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Archive for the ‘Investment in Technological Breakthrough’ Category

Starting a Biotech the European Way

Author:  Stephen J. Williams, Ph.D.

A wonderful post by Tony Marcel in Nature Biotechnology highlights some of the structural differences in the way biotech startups are formed in Europe contrasted with bio-entrepreneurship as conducted in the United States.  Tony Marcel is currently the CEO of FGene S.A. and gives a personal experience  of the European biotech startup scene and highlights the differences, as he sees it, in the unique business development models occurring in Europe versus the US.  This post will highlight features from the article.

  • US model of biotech is not easily transferable to how Europe does business
  • US model involves developing a specific technology platform then selling that tool, service or platform to pharma for R&D $ and royalties
  • European perspective is to build networks instead of platforms which can deliver capabilities or one product to pharma
  • The article discusses three weaknesses identified in the biotech world with respect to Europe and the US

Three ” weaknesses” identified which may affect decision to start a biotech in Europe include:

  1. European academic scientists have trepidation making deals with big pharma
  2. European scientists are not as eager as US counterparts to start a biotech
  3. biotechs still are not as good as pharma in drug development so even their pipeline of “hits” are failing in clinical trials

The article aims to use these weaknesses to define a European way involving

  • defining management players and market niche early on
  • reducing the barriers to entry (i.e. legal)
  • establishing the relationships to increase viability

 

The full article can be found at the following link:

http://www.nature.com/bioent/2003/030101/full/nbt0299supp_9.html

 

An emerging European model for bioentrepreneurship

Tony Marcel

Tony Marcel is CEO of FGene S.A., 91, Avenue Kléber, 75116 Paris, France

e-mail:  tonymftmcgene@compuserve.com.

The US model for biotechnology is not easily exportable to Europe, but an alternative European business model may be adaptable everywhere.

There is a widespread opinion that biotechnology companies worldwide need to follow business models initiated in the US. These models, generally speaking, are based on development of a specific technology platform. The prevailing wisdom suggests this technology can be sold as a tool or service to pharmaceutical companies or can be used to develop a lead compound that can then be sold to big pharma for R&D dollars and single-digit downstream royalties.

But my experience as a former academic medical researcher who has helped discover, develop, and market drugs for Hoechst, Laboratoires Roussel, Roussel-Uclaf, Rhône-Poulenc Sante, and Amgen has taught me that there is an appealing alternative to this model that may be more practical from the European perspective. Rather than building technologies, one can build networks that have the capability of delivering to big pharma the one product they cannot refuse: validated lead compounds for unmet medical needs.

Identifying a market niche

My background has taught me that an effective way to find solutions is to look at weaknesses perceived by the status quo, and then to develop a strategy to turn them into strengths. Biotechnology’s biggest weakness was its lack of products, in traditional pharmaceutical terms. Relatively few lead compounds have made their way through clinical trials and onto the market. So to separate your company from the crowd, my first conclusion is that it needs to be product-based. It should develop lead compounds that can be sold to big pharma, or take those compounds through clinical trials and to the market.

How do you accomplish this in Europe? I identified three weaknesses from a traditional biotechnology or pharmaceutical perspective that I felt could be developed into strengths. The first was that European scientists are much more risk averse than their American counterparts when it comes to setting up their own business. The legal, financial, and cultural infrastructure to take such a step is far more developed in the US than elsewhere.

The second was that European academic scientists tended to be mistrustful of big pharma’s intentions in licensing discussions. Taking the fruits of their research and developing it into a business is an uncharted area for most, and their unfamiliarity with this process made them cautious.

Finally, biotechnology startups everywhere, not just in Europe, are usually not very efficient in conducting pharmaceutical development. In general, they are discovery-focused companies that lack both the expertise and the contacts in these areas to efficiently manage this process.

These three weaknesses provide the basis for my product-based business plan. The fact that European scientists are not as ready to start companies as in the US makes Europe a source of world-class research not already tied up commercially. In addition, my experience in the pharmaceutical world has demonstrated that a commitment to building a relationship based on trust with scientists and their university licensing departments tremendously enhances the quality of these exchanges and, over time, provides remarkable access to a pipeline of innovative lead compounds.

Finally, the pharmaceutical industry’s move to outsource much of the development and clinical trials process has created a remarkable infrastructure for moving lead compounds through development. One only needed to know when this was appropriate and to have the money to commit to that project to realize a major portion of the development process.

The business model that results from uniting these strengths is a company dedicated not to a specific technology platform, but rather to the development of innovative compounds discovered and patented by academia. The company’s niche is to license in molecules at an early stage and demonstrate proof of principle, and take them through regulatory preclinicals, as well as phase I/II clinicals. At that point, the company licenses its products to big pharma. Profit is generated by the substantial risk-to-reward ratio between the cost of licensing in molecules and the outlicensing price to big pharma.

Management

Contrary to the way many US biotechnology companies are run, the management structure of such a company is not a one-person show. This strategy relies heavily on a supervisory board made up of representatives from European ministries and major European banks. It is also dependent on a scientific advisory board (SAB) with members from key European states. Unlike the boards of some biotechnology companies, the individuals selected are not merely figureheads. They must be committed to an operational role in which they are regularly consulted about the company’s plans.

The key to making this work is to maintain permanent links with academia, the source of new molecules, through publications, meetings, and also through SAB members. One also needs to develop comparable relationships in the pharmaceutical industry in order to keep abreast of licensing-in needs. Using this dual approach, a company will be able to identify discoveries relevant to a major pharmaceutical market before they are published. The company can then select candidates for licensing based on demonstrations of their potentially useful activity, the proof of pilot synthesis and purification capability, and sufficient intellectual property protection.

Given the academic scientist’s aversion to starting a business, where will this network of managers come from? In Europe, the merger and acquisition fever that has hit both the pharmaceutical and banking industries has created a large pool of experienced professionals, acquainted with science, marketing, and business. Some of these individuals will be at a point in their lives where setting up companies is an exciting alternative career.

The challenge for this new generation of European bioentrepreneurs will be to develop their ability to create a new level of cross-talk between inventors and developers. Their core responsibility will be much in keeping with their training: Build and nurture a portfolio of molecules at various stages of development.

Barriers to entry

If this model is so straightforward, why do pharmaceutical companies not eliminate the biotechnology middleman and reap the rewards directly? One of the three premises of this model is that a small biotech company is more able to concentrate on an academic alliance than a large pharmaceutical company. Biotechnology’s close identification with academia through the training of both its management and staff gives it a cultural advantage in assuming this role.

Historically, the model in which big pharma establishes a direct relationship with academia has never proven successful. For example, SmithKline and French invested much of its Tagamet earnings into developing academic alliances to fill its pipelines. Nonetheless, investing a substantial amount of money in these relationships over a significant period of time did not prevent this group from having to merge with Beecham. Nearly every working pharmaceutical executive today has a similar war story.

The reason it has failed for the past 20 years, and is likely to continue to fail for the next 20, is that it concentrates efforts in the hands of the most powerful pharmaceutical companies and key research institutions. The resulting bureaucracy is so overwhelming it not only alienates the scientific innovators, but creates a stifling atmosphere in which decisions simply cannot be made.

But old habits die hard, and this model has long been a tradition in Europe—particularly in France. Therefore, it is likely, if for no other reason than to reap the potential financial returns of such a model, that pharmaceutical companies will continue to make this model work.

However, the important role that biotechnology can play in this process is being recognized by some individuals now in positions of responsibility in pharmaceutical companies, academic institutions, and government offices. These individuals are doing their best to support biotechnology’s role in the development of innovative new medicines.

Viability

If you have read this far, you are probably persuaded by the arguments, but may wonder, “If it is such a great business model, why hasn’t anyone done it before?” Well, they have. In 1995, FGene was founded in France as a company devoted to the development of biopharmaceutical products. The company was initiated by the willingness of the Paris-based Institut Pasteur, a major European academic institution, to license molecules to it. This relationship allowed the beginning of the process I have just described.

The resolve of the French government, key players in academia, the investment community, and the pharmaceutical industry to enhance the growth of biotechnology in France is an opportunity we have seized. We have tried to duplicate in Europe the remarkable links developed between biotechnology startups and academia in the US, and hope to create a viable business serving the needs of the world’s largest pharmaceutical companies that are literally in our backyard.

In three years of existence, FGene already boasts five products in its active development portfolio: a recombinant protein for the treatment of traumatic spinal section; a peptide for the prevention and therapy of cardiovascular and cerebrovascular ischemia, such as coronary diseases; a selective IL2 receptor agonist for the treatment of cancer; a peptide active on kidney and bone for the treatment of bone and mineral balance disorders, such as osteoporosis; and a peptide for improving male pattern sexual arousal.

We are encouraged that we have made this much progress in such a short time. While this model is still not proven in terms of financial success, it provides a much stronger foundation for growing a biotechnology company than most biotechnology business plans currently in use because costs are directly related to the development of marketable products.

Conclusions

For budding European bioentrepreneurs, this model recommends itself for three reasons: First, it uses unexploited resources that are difficult to access through traditional biotechnology or pharmaceutical models. Second, it is based on pharmaceutical customers’ high-priority needs. And third, it provides a company with a burn rate that is in direct proportion to the realization of a marketable product.

This model has first taken hold in France because of a unique set of circumstances, but its applicability seems uthe commitment of a network of individuals to build a new kind of biotechnology company.

