

A deeper understanding of the complex biochemical processes occurring within tumor cells and tissues requires a knowledge of the spatial and temporal expression of individual proteins. Currently, such information is mainly obtained by IHC staining for specific proteins in patient tissues.[8,24,25] Nevertheless, IHC has limited use in high-throughput proteomic biomarker discovery because only a few proteins can be immunostained simultaneously. MALDI IMS allows researchers to analyze proteomic expression profiles directly from patient tissue sections.[26-28] The protocol begins with mounting a tissue section onto a sample plate (Figure 2). MALDI matrix is then applied onto the tissue sample, which is analyzed by MALDI MS in order to obtain mass spectra from predefined locations across the entire patient tissue section. The mass spectrum from each location is a complete proteomic profile for that particular area. All acquired mass spectra from the entire tissue are then compiled to create a 2D map for that tissue sample. This map could then be compared with those from other tissue samples to identify changes in protein or peptide expression or comparisons of the maps from different areas within the same tissue section could be performed. This technology  importantly allows the high-throughput discovery of novel protein markers. In addition, correlations between protein expression and tissue histology can also be studied easily.

Most studies using MALDI IMS have been performed on frozen tissue sections ranging from 5 to 20 µm in thickness.[26,27,29] After sectioning, a MALDI matrix is applied either by automated spraying or spotting. The matrix of choice is usually α-cyano-4-hydroxy-cinnamic acid for peptides and sinapinic acid (3,5-dimethoxy-4-hydroxycinnamic acid) for proteins.

Figure 2.  Procedures for MALDI imaging. IMS: Imaging mass spectrometry; MS: Mass spectrometry.

Spotting allows the precise application of matrix to areas of interest and minimizes the diffusion of analyte material across the sample, although the imaging resolution achieved by spotting is lower (~150 µm). A laser beam is then fired towards the area of interest on the tissue section to generate protein ions for analysis by a mass analyzer.[29] Among the different mass analyzers, TOF analyzers are the most commonly used owing to their high sensitivity, broad mass range and suitability for detection of ions generated by MALDI. Use of other mass analyzers such as TOF-TOF, quadrupole TOF (QTOF), ion traps (ITs) and Fourier transform-ion cyclotron resonance (FT-ICR) have also been reported in other studies.[30-33]

After obtaining the mass spectra, statistical analysis needs to be performed to identify statistically significant features that could have potential use as biomarkers. But before such analyses can be applied, there has to be background-noise subtraction, spectral normalization and spectral alignment.[34,35,34] Statistical methods used to identify significant differences in peak intensity are symbolic discriminant analysis and principal component analysis. Symbolic discriminant analysis determines discriminatory features and builds functions based on such features for distinguishing samples according to their classification.[36,37] Using this approach, Lemaire et al. found a putative proteomic biomarker from ovarian cancer tissues by MALDI IMS that was later identified to be the Reg-α protein, a member of the proteasome activator 11S.[37] This result was later successfully validated by western blot (protein expression found in 88.8% carcinoma cases vs 18.7% benign disease) and IHC (protein expression found in 63.6% carcinoma tissues vs 16.6% benign tissues).[37] On the other hand, principal component analysis reduces data complexity by transforming data based on peak intensities to information based on data variance, termed ‘principal components’, resulting in a list of significant peaks (principal components) ordered by decreasing variance.[35,38,39] Neither symbolic discriminant analysis or principal component analysis is capable of performing unsupervised classification. This aim requires the use of other methods such as hierarchical clustering.[39,40] In this method identified peaks are clustered as nodes in a pair-wise manner according to similarity until a dendogram is obtained, providing information as to the degree of association of all peak masses in a hierarchical fashion. Peaks that are capable of differentiating between different histological/pathological features could then be chosen for further validation of their value as tumor markers.[39]