My vision is that companies formed will reinvigorate the European pharmaceutical industry. In the end, everyone wins. Academic science has a new route to receive fair payment for their innovations, biotechnology companies show a rapid timeline to profitability, making investors happy, and pharmaceutical companies fill their pipelines with truly innovative medicines. But the real winner in the end will be the consumer—the rapid translation of genomic products will lead to medicines that improve healthcare at an affordable price, in a much shorter time frame than previously possible.

 

source: http://www.nature.com/bioent/2003/030101/full/nbt0299supp_9.html

More articles on BioEntrepreneurship in this Online Open Access Journal Include:

11:00AM – 10/1/2014: Scientific Collaborations @14th Global Partnering & Biotech Investment, Congress Center Basel – SACHS Associates, London

9:00AM 10/1/2014: Partnering I @14th Global Partnering & Biotech Investment, Congress Center Basel – SACHS Associates, London

BioTech Partnerships and the National Model in Israel

Four Startups After One Year: BioDesign Entrepreneurship Program @ Hebrew University-Hadassah Medical Center

Biotech Chinese and Israeli Strategic Collaboration: Pontifax and WuXi PharmaTech (Cayman) Inc. (NYSE: WX)

Top 10 Israeli medical advances to watch in 2014 @ ISRAEL21c

Israel’s Innovation System: A Triple Helix with Four Sub-helices

Helix Model of Innovation in Israel: The Global Scheme and its Local Application

i-CORE Participation In Israel: Hebrew University faculty leads and holds Scientific Management Positions in Five I-CORE Centers

Stem Cell Research — The Frontier is at the Technion in Israel

Next-generation Universal Cell Immunotherapy startup Adicet Bio, Menlo Park, CA is launched with $51M Funding by OrbiMed

Recent Breakthroughs in Cancer Research at the Technion-Israel Institute of Technology- 2015

BEYOND THE “MALE MODEL”: AN ALTERNATIVE FEMALE MODEL OF SCIENCE, TECHNOLOGY AND INNOVATION

Read Full Post »

 

AGTC (AGTC) , An adenoviral gene therapy startup, expands in Florida with help from $1 billion deal with Biogen

Reporter: Stephen J. Williams, Ph.D.

from Biospace News

AGTC Sets Up Shop in Florida, New Facility to House 75 Employees
February 17, 2016
By Alex Keown, BioSpace.com Breaking News Staff

GAINESVILLE, Fla. — Applied Genetic Technologies Corporation (AGTC), a biotechnology company researching adeno-associated virus (AAV)-based gene therapies for the treatment of rare diseases, is expanding into the rapidly growing north central Florida biotech corridor.

The company, which was founded on technology developed at the University of Florida, is opening a combined use corporate office and laboratory facility in Alachua, Fla. AGTC’s portion of the new multi-tenant facility is expected to accommodate up to about 75 people and consists of approximately 20,000 square feet including state-of-the-art lab and office space as well as space for future expansion, the company announced this morning.

“The new facility will help us to accelerate our research and development efforts for novel AAV-based gene therapies for rare diseases and house critical corporate functions including finance, quality assurance and project management, while providing ample space as we continue to bring new talent to our team,” Sue Washer, president and chief executive officer of AGTC said in a statement.

AGTC’s lead product candidates focus on X-linked retinoschisis, achromatopsia and X-linked retinitis pigmentosa, which are inherited orphan diseases of the eye, caused by mutations in single genes that significantly affect visual function and currently lack effective medical treatments. Retinoschisis is a condition in which an area of the retina has separated into two layers. The part of the retina that is affected by retinoschisis will have suboptimal vision, according to the University of Michigan’s Kellogg Eye Center. Achromatopsia is a condition of the eye that is characterized by an absence (partial or total) of color vision. People with the complete form of achromatopsia are unable to perceive any colors and can only see black, white and shades of gray.

AGTC is also pursuing pre-clinical development of treatments for wet AMD using the company’s experience in ophthalmology to expand into disease indications with larger markets.

In August, AGTC’s research was bolstered by a $1 billion deal withBiogen (BIIB) to support the company’s gene-based therapies. As part of the deal, Biogen holds a license to AGTC’s XLRS and XLRP programs and an additional three licenses, BioSpace (DHX) reported in August.

David Day, assistant vice president & director of the Office of Technology Licensing at the University of Florida, touted the growth of the biotech sector in north central Florida.

“AGTC’s progress in developing novel treatments for rare diseases without adequate therapeutic options is a particularly good model for the entire biotechnology sector,” Day said in a statement.

Read Full Post »

Fluidigm Microfluidic Technology: Contributions to Life Science Industry – the Biomark™ HD and C1™systems.

Reporter: Aviva Lev-Ari, PhD, RN

 

Technology

https://www.fluidigm.com/about/technology

Products

https://www.fluidigm.com/products

Applications

  • Ag-Genomics

A look at the latest agricultural biology DNA sampling applications and approaches

  • Single-Cell Analysis

Fluidigm supports six significant single-cell biology methods to help accomplish more

  • Sample Identification

Discover solutions to persistent issues with sample collection and biorepository work

https://www.fluidigm.com/applications

Company Profile

Fluidigm creates and manufactures innovative technologies and life-science tools designed to revolutionize biology through a relentless pursuit of scientific truth. Its core technologies are based on microfluidics and mass cytometry, and enable the exploration and analysis of individual cells, as well as the industrial application of genomics.

Most microfluidics experts in the 1990s worked with rigid substances like silicon, glass or plastic, but a young Stephen Quake, PhD, endeavored to create complex microplumbing from a novel rubber substrate. He and co-inventor Marc Unger built a microscopic valve to control the flow of fluids within microchannels—and a new approach to integrating biological liquid handling was born.

Meanwhile, Gajus Worthington, a college classmate of Quake’s, was acquiring the skills and experience necessary to build a successful company. Mentored in his early 20s by thought leaders such as Jim Collins, he set upon his personal mission to create an organization that would make lasting contributions to science and technology. In 1999 Worthington and Quake united the possibilities of Quake’s breakthrough with the desire to enable ever greater biological discoveries and co-founded Fluidigm. Today the company’s integrated fluidic circuits (IFCs) offer rapid, efficient, highly parallel and reproducible analysis of up to hundreds of genetic markers across thousands of DNA samples in just hours, rather than days or weeks, all the way down to the level of the individual cell.

The Fluidigm microfluidic technology supports genomics-based applications such as single-cell gene expression, high-throughput SNP genotyping, protein expression analysis, digital PCR, mutant detection and more. Additionally, two of the company’s instruments have proven to be workhorses within the life science industry: the Biomark™ HD and C1™systems.

Originally introduced in 2006 and updated in 2011, Biomark HD stands alone in the world of analytical instrumentation as a multiapplication platform without compromise, providing high quality results for every experimental approach. Since its debut in 2012, the C1 system has been revolutionizing single-cell research by enabling researchers to rapidly and reliably isolate, process and profile individual cells for genomic analysis.

C1 researchers study cell differentiation, measure individual cell responses to specific stimuli, verify critical disease biomarkers, validate RNAi knockdown and conduct candidate drug screens. Select BioSciences, an independent research company, said in its January 2011 report on Single Cell Analysis (SCA) that “Fluidigm is the leading microfluidics company for SCA…[and] Fluidigm is well-positioned to become a leader in SCA.”

By 2013 the company’s position in the single-cell movement was clear: Independent research firm DeciBio in its August report entitled Single Cell Genomics (SCG): Market Size, Segmentation, Growth, Competition and Trends identified Fluidigm as the “undisputed leader in single-cell genomics.”

In 2014 Fluidigm expanded into single-cell proteomics with its acquisition of technology leader DVS Sciences, the inventor of CyTOF®, a multi-parameter single-cell protein analysis system. The CyTOF 2 mass cytometer analyzes antibody and metal complexes using an innovative method of atomic mass spectrometry, and solidifies Fluidigm’s position at the leading edge of single-cell biology.

Today more than 400 people work for Fluidigm worldwide. The company works with more than 1,000 valued customers pioneering the field of single-cell biology or using applied genomics in industrial applications to improve and protect our food supplies, track samples in the world’s largest biobanks and in general provide faster, more accurate, lower cost workflows to help improve people’s lives.

Fluidigm is headquartered in South San Francisco, California, with sales and sales support operations from Beijing to Tokyo to Paris to San Francisco. Fluidigm conducts its Research and Development activities and manufactures its instruments, integrated fluidic circuits and reagents in its factories in South San Francisco, Singapore and Markham, Ontario.

1999

Founding of Fluidigm Corporation (originally Mycometrix) to commercialize IFC technology developed in the Caltech laboratory of biophysicist Stephen Quake, PhD.

2003

Launch of the TOPAZ® System for Protein Crystallization, including integrated fluidic circuits (IFCs) that assemble 768 crystallization conditions in parallel and instrumentation and software that automate the digital imaging and analysis of experiments.

2004

Development of intellectual property around a new class of IFCs referred to as Dynamic Array™ IFCs and of prototypes yielding as many as 9,216 parallel data points.

DVS Sciences, founded by Dmitry Bandura, Vladimir Baranov, Scott Tanner, and Olga Ornatsky, was spun out of MDS Sciex.

2005

Opening of a 15,000 square-foot IFC fabrication facility in Singapore

2006

Launch of the Biomark™ system for Genetic Analysis, a multi-application hardware/software platform based on Fluidigm Dynamic Array IFCs. Introduction of the Biomark™ system heralded a practical solution for ultra-sensitive detection by PCR.

Launch of the 12.765 Digital Array™ IFC to provide absolute counting of target molecules, often within samples as small as a single cell. The Digital Array™ IFC is the method of choice to achieve such quantification known as digital PCR, which had been too impractical for routine use until this product was available.

2007

Launch of high-throughput SNP genotyping on the Biomark system, enabling breakthroughs for the study of genetic variation within large populations.

Launch of the Fluidigm 48.48 Dynamic Array IFC that, for the first time in microfluidics, provided a matrixed chip architecture which enabled both a high density of experiments (2,304 per chip) and effective mixing of nano-volume scale fluids.

2008

Launch of the Fluidigm 96.96 Dynamic Array IFC which is capable of performing 9,216 simultaneous real-time PCR experiments in nanoliter quantities. This new generation IFC enabled life science researchers to achieve new levels of cost and logistical efficiency and flexibility, as well as comprehensive profiling from miniscule amounts of sample down to the scale of individual cells.

Launch of the Fluidigm EP1™ System for genetic analysis. This is Fluidigm’s most efficient system for high sample throughput SNP genotyping and end point digital PCR. It allows extremely low running costs and provides the easiest workflow for low to mid multiplex SNP genotyping.

Launch of the DVS Sciences CyTOF Single-cell Protein Analysis System technology which identifies proteins in individual cells by seeding them with antibodies that have metal labels. It uses an atomic mass spectrometer to measure the metal labels informing the researcher about the protein composition of the cell.

2009

Launch of the Fluidigm 48.770 Digital Array IFC, the highest density commercially available integrated fluidic circuit (IFC) to date. This IFC can test up to 48 individual samples at a time and automatically partition each of the samples into separate sets of 770 reaction chambers—delivering a total of 36,960 simultaneous digital PCR reactions.

Launch of the Fluidigm Access Array™ System specifically designed to support high-throughput re-sequencing, targeted enrichment, sample barcoding, and library preparation for sequencing using amplicon tagging.

2010

MIT’s Technology Review magazine selects Fluidigm Corporation as one of the top 50 most innovative companies in the world.

Launch of the reusable FR48.48 Dynamic Array IFC—the world’s first reusable bio-chip for the SNP genotyping market.

DVS Sciences Toronto manufacturing facility established.

2011

Launch of the Biomark™ HD Real-time PCR System, the company’s most advanced instrument for genomic analysis. The Biomark HD System provides the sensitivity and throughput needed to study gene expression down to the single-cell level—especially those who have limited amounts of sample or study rare populations of cells.

Fluidigm complete its initial public offering. Shares trade on The NASDAQ Global Market under the symbol “FLDM.”

Fluidigm Singapore factory achieves a manufacturing milestone, building and shipping more than 1 billion microscopic NanoFlex™ valves since its inception. Each NanoFlex valve is so small that it takes 10 of them to span the width of a human hair.

Launch of Fluidigm assays and primers optimized for the company’s integrated fluidic circuit technology. The products are marketed as Delta Gene™ Assays (gene expression), SNP Type™ Assays (SNP genotyping), and Access Array™ Target-specific Primers (target enrichment for next-generation sequencing).

Launch of the 192.24 Dynamic Array™ IFC, designed to genotype 192 samples against 24 SNP assays in a single run, providing 4,608 data points in just one hour.

2012

Launch of the C1™ Single-Cell Auto Prep System which revolutionizes single-cell research. The C1 enables researchers to rapidly and reliably isolate, process, and profile individual cells for genomic analysis. For the first time, single-cell researchers could extract, reverse transcribe, amplify, and ultimately detect and analyze cell activity using just one technology, reducing the variability caused by multi-platform technical errors.

Fluidigm China office opens.

The Broad Institute and Fluidigm launch the world’s first research center dedicated to accelerating the development of research methods and discoveries in mammalian single-cell genomics. The Single-Cell Genomics Initiative is a hub for collaboration among single-cell genomics researchers in many pioneering fields, including stem cells and cancer biology.

2013

Fluidigm and the Genome Institute of Singapore open the Singapore Single-Cell Research Centre opening the door for Asian biological discoveries. It is the first single-cell centre of excellence in Asia.

Launch of the DVS Sciences CyTOF 2 Single-Cell Protein Analysis System a multi-parameter single-cell protein analysis system which analyzes antibody/metal complexes using atomic mass spectrometry. The technology enables high-parameter single-cell protein analysis for applications in biological research.

2014

Fluidigm Completes Acquisition of DVS Sciences—Creating a Single-Cell Technology Powerhouse.

SOURCE

https://www.fluidigm.com/about/aboutfluidigm

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UPDATED on 3/28/2016

SAN FRANCISCO — What briefly appeared to be a potential bidding war for Affymetrix, a genetics analysis technology maker, fizzled out on Monday after the company chose to stick with a takeover bid from Thermo Fisher Scientific over a higher bid from a Chinese-backed suitor.

In a statement, Affymetrix reiterated its support for the $14-a-share offer from Thermo Fisher that it accepted in January.

http://www.nytimes.com/2016/03/29/business/dealbook/affymetrix-to-stick-with-thermo-fishers-takeover-proposal.html?&moduleDetail=section-news-3&action=click&contentCollection=DealBook&region=Footer&module=MoreInSection&version=WhatsNext&contentID=WhatsNext&pgtype=article 

UPDATED on 3/23/2016

Affymetrix Postpones Stockholder Meeting as Origin Ups Acquisition Offer; Board Backs Thermo Bid

UPDATED on 3/21/2016

Former Affymetrix Execs Offer to Buy Company in Alternative to Thermo Fisher Deal

NEW YORK (GenomeWeb) – Origin Technologies Corporation, founded by former Affymetrix executives for the purpose of purchasing the company, proposed today to acquire Affy for $16.10 per share in an all-cash transaction valued at approximately $1.5 billion.

The proposal comes about a week before Affy shareholders are scheduled to vote on a different deal, Thermo Fisher Scientific’s proposed acquisition of Affy for approximately $1.3 billion, which the boards of directors of both firms unanimously approved in January.

According to a letter sent by Origin to Affymetrix today, its proposal represents a 75 percent premium to Affymetrix’s unaffected closing share price of $9.21 on the last trading day prior to the announcement of Thermo Fisher’s proposed acquisition.

Fully financed by SummitView Capital, Origin said its all-cash offer represents a 15 percent premium for Affy stockholders relative to the proposed transaction with Thermo, under which stockholders would receive $14.00 per share in cash.

As part of the offer, Origin also pledged to fund payment of the $55 million termination fee that would be due to Thermo under the terms of Thermo and Affy’s January agreement.

Wei Zhou, president of the newly formed Origin, wrote in the letter to Affy today that Origin strongly believes that its offer is superior to Thermo’s based on several criteria.

First, it offers substantially higher value to Affy’s stockholders, he said. Additionally, Origin believes it is in a better position to help Affy achieve its potential as a standalone, global company focused on genomics and proteomics. The deal would also offer an opportunity to acquire new technologies in the complete human genome sequencing space, Zhou wrote.

If the Origin-Affy merger goes through, Origin would have a separate option of combining with another company founded by Zhou in 2009, Centrillion Technology Holdings Corporation.

SOURCE

https://www.genomeweb.com/business-news/former-affymetrix-execs-offer-buy-company-alternative-thermo-fisher-deal

 

Affymetrix: Sales $350 million, Acquisition Price $1.3 billion – Advantages: Cytogenetics, Genotyping and Gene Expression Analysis

Reporter: Aviva Lev-Ari, PhD, RN

Thermo Fisher Scientific Inc.

NYSE: TMOJan 12 1:13 PM EST
136.60Price increase1.72 (1.28%)

Thermo Fisher Scientific to acquire Affymetrix for $1.3 billion

WALTHAM, Mass. – Thermo Fisher Scientific Inc., announced Jan. 8 that it has agreed to acquire Affymetrix Inc. for $14.00 per share in cash, or roughly $1.3 billion. The transaction, approved by the boards of directors of both companies is pending shareholder approval and is expected to close in the second quarter this year.

Santa Clara, Calif.-based Affymetrix was founded in 1992 and is a pioneer in the field of

  • microarray technology, launching its
  • GeneChip line in 1994. Today, the company serves both the
  1. life sciences research and
  2. clinical markets

Over the past ten years, the company has broadened its portfolio of tools that enable both

  • multiplexed and
  • parallel analysis of
  • biological systems at the cell, protein and genetic level.

Notable acquisitions for Affymetrix have included genetic tools company ParAllele Bioscience (2005), genetic, protein and cellular analysis provider Panomics (2008), and eBioscience (2012), which included one of the world’s largest selections of

  • antibodies,
  • ELISAs, and
  • proteins

for life science research and diagnostics.

“The acquisition of Affymetrix will strengthen our leadership in biosciences and create new market opportunities for us in genetic analysis,” said Marc N. Casper, president and CEO of Thermo Fisher Scientific. “In biosciences, the company’s antibody portfolio will significantly expand our offering in the fast-growing flow cytometry market, and customers will have greater access to these products through our global scale and commercial reach. In genetic analysis, Affymetrix’s technologies are highly complementary and present new opportunities for us in targeted

  • clinical and
  • applied markets.”

According to Frank Whitney, president and CEO of Affymetrix, the acquisition will allow the company to continue to build upon the close relationships it has created with customers, while deepening its reach into the biopharma market. “We are excited about the opportunity to combine our portfolios and strengthen our position in high-growth markets such as

  • single-cell biology
  • reproductive health and
  • AgBio

According to information provided by Thermo Fisher, benefits of the acquisition include expanding its offerings of its antibody portfolio via the eBioscience line of products, which also includes

  • multiplex RNA,
  • protein assay
  • single-cell assays
  • genetic analysis capabilities via complementary products used in
  1. cytogenetics
  2. genotyping and
  3. gene expression.