In MALDI IMS, protein identification cannot be performed with confidence solely on the molecular weight. However, Groseclose et al. have developed a method using in situ digestion of proteins directly on tissue section.[41] They first used MALDI IMS to obtain a map of the protein and peptide spectra, then spotted a consecutive section of the same tissue sample with trypsin for protein digestion, and then spotted matrix solution onto the digested spots and the resulting peptides are identified directly from the tissue by MS/MS. This modification increases the confidence in protein identification. The time required for MALDI IMS analysis per tissue section is as follows: tissue sectioning, mounting and matrix application: 4-8 h; MALDI image acquisition: 1-2 days; spectral analysis: 1-2 h.[33,39]

Recently, in situ enzymatic digestion has been successfully applied for improving the retrieval of peptides directly from formalin-fixed, paraffin-embedded FFPE tissue samples.[27] Such development has greatly facilitated the application of MALDI IMS in FFPE tissues.[26,42] In fact, Stauber et al. identified the downregulation of ubiquitin, transelongation factor 1, hexokinase and neurofilament M from FFPE brain tissues of rat models of Parkinson disease using this modified technique.[42] The success of performing proteomic profiling using MALDI IMS directly on FFPE tissues opens up great possibility for using archival patient materials in high-throughput biomarker discovery. Novel cancer biomarkers identified using MALDI IMS still require validation by other techniques such as IHC.

Electron Transfer Dissociation MS

Post-translational modifications play important roles in the structure and function of proteins such as protein folding, protein localization, regulation of protein activity and mediation of protein-protein interaction. Two common forms of PTM that have been implicated in cancer development are phosphorylation and glycosylation. Previously, phosphoproteomic studies have led to the identification of novel tyrosine kinase substrates in breast cancer,[43] discovery of novel therapeutic targets for brain cancer[44] and increased understanding of signaling pathways involved in lung cancer formation.[45,46] Conversely, the identification of abnormally glycosylated proteins, such as mucins, has provided novel biomarkers and therapeutic targets for ovarian cancer.[47]

The study of PTM begins with digesting the target protein using enzymes such as trypsin,   introducing the fragments into MS for determination of the sites and types of modification and, at the same time, identification of the protein. The analysis is conventionally carried out using collision-induced dissociation (CID) MS, where peptides are collided with a neutral gas for cleavage of peptide bonds to produce b- and y-type ions (Figure 3). A complete series of peptides differing in length by one amino acid is produced, leading to identification of the protein by peptide-sequence determination. However, for phosphopeptides, the presence of phosphate groups would compete with the peptide backbone as the preferred cleavage site. The end result is a reduced set of peptide fragments, which hinders protein identification, and the exact location of the phosphate group on the peptide cannot be determined accurately when there are more than one possible phosphorylation sites.[48,49]

Figure 3.  Peptide bond-cleavage site for a-, b-, c-, x-, y– and z-type ions.