Thermo expects Affymetrix will add $0.10 in adjusted earnings per share in the first full year of ownership, while creating $70 million in operational savings by year three. Affymetrix has annual revenues of approximately $350 million and will be integrated within Thermo Fisher’s Life Sciences Solutions business unit.

SOURCE

http://www.thejournalofprecisionmedicine.com/thermo-fisher-scientific-to-acquire-affymetrix-for-1-3-billion/

 

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

 

Gene Editing: The Role of Oligonucleotide Chips

Curator: Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2016/01/07/gene-editing-the-role-of-oligonucleotide-chips/

 

Articles on Immune-Oncology Molecules In Development @pharmaceuticalintelligence.com

Curators: Stephen J Williams, PhD and Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2016/01/11/articles-on-immune-oncology-molecules-in-development-pharmaceuticalintelligence-com/

 

 

Read Full Post »

Investment Trends in Series A and B by Major and by Micro US Venture Capital Firms

Reporters: Gerard Loiseau, ESQ and Aviva Lev-Ari, PhD, RN

 

Introduction by Gerard Loiseau, ESQ

The Future of Funding for Early-Stage Start-Ups in the Healthcare Businesses

 

 

  • Is Smart Money Pulling Back From Early-Stage Start-ups and if the answer is Yes, why ?
  1. In an article as of Monday, 02 February 2015 originally posted on GigaOM,
  • Bryan Dow, Executive Director at Mooreland Partners was talking about M&A and 3D Printing Collide.
  • As part of his expose, he talks about “the financing: filling the gaps” where he explains that “Strategic investors also currently consider 3D printing to be ‘non-investable’ due to the long lead time for business development. Size plays an important role, too. 3D printing companies just don’t have the revenue or EBITDA necessary to fit the threshold requirements.”
  • So how are Early-Stage Start-ups funding their development in the 3D Printing business ? Mainly Crowdfunding is the answer with companies like Kickstarter and Indiegogo.
  1. In an interview at McKinsey & Co., Eric Schadt, M.D., founding director of the Icahn Institute for Genomics and Multiscale Biology at New York’s Mount Sinai Health System, says questions will become easier to answer as more data is pulled together.
  • How big data will cause an evolution in medicine
  • November 24, 2015 | By Susan D. Hall
  • He says: “Technology is revolutionizing our understanding and treatment of disease”
  • Evolution? Revolution?
  • Big Data will help to build predictive models by aggregating more and more information from all the components of a disease.
  • It is evolution but will be very fast a revolution.
  • Big data are always used by Google, Amazon, (—), and the same processes can be applied to medicine. (The first subsidiary of Alphabet is Life Sciences Group@Google, now Verily)
  • About Wearables.
  • Mobile health apps utilization represents the future, and wearable-device allows anyone to manage one’s situation and/or to be managed in case of deviations from the “baseline”.
  • Big Data, patients, payers and pharma.
  • It introduces a partnership with the Patients, who will get a dashboard about their health situation.
  • Payers will be able to control the slide into a disease state and so to save money.
  • They will get better risk profiles.
  • Device makers can taka advantage of this new business model.
  • Pharma will be able to better understand the causal players of disease.
  • Talents
  • Experts have to be recruited according to this nearby new “ecosystem”
  • Translation will be a key item.
  • A major problem is the transformation of the life sciences, driven by this quantitative, statistical, computational model.
  • Mathematics and computer science will be essential.
  1. Gina Hall , Contributor, Silicon Valley Business Journal, says : Startup founders may have to work a little harder for funding as top venture capital firms pull out of early stage investing.
  • Gina Hall mentions a CB Insights report « The investment research firm said there were only 67 angel and Series A deals in the third quarter of 2015, the lowest quarterly count since the fourth quarter of 2010, which saw 64 deals”
  • Bill Maris, president and chief executive of Google Ventures and Andreessen Horowitz both said that they scaled down seed investments about two years ago.
  • They do consider that the number of candidates is increasing in huge proportions.
  1. Tess Townsend, Staff reporter, Inc.com@Tess_Townsend says : ‘Smart Money’ Is Getting Scarce for Startups
  • Investment in tech is rising, but less and less money is coming from top venture capital firms. What do they know that everyone else is just figuring out?
  • “Filling the place of smart money venture capitalists are investors with less experience in the market, such as mutual funds better known for public-market investing,” states The Information.  
  1. Digital Health : CB Insights October 5, 2015
  • “Four of the last 5 quarters have seen more than $200M in digital health financings involving the top 20 smart money VCs.”
  • Even if CB Insights comments on December 14 :
  • Data points on active corporates:
  • “The number of digital health investments in total was small, with pharma corps with only 28 deals involving pharma corps since 2013”
  1. Healthcare Start-ups Boom: 2015 Could See More Than $12B Invested Into VC-Backed Companies : CB Insights September 1/, 2015
  • There have been more than 400 healthcare deals in the first half of 2015, and the year is on track for a five-year high in funding.

 

 

Investment by Blue Chip VCs
Series A Series B Private Tech Global Financing First 9 month Stage A Funding # of Seres A Rounds
% % $ $Billion # of Transactions
2012 137.4
2013 7.5 11.4 165.2 2.0 243
2014 6.1 11.2 278.1 2.0 219
Est. 2015 5.3 9.0 241.7 1.3 115
SOURCE SignalFire, San Francisco
COMMENT: That growth is occurring in later-stage companies, series B and later; funding in the seed and series A rounds is down 20.5% and 28% in the first nine months compared with the same period last year, respectively.

DEFINITIONS by SignalFire:                                                   Series A: $4 million and $12 million

 

Investment Firm Type by Name 

14 “micro” VCs and 15 “major” VCs

Major VC Micro VC
General Catalyst Partners Harrison Metal
Khosla Ventures Lerer Hippeau Ventures
Kleiner Perkins Caufield & Byers O’Reilly AlphaTech Ventures
Lightspeed Venture Partners Y Combinator (Accelerator)
New Enterprise Associates (NEA) Forerunner Ventures
Redpoint Ventures Red Swan Ventures
Spark Capital LLC Lowercase Capital
Sequoia Capital Baseline Ventures
Greylock Partners Crosscut Ventures
Founders Fund Data Collective
Union Square Ventures First Round Capital
Andreessen Horowitz Founder Collective
Accel Partners Floodgate
Benchmark Felicis Ventures
Bessemer Venture Partners

SOURCE

https://www.theinformation.com/smart-money-pulls-backs-from-early-stage-startups?unlock=92821f&token=2053453a7297bdd5b8a501d6ea4fea0d4e1d2cbe

 

Conclusions by Gerard Loiseau, ESQ

  • Start-ups will have to adapt to these new challenges.
  • The biggest evolution is linked to Big Data and so to the New Entrants like Alphabet and Apple.
  • They are designing the future and the Cloud is their battlefield, following the pioneer, Amazon.com
  • People will wear the sensors allowing to identify variation in vital signs and indications of the state of their diseases. The transmission will be done through watches and other mobile devices in the Internet of Things (IoT) to the cloud and they will get a direct ping as their answer.
  • Labs and hospitals will be managed by their IT Data managed trough out the Cloud.
  • The New Entrants will create THEIR own “medical centres”  that will be Virtual.
  • They will provide the data, infrastructure, information and training to all the constituencies including Patient’s access to EMR.
  • Intelligent Medical Centre will operate the representation of completely reshaped existing workflows.
  • Start-ups will have to adapt to these new challenges by embracing the new reality.

The following article concerns trends seen in early round investment landscape in the United States, focusing on Seed Round and Series A and B Venture Capital and can be read at

Source: http://tomtunguz.com/us-it-fundraising-early-2016/?utm_content=bufferd960d&utm_medium=social&utm_source=linkedin.com&utm_campaign=buffer

by

What’s Really Happening In The US Venture Fundraising Market In Early 2016

The startup fundraising market in 2016 has been difficult to characterize. Punctuated by a concentrated decline in public tech stocks, the sentiment in Startupland has changed from resolute ebullience to a calmness approaching caution. Two months in, we can analyze January and February data. This posts analyses US headquartered information technology companies which VC-led investment rounds, except for the $793M Series C in Magic Leap, which I excluded as an outlier.

VCs invested about $2B in January and February 2016. The January figure equals the previous year, but February dollars deployed halved compared to 2015, reverting to 2014 levels.

The count of investments fell in January by 44% to roughly 130 and remained there in February.

For January investment round volumes to fall and for total dollars invested to remain the same, VCs must have invested in a disproportionate share of large, later stage rounds. As the year continued, round volumes held steady, but total dollars invested halved indicating the typical investment fell substantially. And the median investment chart above supports this hypothesis.

Let’s break this overall figure into Series A, B, C and Seed median investment sizes. Series As have fallen from their late 2015 highs by about 20%. The median Series B totals less than $15M, down 25% from the 2015 highs. Series Cs are stable at about $35M, and seed rounds continue their ascent with the typical Seed round at more than $2M.

The Seed round figure might be spurious. Without a fixed definition of a seed round, this number can move as the market includes a greater or lesser number of financings in this colloquial term.

We can segment the data by round size: rounds less than $2.5M, $15M, $50M, and greater 50+. Median seed rounds are then dominated by the +/- $150k initial investments of incubators and accelerators with large new portfolios like YCombinator and 500Startups whose demo days are fast approaching. The differing data points suggest to me small Series As and Seeds are being further conflated; for entrepreneurs it’s often better to characterize a $3M round as a seed, rather than a Series A.

No analysis is perfect. But this data does provide a lens into the state of the fundraising market. Series A and B sizes are down from their highs. Overall investment in February halved. But the data raises more questions.

What is really happening with seed round size? Was VC activity in February an aberration or representative of a deeper change in sentiment? In all likelihood, February was a bit of a wait-and-see month. Most importantly, the data supports the notion that investors are still looking to invest, and round sizes are relatively stable. with the exception of the B. The Series B will likely be the most challenging round to raise in the beginning of this year.

Read Full Post »

TSUNAMI in HealthCare under the New Name Verily.com, Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 1: Next Generation Sequencing (NGS)

TSUNAMI in HealthCare under the New Name Verily.com

Curator: Aviva Lev-Ari, PhD, RN

 

UPDATED on 6/8/2016

The Tricorder project was announced only 3 months after Google entered the life sciences field, according to the report, and came from the same incubator which rolled out the company’s self-driving car and recently cancelled Google Glass.

Verily CEO Andrew Conrad said the scientific basis for the device was proven upon unveiling in 2014, but experts have presented conflicting views on the reality of such a device, STAT Newsreports.

“What (Verily is) really good at is physical measurements — things like temperature, pulse rate, activity level. They are not particularly good at … the chemical and the biological stuff,” Walt toldSTAT news.

Four former Verily employees said the Tricorder “has been seen internally more as a way to generate buzz than as a viable project,” according to the report.

SOURCE

http://www.massdevice.com/googles-star-trek-tricorder-bid-flops/?spMailingID=9031578&spUserID=MTI2MTQxNTczMjM5S0&spJobID=940786327&spReportId=OTQwNzg2MzI3S0

 

UPDATED on 4/16/2016

SOURCE

http://recode.net/2016/04/13/verily-alphabet-profitable/

Verily, Alphabet’s medical business, is profitable, Sergey Brin tells Googlers

20160413-verily-google-life-sciences

Verily | YouTube

SCIENCE

Publicly, Alphabet has said very little about its assortment of companies not named Google.

But internally, Alphabet is a little more forthcoming.

As we reported earlier, Nest CEO Tony Fadell appeared before Google’s all-hands meeting two weeks ago to address recent criticism of his company. During that meeting, Google co-founder and Alphabet exec Sergey Brin also defended another company under the holding conglomerate: Verily, the medical tech unit previously called Google Life Sciences.

Lumped together, Alphabet’s moonshots aren’t making money yet — but Verily is, Brin said.

Verily was the target of a scathing article — in Stat, a medical publication from the Boston Globe — scrutinizing its CEO, Andy Conrad. Several former employees told Stat that Verily suffered a talent exodus due to “derisive and impulsive” leadership by Conrad.

Here’s what Brin said in response at Google’s TGIF meeting:

I have seen a smattering of articles. And, you know, it’s actually sad to see sometimes where it appeared that … former employees or soon-to-be former employees talked to the press. But, anyhow, I can tell you what’s going on with these companies, fortunately. So in Verily’s case, despite a handful of examples, their attrition rate is below Google’s and Alphabet’s as a whole. And also, there are articles that have generally said we are blowing a lot of money and so forth. It’s true that, you know, as whole our Other Bets are not yet profitable, but some of them are, including Verily on a cash basis and increasingly so. So we’re pretty excited about these efforts.

Verily makes money through

  • partnerships with pharmaceutical companies — such as Novartis, which is licensing and planning to sell Verily’s smart contact lens — and
  • medical institutions.

It is one of three units contributing to the Other Bets total revenue ($448 million) in 2015, along with

  • Google Fiber and
  • Nest.

As we reported earlier, Nest likely brought in around $340 million of that and Fiber pulled close to $100 million, meaning that Verily’s sales were somewhere around $10 million. During the year, all the moonshot units combined reported operating losses of $3.6 billion.

Note Brin’s stipulation that Verily’s profit comes on a “cash basis.” That probably means that it’s not making profit on the normal basis, meaning when you take into account total sales minus total costs. But “cash positive” suggests they’re booking sales faster than they’re spending money, which is a positive sign. Companies normally report financials accounting for all costs. And that’s how Alphabet will next week, when it shares first-quarter results for Google and the Other Bets — although we almost certainly won’t see figures on Verily’s profitability.

We reached out to Alphabet and Verily reps for more clarity, but didn’t get any.

SOURCE

http://recode.net/2016/04/13/verily-alphabet-profitable/

 

Original Curation dated 12/14/2015

  1. Part 1: Verily in Action
  2. Part II: Innovations at a Different Scale: GDE Enterprises – A Case in Point of Healthcare in Focus – Work-in-Progress

12/31/2015 – All time

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Part 1: Verily in Action

They write @ https://verily.com/

When Google[x] embarked on a project in 2012 to put computing inside a contact lens — an immensely challenging technical problem with an important application to health — we could not have imagined where it would lead us. As a life sciences team within Google[x], we were able to combine the best of our technology heritage with expertise from across many fields. Now, as an independent company, Verily is focused on using technology to better understand health, as well as prevent, detect, and manage disease.

Andy Conrad, Ph.D.

Chief Executive OfficerFormerly the chief scientific officer of LabCorp, Andy is a cell biologist with a doctorate from UCLA. He has always been passionate about early detection and prevention of disease: Andy co-founded the National Genetics Institute, which developed the first cost-effective test to screen for HIV in blood supply.

Brian Otis, Ph.D.

Chief Technical OfficerBrian’s team focuses on end-to-end innovation ranging from integrated circuits to biocompatible materials to sensors. He joined Google[x] as founder of the smart contact lens project and now leads our efforts across all hardware and device projects, including wearables, implanted devices, and technology like Liftware.

Jessica Mega, M.D., MPH

Chief Medical OfficerJessica leads the clinical strategy and research team at Verily. She is a board-certified cardiologist who trained and practiced at Massachusetts General Hospital and Brigham and Women’s Hospital. As a faculty member at Harvard Medical School and a senior investigator with the TIMI Study Group, Jessica directed large, international trials evaluating novel cardiovascular therapies.

Linus Upson

Head of EngineeringA long-time Google software engineer, Linus has been a team lead in developing products that now help billions of people worldwide find the information they need on the Internet, including Chrome and Chrome OS. He now oversees our engineering teams.

Tom Stanis

Head of SoftwareTom spent nine years working on core Google products before joining Google[x] in 2014 to work on the Baseline Study. He now leads all our Software projects, including the development of machine learning algorithms for applications ranging from robotic-assisted surgery to diabetes management.

Vikram (Vik) Bajaj, Ph.D.

Chief Scientific OfficerVik’s broad research interests in industry and as a former academic principal investigator have included structural and systems biology, molecular imaging, nanoscience, and bioinformatics. Vik now leads the Science team in research directions related to our mission.

What are the Dimensions of the Tsumani in Healthcare?

  • prevention,
  • detection,
  • management of disease

 

Hardware

  • contact lens with an embedded glucose sensor for measuring the glucose in human tears.

Software

  • multiple sclerosis, for example, combines wearable sensors with traditional clinical tests
  • signals that could lead to new knowledge about the disease and why it progresses differently among individuals.

Clinical

  • Constituencies industry, hospitals, government, academic centers, medical societies, and patient advocacy groups
  • The Baseline Study is one of these dedicated efforts, a multi-year initiative that aims to identify the traits of a healthy human by closely observing the transition to disease.

Science

  • Understand processes that lead to conditions like cancer, heart disease, and diabetes
  • computational systems biology platforms and life sciences tools
  • bio-molecular nanotechnology for precision diagnostics and therapeutic delivery
  • advanced imaging methods for applications ranging from early diagnosis to surgical robotics.

 

FOLLOW the LEADER of Parish in the Tsunami

 

Google[x] searches for ways to boost cancer immunotherapy | Science/AAAS | News

http://news.sciencemag.org/math/2015/01/googlex-searches-ways-boost-cancer-immunotherapy

 

Google Life Sciences and American Heart Association commit $50M to study heart disease | VentureBeat

http://venturebeat.com/2015/11/08/google-life-sciences-and-american-heart-association-commit-50m-to-study-heart-disease/

 

Google Life Sciences Division Is Now Called… Verily?

http://gizmodo.com/google-life-sciences-division-is-now-called-verily-1746729894

 

WIRED: Google’s Verily Is Spinning Off ‘Verb,’ a Secretive Robot-Surgery Startup

Alphabet’s Verily, née Google Life Sciences, has announced its first spinoff, a brand new robot-assisted surgery company.

http://www.wired.com/2015/12/googles-verily-is-spinning-off-verb-a-secretive-robot-surgery-startup/

 

Google Life Sciences Rebrands as Verily under Alphabet – Fortune

Vik Bajaj, CSO

http://fortune.com/2015/12/08/google-alphabet-verily/

Verily, I Swear, Google Life Sciences debuts a New Name

By CHARLES PILLER  DECEMBER 7, 2015

http://www.statnews.com/2015/12/07/verily-google-life-sciences-name/

 

Why biomedical superstars are signing on with Google Tech firm’s ambitious goals and abundant resources attract life scientists.