Electron transfer dissociation is a recently developed dissociation technique for the analysis of peptides by MS, utilizing radiofrequency quadrupole ion traps such as 2D linear IT, spherical IT and Orbitrap™ (Thermo Fisher Scientific Inc., MA, USA) mass analyzers.[48,49] In this technology, peptides are fragmented by transfer of electrons from anions to induce cleavage of Cα-N bonds along the peptide backbone, hence producing c- and z-type ions (Figure 3). In contrast to CID, ETD preserves the localization of labile PTM and also provides peptide-sequence information.[48] But ETD fails to fragment peptide bonds adjacent to proline, which are readily cleaved by CID.[50] A study that compared the performance of CID with that of ETD found that only 12% of the identified peptides were commonly detected between the two techniques. A study reported that CID successfully identified more peptides with charge states of +2 and below, whereas ETD was found to be better at identifying peptide ions with charge states of greater than +2.[51] Therefore, it is suggested that CID and ETD should be used together to complement each other.[52]  Han et al. successfully differentiated the isobaric amino acids isoleucine and leucine from one another by performing CID on the resulting z-ions after ETD. The presence of isoleucine residue was then confirmed by the detection of a specific 29-Da loss from the peptide.[53]  A clear advantage of using ETD for the analysis of phosphopeptides is a near complete series of c- and z-ions without loss of phosphoric acid,[48] greatly facilitating the determination of the phosphorylation sites and the identification of phosphopeptides. Recently, an analysis of yeast phosphoproteome using ETD successfully identified 1252 phosphorylation sites on 629 proteins, whose expression levels ranged from less than 50 to 1,200,000 copies per cell.[54] In another study using ETD, a total of 1435 phosphorylation sites were identified from human embryonic kidney 293T cells, of which 1141 (80%) were previously unidentified. Finally, a study by Molina et al. successfully identified 80% of the known phosphorylation sites in more than 1000 yeast phosphopeptides in one single study using a combination of ETD and CID.[55] In addition, ETD could be applied to investigate other forms of PTM, such as N-linked glycosylations.[56,57] N-linked glycans contain a common core with branched structures. These can be processed by stepwise addition or removal of monosaccharide residues linked by glycosidic bonds, producing highly varied forms of N-linked glycan structures.[58-60] A weakness of analyzing glycopeptides using CID is that cleavage of glycosidic bonds occurs with little peptide backbone fragmentation, so that only the glycan structure is available.[61]  Hogan et al. used CID and ETD together to overcome this problem determining the glycan structure and glycosylation site.[61] ICID was initially used for cleavage of glycosidic bonds that allowed the entire glycan structure to be inferred from the CID spectrum alone. ETD was later performed to dissociate the same peptide that resulted in a contiguous series of fragment ions with no loss of glycan molecules, allowing the identification of both the site of glycosylation and the identity of the glycoprotein.[61] Readers are strongly encouraged to refer to[49] and.[62] In a comprehensive comparison of CID versus ETD for the identification of peptides without PTMs, CID was found to identify 50% more peptides than ETD (3518 by CID vs 2235 by ETD), but ETD provided somewhat better sequence coverage (67% for CID vs 82% for ETD). It turns out that ETD produced more uniformly fragmented ions with intensities that were five- to ten-times lower than those produced by CID.[55] Finally, the best sequence coverage of up to 92% was achieved when consecutive CID and ETD were performed.[55]

This increase in sequence coverage using the combined approach is needed for studies requiring de novo peptide identifications. As such, this strategy is particularly suited for studies involved in the discovery, identification and characterization of novel peptides or proteins and their PTMs for biomarker use. A prerequisite of this technique is that the biological samples under investigation must undergo some form of fractionation before they are amenable to analysis by ETD or CID. This is achieved by the use of LC techniques, such as reverse-phase, strong cation exchange or strong anion exchange chromatography, and serves to reduce the complexity and wide dynamic range of protein-expression levels commonly found in biological specimens. Given the important roles of PTM in the function and activity of proteins, this technology paves the way for exploring the intricate cellular activities within a cancer cell.

References

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Advanced Proteomic Technologies for Cancer Biomarker Discovery

Part II

Reverse-phase Protein Array

One of the goals of proteomics is to identify protein changes associated with the development of diseases such as cancer.  Even with the rapid development of proteomic technologies during the past few years, analysis of patient samples is still a challenge. Difficulties arise from the fact that[63,64]:

  • Proteomic patterns differ among cell types;
  • Protein expression changes occur over time;
  • Proteins have a broad dynamic range of expression levels spanning several orders of magnitude;
  • Proteins can be present in multiple forms, such as polymorphisms and splice variants;
  • Traditional proteomic methods require relatively large amounts of protein
  • Many proteomic technologies cannot be used to study protein-protein interactions.

The principle of RPA is simple and involves the spotting of patient samples in an array format onto a nitrocellulose support (Figure 4). Hundreds of patient specimens can be spotted onto an array, allowing a comparison of a large number of samples at once.[65] Each array is incubated with one particular antibody, and signal intensity proportional to the amount of analyte in the sample spot is generated.[66] Signal detection is commonly performed by fluorescence, chemiluminescence or colorimetric methods. The results are quantified by scanning and analyzed by softwares such as P-SCAN and ProteinScan, which can be downloaded from[84] for free.[67,68]

Figure 4.  Principle of reverse-phase protein array.