Erika Check Hayden 21 October 2015

http://www.nature.com/news/why-biomedical-superstars-are-signing-on-with-google-1.18600

 

GOOGLE LIFE SCIENCES MAKES DIABETES ITS FIRST BIG TARGET

http://www.wired.com/2015/08/google-life-sciences-makes-diabetes-first-big-target/

 

GOOGLE WON THE INTERNET. NOW IT WANTS TO CURE DISEASES

http://www.wired.com/2015/08/google-won-internet-now-wants-cure-diseases/

 

Google Reveals Health-Tracking Wristband

Caroline Chen and Brian Womack

June 23, 2015 — 9:30 AM EDT

http://www.bloomberg.com/news/articles/2015-06-23/google-developing-health-tracking-wristband-for-health-research

 

Google Moves to the Operating Room in Robotics Deal With J&J

ALISTAIR BARR and JOSEPH WALKER

http://blogs.wsj.com/digits/2015/03/27/google-moves-to-the-operating-room-in-robotics-deal-with-jj/

 

Google, Biogen Seek Reasons for Advance of Multiple Sclerosis

Caroline Chen

January 27, 2015 — 9:00 AM EST

http://www.bloomberg.com/news/articles/2015-01-27/google-biogen-seek-reasons-for-advance-of-multiple-sclerosis

 

Google’s Newest Search: Cancer Cells

Google X Team Hopes to Develop Nanoparticles to Provide Early Detection of Cancer, Other Diseases

ALISTAIR BARR and RON WINSLOW

Updated Oct. 29, 2014 11:17 a.m. ET

http://www.wsj.com/articles/google-designing-nanoparticles-to-patrol-human-body-for-disease-1414515602

 

A Spoon That Shakes To Counteract Hand Tremors

Updated May 14, 201411:43 AM ET

INA JAFFE

http://www.npr.org/sections/health-shots/2014/05/13/310399325/a-spoon-that-shakes-to-counteract-hand-tremors

 

Google’s New Moonshot Project: the Human Body

Baseline Study to Try to Create Picture From the Project’s Findings

ALISTAIR BARR

Updated July 27, 2014 7:24 p.m. ET

http://www.wsj.com/articles/google-to-collect-data-to-define-healthy-human-1406246214

 

Novartis Joins With Google to Develop Contact Lens That Monitors Blood Sugar

MARK SCOTT JULY 15, 2014

http://www.nytimes.com/2014/07/16/business/international/novartis-joins-with-google-to-develop-contact-lens-to-monitor-blood-sugar.html

 

Google[x] searches for ways to boost cancer immunotherapy

Jon Cohen

15 January 2015 6:25 am

http://news.sciencemag.org/math/2015/01/googlex-searches-ways-boost-cancer-immunotherapy

 

SOURCE

https://verily.com/

Part II: Innovations at a Different Scale: GDE Enterprises

A Case in Point of Healthcare in Focus –

Work-in-Progress

 

 

Read Full Post »

Kurzweill Reports in Medical Science I

Curator: Larry H. Bernstein, MD, FCAP

 

 

 

E-coli bacteria found in some China farms and patients cannot be killed with antiobiotic drug of last resort

“One of the most serious global threats to human health in the 21st century” — could spread around the world, requiring “urgent coordinated global action”
November 20, 2015

http://www.kurzweilai.net/e-coli-bacteria-found-in-some-china-farms-and-patients-cannot-be-killed-with-antiobiotic-drug-of-last-resort

Colistin antibiotic overused in farm animals in China apparently caused E-coli bacteria to become completely resistant to treatment; E-coli strain has already spread to Laos and Malaysia (credit: Yi-Yun Liu et al./Lancet Infect Dis)

Widespread E-coli bacteria that cannot be killed with the antiobiotic drug of last resort — colistin — have been found in samples taken from farm pigs, meat products, and a small number of patients in south China, including bacterial strains with epidemic potential, an international team of scientists revealed in a paper published Thursday Nov. 19 in the journal The Lancet Infectious Diseases.

The scientists in China, England, and the U.S. found a new gene, MCR-1, carried in E-coli bacteria strain SHP45. MCR-1 enables bacteria to be highly resistant to colistin and other polymyxins drugs.

“The emergence of the MCR-1 gene in China heralds a disturbing breach of the last group of antibiotics — polymixins — and an end to our last line of defense against infection,” said Professor Timothy Walsh, from the Cardiff University School of Medicine, who collaborated on this research with scientists from South China Agricultural University.

Walsh, an expert in antibiotic resistance, is best known for his discovery in 2011 of the NDM-1 disease-causing antibiotic-resistant superbug in New Delhi’s drinking water supply. “The rapid spread of similar antibiotic-resistant genes such as NDM-1 suggests that all antibiotics will soon be futile in the face of previously treatable gram-negative bacterial infections such as E.coli and salmonella,” he said.

Likely to spread worldwide; already found in Laos and Malaysia

The MCR-1 gene was found on plasmids — mobile DNA that can be easily copied and transferred between different bacteria, suggesting an alarming potential to spread and diversify between different bacterial populations.

Structure of plasmid pHNSHP45 carrying MCR-1 from Escherichia coli strain SHP45 (credit: Yi-Yun Liu et al./Lancet Infect Dis)

“We now have evidence to suggest that MCR-1-positive E.coli has spread beyond China, to Laos and Malaysia, which is deeply concerning,” said Walsh.  “The potential for MCR-1 to become a global issue will depend on the continued use of polymixin antibiotics, such as colistin, on animals, both in and outside China; the ability of MCR-1 to spread through human strains of E.coli; and the movement of people across China’s borders.”

“MCR-1 is likely to spread to the rest of the world at an alarming rate unless we take a globally coordinated approach to combat it. In the absence of new antibiotics against resistant gram-negative pathogens, the effect on human health posed by this new gene cannot be underestimated.”

“Of the top ten largest producers of colistin for veterinary use, one is Indian, one is Danish, and eight are Chinese,” The Lancet Infectious Diseases notes. “Asia (including China) makes up 73·1% of colistin production with 28·7% for export including to Europe.29 In 2015, the European Union and North America imported 480 tonnes and 700 tonnes, respectively, of colistin from China.”

Urgent need for coordinated global action

“Our findings highlight the urgent need for coordinated global action in the fight against extensively resistant and pan-resistant gram-negative bacteria,” the journal paper concludes.

“The implications of this finding are enormous,” an associated editorial comment to the The Lancet Infectious Diseases paper stated. “We must all reiterate these appeals and take them to the highest levels of government or face increasing numbers of patients for whom we will need to say, ‘Sorry, there is nothing I can do to cure your infection.’”

Margaret Chan, MD, Director-General of the World Health Organization, warned in 2011 that “the world is heading towards a post-antibiotic era, in which many common infections will no longer have a cure and, once again, kill unabated.”

“Although in its 2012 World Health Organization Advisory Group on Integrated Surveillance of Antimicrobial Resistance (AGISAR) report the WHO concluded that colistin should be listed under those antibiotics of critical importance, it is regrettable that in the 2014 Global Report on Surveillance, the WHO did not to list any colistin-resistant bacteria as part of their ‘selected bacteria of international concern,’” The Lancet Infectious Diseases paper says, reflecting WHO’s inaction in Ebola-stricken African countries, as noted last September by the international medical humanitarian organization Médecins Sans Frontières.

Funding for the E-coli bacteria study was provided by the Ministry of Science and Technology of China and National Natural Science Foundation of China.


Abstract of Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study

Until now, polymyxin resistance has involved chromosomal mutations but has never been reported via
horizontal gene transfer. During a routine surveillance project on antimicrobial resistance in commensal Escherichia coli from food animals in China, a major increase of colistin resistance was observed. When an E coli strain, SHP45, possessing colistin resistance that could be transferred to another strain, was isolated from a pig, we conducted further analysis of possible plasmid-mediated polymyxin resistance. Herein, we report the emergence of the first plasmid-mediated polymyxin resistance mechanism, MCR-1, in Enterobacteriaceae.

The mcr-1 gene in E coli strain SHP45 was identified by whole plasmid sequencing and subcloning. MCR-1 mechanistic studies were done with sequence comparisons, homology modelling, and electrospray ionisation mass spectrometry. The prevalence of mcr-1 was investigated in E coli and Klebsiella pneumoniae strains collected from five provinces between April, 2011, and November, 2014. The ability of MCR-1 to confer polymyxin resistance in vivo was examined in a murine thigh model.

Polymyxin resistance was shown to be singularly due to the plasmid-mediated mcr-1 gene. The plasmid carrying mcr-1 was mobilised to an E coli recipient at a frequency of 10−1 to 10−3 cells per recipient cell by conjugation, and maintained in K pneumoniae and Pseudomonas aeruginosa. In an in-vivo model, production of MCR-1 negated the efficacy of colistin. MCR-1 is a member of the phosphoethanolamine transferase enzyme family, with expression in E coli resulting in the addition of phosphoethanolamine to lipid A. We observed mcr-1 carriage in E coli isolates collected from 78 (15%) of 523 samples of raw meat and 166 (21%) of 804 animals during 2011–14, and 16 (1%) of 1322 samples from inpatients with infection.

The emergence of MCR-1 heralds the breach of the last group of antibiotics, polymyxins, by plasmid-mediated resistance. Although currently confined to China, MCR-1 is likely to emulate other global resistance mechanisms such as NDM-1. Our findings emphasise the urgent need for coordinated global action in the fight against pan-drug-resistant Gram-negative bacteria.

 

Researchers discover signaling molecule that helps neurons find their way in the developing brain

November 20, 2015

http://www.kurzweilai.net/researchers-discover-signaling-molecule-that-helps-neurons-find-their-way-in-the-developing-brain

This image shows a section of the spinal cord of a mouse embryo. Neurons appear green. Commissural axons (which connect the two sides of the brain) appear as long, u-shaped threads, and the bottom, yellow segment of the structure represents the midline (between brain hemispheres). (credit: Laboratory of Brain Development and Repair/ The Rockefeller University)

Rockefeller University researchers have discovered a molecule secreted by cells in the spinal cord that helps guide axons (neuron extensions) during a critical stage of central nervous system development in the embryo. The finding helps solve the mystery: how do the billions of neurons in the embryo nimbly reposition themselves within the brain and spinal cord, and connect branches to form neural circuits?

Working in mice, the researchers identified an axon guidance factor, NELL2, and explained how it makes commissural axons (which connect the two sides of the brain).

The findings could help scientists understand what goes wrong in a rare disease called horizontal gaze palsy with progressive scoliosis. People affected by the condition often suffer from abnormal spine curvature, and are unable to move their eyes horizontally from side to side. The study was published Thursday Nov. 19 in the journal Science.


Abstract of Operational redundancy in axon guidance through the multifunctional receptor Robo3 and its ligand NELL2

Axon pathfinding is orchestrated by numerous guidance cues, including Slits and their Robo receptors, but it remains unclear how information from multiple cues is integrated or filtered. Robo3, a Robo family member, allows commissural axons to reach and cross the spinal cord midline by antagonizing Robo1/2–mediated repulsion from midline-expressed Slits and potentiating deleted in colorectal cancer (DCC)–mediated midline attraction to Netrin-1, but without binding either Slits or Netrins. We identified a secreted Robo3 ligand, neural epidermal growth factor-like-like 2 (NELL2), which repels mouse commissural axons through Robo3 and helps steer them to the midline. These findings identify NELL2 as an axon guidance cue and establish Robo3 as a multifunctional regulator of pathfinding that simultaneously mediates NELL2 repulsion, inhibits Slit repulsion, and facilitates Netrin attraction to achieve a common guidance purpose.

A sensory illusion that makes yeast cells self-destruct

A possible tactic for cancer therapeutics
November 20, 2015

http://www.kurzweilai.net/a-sensory-illusion-that-makes-yeast-cells-self-destruct

 

Effects of osmotic changes on yeast cell growth. (A) Schematic of the flow chamber used to create osmotic level oscillations for different periods of time. (B) Cell growth for these periods. The graphs show the average number of progeny cells (blue) before and after applying stress for different periods (gray shows orginal “no stress” line). The inset shows representative images of cells for two periods. (credit: Amir Mitchell et al./Science)

UC San Francisco researchers have discovered that even brainless single-celled yeast have “sensory biases” that can be hacked by a carefully engineered illusion — a finding that could be used to develop new approaches to fighting diseases such as cancer.

In the new study, published online Thursday November 19 in Science Express, Wendell Lim, PhD, the study’s senior author*, and his team discovered that yeast cells falsely perceive a pattern of osmotic levels (by applying potassium chloride) that alternate in eight minute intervals as massive, continuously increasing stress. In response, the microbes over-respond and kill themselves. (In their natural environment, salt stress normally gradually increases.)

The results, Lim says, suggest a whole new way of looking at the perceptual abilities of simple cells and this power of illusion could even be used to develop new approaches to fighting cancer and other diseases.

“Our results may also be relevant for cellular signaling in disease, as mutations affecting cellular signaling are common in cancer, autoimmune disease, and diabetes,” the researchers conclude in the paper. “These mutations may rewire the native network, and thus could modify its activation and adaptation dynamics. Such network rewiring in disease may lead to changes that can be most clearly revealed by simulation with oscillatory inputs or other ‘non-natural’ patterns.

“The changes in network response behaviors could be exploited for diagnosis and functional profiling of disease cells, or potentially taken advantage of as an Achilles’ heel to selectively target cells bearing the diseased network.”

https://youtu.be/CuDjZrM8xtA
UC San Francisco (UCSF) | Sensory Illusion Causes Cells to Self-Destruct

* Chair of the Department of Cellular and Molecular Pharmacology at UCSF, director of the UCSF Center for Systems and Synthetic Biology, and a Howard Hughes Medical Institute (HHMI) investigator.

** Normally, sensor molecules in a yeast cell detect changes in salt concentration and instruct the cell to respond by producing a protective chemical. The researchers found that the cells were perfectly capable of adapting when they flipped the salt stress on and off every minute or every 32 minutes. But to their surprise, when they tried an eight-minute oscillation of precisely the same salt level the cells quickly stopped growing and began to die off.


Abstract of Oscillatory stress stimulation uncovers an Achilles’ heel of the yeast MAPK signaling network

Cells must interpret environmental information that often changes over time. We systematically monitored growth of yeast cells under various frequencies of oscillating osmotic stress. Growth was severely inhibited at a particular resonance frequency, at which cells show hyperactivated transcriptional stress responses. This behavior represents a sensory misperception—the cells incorrectly interpret oscillations as a staircase of ever-increasing osmolarity. The misperception results from the capacity of the osmolarity-sensing kinase network to retrigger with sequential osmotic stresses. Although this feature is critical for coping with natural challenges—like continually increasing osmolarity—it results in a tradeoff of fragility to non-natural oscillatory inputs that match the retriggering time. These findings demonstrate the value of non-natural dynamic perturbations in exposing hidden sensitivities of cellular regulatory networks.

Google Glass helps cardiologists complete difficult coronary artery blockage surgery

November 20, 2015

http://www.kurzweilai.net/google-glass-helps-cardiologists-in-challenging-coronary-artery-blockage-surgery

 

Google Glass allowed the surgeons to clearly visualize the distal coronary vessel and verify the direction of the guide wire advancement relative to the course of the occluded vessel segment. (credit: Maksymilian P. Opolski et al./Canadian Journal of Cardiology

Cardiologists from the Institute of Cardiology, Warsaw, Poland have used Google Glass in a challenging surgical procedure, successfully clearing a blockage in the right coronary artery of a 49-year-old male patient and restoring blood flow, reports the Canadian Journal of Cardiology.

Chronic total occlusion, a complete blockage of the coronary artery, sometimes referred to as the “final frontier in interventional cardiology,” represents a major challenge for catheter-based percutaneous coronary intervention (PCI), according to the cardiologists.

That’s because of the difficulty of recanalizing (forming new blood vessels through an obstruction) combined with poor visualization of the occluded coronary arteries.

Coronary computed tomography angiography (CTA) is increasingly used to provide physicians with guidance when performing PCI for this procedure. The 3-D CTA data can be projected on monitors, but this technique is expensive and technically difficult, the cardiologists say.

So a team of physicists from the Interdisciplinary Centre for Mathematical and Computational Modelling of theUniversity of Warsaw developed a way to use Google Glass to clearly visualize the distal coronary vessel and verify the direction of the guide-wire advancement relative to the course of the blocked vessel segment.

Three-dimensional reconstructions displayed on Google Glass revealed the exact trajectory of the distal right coronary artery (credit: Maksymilian P. Opolski et al./Canadian Journal of Cardiology)

The procedure was completed successfully, including implantation of two drug-eluting stents.

“This case demonstrates the novel application of wearable devices for display of CTA data sets in the catheterization laboratory that can be used for better planning and guidance of interventional procedures, and provides proof of concept that wearable devices can improve operator comfort and procedure efficiency in interventional cardiology,” said lead investigatorMaksymilian P. Opolski, MD, PhD, of the Department of Interventional Cardiology and Angiology at the Institute of Cardiology, Warsaw, Poland.

“We believe wearable computers have a great potential to optimize percutaneous revascularization, and thus favorably affect interventional cardiologists in their daily clinical activities,” he said. He also advised that “wearable devices might be potentially equipped with filter lenses that provide protection against X-radiation.


Abstract of First-in-Man Computed Tomography-Guided Percutaneous Revascularization of Coronary Chronic Total Occlusion Using a Wearable Computer: Proof of Concept

We report a case of successful computed tomography-guided percutaneous revascularization of a chronically occluded right coronary artery using a wearable, hands-free computer with a head-mounted display worn by interventional cardiologists in the catheterization laboratory. The projection of 3-dimensional computed tomographic reconstructions onto the screen of virtual reality glass allowed the operators to clearly visualize the distal coronary vessel, and verify the direction of the guide wire advancement relative to the course of the occluded vessel segment. This case provides proof of concept that wearable computers can improve operator comfort and procedure efficiency in interventional cardiology.

Modulating brain’s stress circuity might prevent Alzheimer’s disease

Drug significantly prevented onset of cognitive and cellular effects in mice
November 17, 2015

http://www.kurzweilai.net/modulating-brains-stress-circuity-might-prevent-alzheimers-disease

 

Effect of drug treatment on AD mice in control group (left) or drug (right) on Ab plaque load. (credit: Cheng Zhang et al./Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association)

In a novel animal study design that mimicked human clinical trials, researchers at University of California, San Diego School of Medicine report that long-term treatment using a small-molecule drug that reduces activity of  the brain’s stress circuitry significantly reduces Alzheimer’s disease (AD) neuropathology and prevents onset of cognitive impairment in a mouse model of the neurodegenerative condition.

The findings are described in the current online issue of the journal Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association.