Main advantages of RPA technology include[69-71]:

  • Various types of biological samples can be used;
  • The possibility of investigating PTMs;
  • Protein-protein interactions can be studied;
  • Labeling of patient samples with fluorescent dyes (e.g., 2D DIGE) or mass tags (e.g., isotope-coded affinity tag [ICAT]) are not required;
  • Any samples spotted as a dilution allows quantifying in the linear range of detection;
  • Quantitative measurement of any protein is possible compared to reference standards of known amounts on the same array.

It has been shown that RPA is extremely sensitive as it is capable of detecting up to zeptomole (1 x 10-21 mole) levels of target proteins with less than 10% variance. The analysis of few cell signaling events is known.[65,70,71] The assay sensitivity depends on antibody affinity, which depends upon antigen-antibody pairs.[68] Of course, only known proteins with available antibodies can be identified. Therefore, this method is more suitable for biomarker screening or validation than discovery of novel proteins. To assist researchers in selecting suitable antibodies, two open antibody databases show their western blot results using cell lysates.[72,73,85,86]

One application of RPA is to investigate the signaling pathways in human cancers. Zha et al. compared the survival signaling events between Bcl 2-positive and -negative lymphomas and found that survival signals, independent of Bcl 2 expression, were detected in follicular lymphoma and confirmed by validation with IHC.[71] In another study, patient-specific signaling pathways have been identified in breast cancers using RPA. Bayesian clustering of a set of 54 subjects successfully separated normal subjects from cancer patients based on an epithelial signaling signature. Principal component analysis was capable of distinguishing normal from cancer patient samples by using a signature composed of a panel of kinase substrates.[69] Differences in cell signaling between patient-matched primary and metastatic lesions have also been found using RPA. In the study, six patient-matched primary ovarian tumors probed with antibodies against signaling proteins, and the signaling profiles differed significantly between primary and metastatic tumors and upregulation of phosphor c-kit was capable of distinguishing five of the six metastatic tumors from the primary lesions.[70] These findings suggest that treatment strategies may need to target signaling events among disseminated tumor cells.

Reverse-phase protein array has also been used to validate mathematical models of cellular pathways. The p53-Mdm2 feedback loop is one of the most well-studied cellular-feedback mechanisms.[74] Normally, p53 activates transcription and expression of Mdm2, which, in turn, suppresses p53 activity. This negative-feedback loop ensures the low-level expression of p53 under normal conditions. Mathematical models have previously been used to investigate this negative-feedback loop.[67] Ramalingam et al. has shown, by using RPA, that part of the mechanism of the p53-Mdm2 feedback loop can be explained by current mathematical models.[75]

Another important application of RPA is for the identification of cancer specific antigens.  Using this method serum from 14 lung cancer patients, colon cancer patients and normal subjects were incubated and eight fractions of the cell lysate were recognized by the sera from four patients, while none of the sera from normal individuals was positive.[76] This study demonstrates the diagnostic potential of identifying cancer antigens that induce immune response in cancer patients by using RPA.

Expert Commentary and Five-year View

The development of 2D DIGE in the past few years has provided researchers with a more accurate method for relative quantification of proteins substantially reducing the number of replicates required for 2D gels and increased its applicability for high-throughput biomarker discovery. MALDI MS has immensely facilitated the direct discovery of biomarkers from patient tissue. Even though archival patient tissue samples are a potential source of materials for tumor marker research, high-throughput techniques for biomarker discovery using such samples has been problematic. With the development of MALDI IMS, investigators can now perform studies that aim to discover novel biomarkers directly from tissue sections and are able to correlate their expression with the histopathological changes of tumors. Previously, investigation into the sites of protein PTM has been difficult since MS-dissociation techniques, such as CID, would lead to preferential loss of PTM, but the use of ETD as a complementary peptide ion-dissociation method has allowed researchers to investigate the precise location and structure of the PTM, and to identify peptide sequence with higher confidence.

The rapid technological improvements in proteomic technologies will identify potential biomarkers for clinical use. Independent validation studies using clinical specimens must be performed before such markers can be applied clinically,. In this regard, RPA has added a potential for high-throughput screening or validation of newly found markers. Using this technique, it will be possible for researchers to quantitatively measure and validate novel markers on hundreds of patient samples simultaneously.

A big problem for proteomic researchers iincludes the abundance of proteins in biological samples. This could be partially solved by depletion of abundant proteins or by fractionation of protein samples according to characteristics. It is envisaged that, in the future, proteomic technologies will be developed to a stage that is capable of analyzing complex protein mixtures without preparatory fractionation. Such progress has recently been achieved in LC-MS, where the use of a high-field, asymmetric waveform, ion-mobility spectrometry device as an interface to an IT MS resulted in a more than fivefold increase in dynamic range without increasing the length of the LC-MS analysis.[77]

Another area that needs improvement is the standardization of protocols for patient-sample collection because results were found to be inconsistent among various studies using MS.[78] It is also considered that part of the reason for this inconsistency is due to the differences in sample-collection or sample-handling procedures.[78,79] The Human Proteome Organization previously published its findings on pre-analytical factors that affect plasma proteomic patterns and provides suggestions for sample handling.[80,81] In addition to the pre-analytical stages, it is imperative to stress that consistent and strict adherence to predefined procedures or standards, from sample collection, sample processing, experimentation, data analysis through to result validation, are of utmost importance to minimize variations and achieve consistent and reproducible results.

Any newly identified potential biomarker must also be validated using an independent cohort of patients in order to establish its clinical value, but the translation of results from the laboratory to the clinic has been slow. Consequently, it has been suggested that quantitative MS could be used for the detection of proteins.[82] The increasing availability of MS facilities to researchers worldwide will facilitate the detection, measurement and validation of protein biomarkers using quantitative MS techniques. Even after validation of such results in the laboratory, diagnostic tests will need to be developed for the marker and large-scale clinical trials would also have to be performed to confirm the results.  All these efforts require cooperation of personnel from various disciplines, such as scientists, medical professionals, pharmaceutical companies and governments. Finally, it is hoped that, through improved understanding of the protein expression as cancer progresses will lead to the discovery and development of useful cancer biomarkers for patient diagnosis, prognosis, monitoring and treatment.

Key Issues

  • 2DE coupled with mass spectrometry has been the main workhorse for the proteomic discovery of novel biomarkers in the past 10 years, and the development of 2D difference gel electrophoresis has substantially improved the quantification accuracy of 2DE.
  • MALDI imaging mass spectrometry has allowed the identification of novel proteomic features directly from patient tissue section for correlation with histopathological changes.
  • Electron transfer dissociation mass spectrometry has opened up the possibility of identifying the structure and localization of the post-translational modification and the peptide/protein.
  • Reverse-phase protein array is a powerful tool for the high-throughput validation of novel biomarkers across hundreds of patient samples simultaneously.

References

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•• Excellent review on the clinical application of reverse-phase protein array.

65. Tibes R, Qiu Y, Lu Y et al. Reverse phase protein array: validation of a novel proteomic technology and utility for analysis of primary leukemia specimens and hematopoietic stem cells. Mol. Cancer Ther. 5(10),2512-2521 (2006).

66. LaBaer J, Ramachandran N. Protein microarrays as tools for functional proteomics. Curr. Opin. Chem. Biol. 9(1),14-19 (2005).

67. Ramalingam S, Honkanen P, Young L et al. Quantitative assessment of the p53-Mdm2 feedback loop using protein lysate microarrays. Cancer Res. 67(13),6247-6252 (2007).

68. Nishizuka S, Ramalingam S, Spurrier B et al. Quantitative protein network monitoring in response to DNA damage. J. Proteome Res. 7(2),803-808 (2008).

69. Petricoin EF 3rd, Bichsel VE, Calvert VS et al. Mapping molecular networks using proteomics: a vision for patient-tailored combination therapy. J. Clin. Oncol. 23(15),3614-3621 (2005).

70. Sheehan KM, Calvert VS, Kay EW et al. Use of reverse-phase protein microarrays and reference standard development for molecular network analysis of metastatic ovarian carcinoma. Mol. Cell Proteomics 4(4),346-355 (2005).

71. Zha H, Raffled M, Charboneau L et al. Similarities of prosurvival signals in Bcl 2-positive and Bcl 2-negative follicular lymphomas identified by reverse phase protein microarray. Lab. Invest. 84(2),235-244 (2004).

72. Major SM, Nishizuka S, Morita D et al. AbMiner: a bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies. BMC Bioinformatics 7,192 (2006).

73. Spurrier B, Washburn FL, Asin S, Ramalingam S, Nishizuka S. Antibody screening database for protein kinetic modeling. Proteomics 7(18),3259-3263 (2007).

74. Ciliberto A, Novak B, Tyson JJ. Steady states and oscillations in the p53/Mdm2 network. Cell Cycle 4(3),488-493 (2005).

75. Ma L, Wagner J, Rice JJ, Hu W, Levine AJ, Stolovitzky GA. A plausible model for the digital response of p53 to DNA damage. Proc. Natl Acad. Sci. USA 102(40),14266-14271 (2005).

76. Madoz-Gurpide J, Kuick R, Wang H, Misek DE, Hanash SM. Integral protein microarrays for the identification of lung cancer antigens in sera that induce a humoral immune response. Mol. Cell. Proteomics 7(2),268-281 (2007).

77. Canterbury JD, Yi X, Hoopmann MR, MacCoss MJ. Assessing the dynamic range and peak capacity of nanoflow LC-FAIMS-MS on an ion trap mass spectrometer for proteomics. Anal. Chem. 80(18),6888-6897 (2008).

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79. Omenn GS, States DJ, Adamski M et al. Overview of the HUPO plasma proteome project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics 5(13),3226-3245 (2005).

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• Concise report on several pre-analytical factors that impact the results of plasma proteomic profiling.

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Update from LC/GC North America.

Solutions for Separation Scientists. Aug 2012; 30(8).

30 years of LCGC

www.chromatographyonline.com

The key advances in separation science is covered in five areas of the discipline:

  1. sample preparation
  2. gas chromatography(GC) columns
  3. GC instrumentation
  4. liquid cheomatography (LC) columns
  5. LC instrumentation

In the first, there is automated sample preparation in kit form (QuEChERS). A short list of automated sample preparation techniques includes: supercritical fluid extraction (SFE), microwave extraction, automated solvent extraction (ASE), and solid phase extraction (SPE). A panel of experts views the bast basic method of extraction is SPE, and one uses solid phase microextraction with direct immersion and static headspace extraction, along with liquid-liquid extraction.[2] In GC incremental improvements have been made with ionic liquids, multidimentional GC, and fast GC. LC has advanced dramatically with ultra-high pressure LC and superficially porous particles. LC-MS has become standard equipment routinely used in many labs.[1]

Biomarkers have to be detected in a background of 104-106 other components of comparable concentration that also partition with the stationary phase. The partition coefficients of many species are similar, or identical to the biomarker target. The issue is how to select and resolve fewer than 100 biomarkers from a milieu of 1 million components in a complex mixture. The novel idea is to target structure instead of general properties of molecules.[3] How might this work?  A single substrate, metabolite, hormone, or toxin is identified in milliseconds by specific protein receptors. The combinatorial chemistry community has shown that synthetic polynucleotides (aptamers) can be found and amplified that have selectivities approaching antibodies.This is a method well know for years as affinity chromatography. A distinct problem has been the natural process of post translational modification (PTMs), which may create isoforms by addition of a single phosphate ester to be found in the proverbial soup.

1. Bush L. Separation Science: Past, Present and Future. LCGC NA 2012; 30(8):620.

2.McNally ME. Analysis of the State of the Art: Sample Preparation. LCGC NA 2012; 30(8):648-651.

2. Regnier FE. Plates vs Selectivity: An Emerging Issue with Complex Samples.  LCGC NA 2012; 30(8):622.

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