Previous research has shown a link between the brain’s stress signaling pathways and AD. Specifically, the release of a stress-coping hormone called corticotropin-releasing factor (CRF), which is widely found in the brain and acts as a neurotransmitter/neuromodulator, is dysregulated in AD and is associated with impaired cognition and with detrimental changes in tau protein and increased production of amyloid-beta protein fragments that clump together and trigger the neurodegeneration characteristic of AD.

“Our work and that of our colleagues on stress and CRF have been mechanistically implicated in Alzheimer’s disease, but agents that impact CRF signaling have not been carefully tested for therapeutic efficacy or long-term safety in animal models,” said the study’s principal investigator and corresponding author Robert Rissman, PhD, assistant professor in the Department of Neurosciences and Biomarker Core Director for the Alzheimer’s Disease Cooperative Study (ADCS).

The researchers determined that modulating the mouse brain’s stress circuitry mitigated generation and accumulation of amyloid plaques widely attributed with causing neuronal damage and death. As a consequence, behavioral indicators of AD were prevented and cellular damage was reduced.  The mice began treatment at 30-days-old — before any pathological or cognitive signs of AD were present — and continued until six months of age.

One particular challenge, Rissman noted, is limiting exposure of the drug to the brain so that it does not impact the body’s ability to respond to stress. “This can be accomplished because one advantage of these types of small molecule drugs is that they readily cross the blood-brain barrier and actually prefer to act in the brain,” Rissman said.

“Rissman’s prior work demonstrated that CRF and its receptors are integrally involved in changes in another AD hallmark, tau phosphorylation,” said William Mobley, MD, PhD, chair of the Department of Neurosciences and interim co-director of the Alzheimer’s Disease Cooperative Study at UC San Diego. “This new study extends those original mechanistic findings to the amyloid pathway and preservation of cellular and synaptic connections.  Work like this is an excellent example of UC San Diego’s bench-to-bedside legacy, whereby we can quickly move our basic science findings into the clinic for testing,” said Mobley.

Rissman said R121919 was well-tolerated by AD mice (no significant adverse effects) and deemed safe, suggesting CRF-antagonism is a viable, disease-modifying therapy for AD. Drugs like R121919 were originally designed to treat generalized anxiety disorder, irritable bowel syndrome and other diseases, but failed to be effective in treating those disorders.

Rissman noted that repurposing R121919 for human use was likely not possible at this point. He and colleagues are collaborating with the Sanford Burnham Prebys Medical Discovery Institute to design new assays to discover the next generation of CRF receptor-1 antagonists for testing in early phase human safety trials.

“More work remains to be done, but this is the kind of basic research that is fundamental to ultimately finding a way to cure — or even prevent —Alzheimer’s disease,” said David Brenner, MD, vice chancellor, UC San Diego Health Sciences and dean of UC San Diego School of Medicine. “These findings by Dr. Rissman and his colleagues at UC San Diego and at collaborating institutions on the Mesa suggest we are on the cusp of creating truly effective therapies.”


Abstract of Corticotropin-releasing factor receptor-1 antagonism mitigates beta amyloid pathology and cognitive and synaptic deficits in a mouse model of Alzheimer’s disease

Introduction: Stress and corticotropin-releasing factor (CRF) have been implicated as mechanistically involved in Alzheimer’s disease (AD), but agents that impact CRF signaling have not been carefully tested for therapeutic efficacy or long-term safety in animal models.

Methods: To test whether antagonism of the type-1 corticotropin-releasing factor receptor (CRFR1) could be used as a disease-modifying treatment for AD, we used a preclinical prevention paradigm and treated 30-day-old AD transgenic mice with the small-molecule, CRFR1-selective antagonist, R121919, for 5 months, and examined AD pathologic and behavioral end points.

Results: R121919 significantly prevented the onset of cognitive impairment in female mice and reduced cellular and synaptic deficits and beta amyloid and C-terminal fragment-β levels in both genders. We observed no tolerability or toxicity issues in mice treated with R121919.

Discussion: CRFR1 antagonism presents a viable disease-modifying therapy for AD, recommending its advancement to early-phase human safety trials.

Allen Institute researchers decode patterns that make our brains human
Conserved gene patterning across human brains provide insights into health and disease
November 17, 2015

http://www.kurzweilai.net/allen-institute-researchers-decode-patterns-that-make-our-brains-human

 

Percentage of known neuron-, astrocyte- and oligodendrocyte-enriched genes in 32 modules, ordered by proportion of neuron-enriched gene membership. (credit: Michael Hawrylycz et al./Nature Neuroscience)

Allen Institute researchers have identified a surprisingly small set of just 32 gene-expression patterns for all 20,000 genes across 132 functionally distinct human brain regions, and these patterns appear to be common to all individuals.

In research published this month in Nature Neuroscience, the researchers used data for six brains from the publicly available Allen Human Brain Atlas. They believe the study is important because it could provide a baseline from which deviations in individuals may be measured and associated with diseases, and could also provide key insights into the core of the genetic code that makes our brains distinctly human.

While many of these patterns were similar in human and mouse, many genes showed different patterns in human. Surprisingly, genes associated with neurons were most conserved (consistent) across species, while those for the supporting glial cells showed larger differences. The most highly stable genes (the genes that were most consistent across all brains) include those associated with diseases and disorders like autism and Alzheimer’s, and these genes include many existing drug targets.

These patterns provide insights into what makes the human brain distinct and raise new opportunities to target therapeutics for treating disease.

The researchers also found that the pattern of gene expression in cerebral cortex is correlated with “functional connectivity” as revealed by neuroimaging data from the Human Connectome Project.

“The human brain is phenomenally complex, so it is quite surprising that a small number of patterns can explain most of the gene variability across the brain,” says Christof Koch, Ph.D., President and Chief Scientific Officer at the Allen Institute for Brain Science. “There could easily have been thousands of patterns, or none at all. This gives us an exciting way to look further at the functional activity that underlies the uniquely human brain.”


Abstract of Canonical genetic signatures of the adult human brain

The structure and function of the human brain are highly stereotyped, implying a conserved molecular program responsible for its development, cellular structure and function. We applied a correlation-based metric called differential stability to assess reproducibility of gene expression patterning across 132 structures in six individual brains, revealing mesoscale genetic organization. The genes with the highest differential stability are highly biologically relevant, with enrichment for brain-related annotations, disease associations, drug targets and literature citations. Using genes with high differential stability, we identified 32 anatomically diverse and reproducible gene expression signatures, which represent distinct cell types, intracellular components and/or associations with neurodevelopmental and neurodegenerative disorders. Genes in neuron-associated compared to non-neuronal networks showed higher preservation between human and mouse; however, many diversely patterned genes displayed marked shifts in regulation between species. Finally, highly consistent transcriptional architecture in neocortex is correlated with resting state functional connectivity, suggesting a link between conserved gene expression and functionally relevant circuitry.

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Muscular dystrophy has deficient stem cell dystrophin

Larry H. Bernstein, MD, FCAP, Curator

LPBI

Article ID #198: Muscular dystrophy has deficient stem cell dystrophin. Published on 11/21/2015

WordCloud Image Produced by Adam Tubman

Dystrophin Deficient Stem Cell Pathology

Muscular Dystrophy is a Stem Cell-Based Disease

Because DMD results from mutations in the dystrophin gene, the vast majority of muscular dystrophy research was based on a simple model in which the Dystrophin protein played a structural role in the structural integrity of muscle fibers. Abnormal versions of the Dystrophin protein caused the muscle fibers to become damaged and die as a result of contraction.  Dystrophin anchors the cytoskeleton of the muscle fibers, which are essential for muscle contraction, to the muscle cell membrane, and then to the extracellular matrix outside the cell that serves as a foundation upon which the muscle cells are built.

gb-2001-2-4-reviews3006-3

However in this current study, Rudnicki and his team discovered that muscle stem cells also express the dystrophin protein. This is a revelation because Dystrophin was thought to be protein that ONLY appeared in mature muscle. However, in this study, it became exceedingly clear that in the absence of Dystrophin, muscle stem cells generated ten-fold fewer muscle precursor cells, and, consequently, far fewer functional muscle fibers. Dystrophin is also a component of a signal transduction pathway that allows muscle stem cells to properly ascertain if they need to replace dead or dying muscle.  Muscle stem cells repair the muscle in response to injury or exercise by dividing to generate precursor cells that differentiate into muscle fibers.

Even though Rudnicki used mice as a model system in these experiments, the Dystrophin protein is highly conserved in most vertebrate animals. Therefore, it is highly likely that these results will also apply to human muscle stem cells.

Gene therapy experiments and trials are in progress and even show some promise, but Rudnicki’s work tells us that gene therapy approaches must target muscle stem cells as well as muscle fibers if they are to work properly.

“We’re already looking at approaches to correct this problem in muscle stem cells,” said Dr. Rudnicki.

This paper has received high praise from the likes of Ronald Worton, who was one of the co-discovers of the dystrophin gene with Louis Kunkel in 1987.

Early pathogenesis of Duchenne muscular dystrophy modelled in patient-derived human induced pluripotent stem cells

Emi Shoji, Hidetoshi Sakurai, Tokiko Nishino, Tatsutoshi Nakahata, Toshio Heike, Tomonari Awaya, Nobuharu Fujii, Yasuko Manabe, Masafumi Matsuo & Atsuko Sehara-Fujisawa

Scientific Reports 5, Article number: 12831 (2015)   http://dx.doi.org:/10.1038/srep12831

Duchenne muscular dystrophy (DMD) is a progressive and fatal muscle degenerating disease caused by a dystrophin deficiency. Effective suppression of the primary pathology observed in DMD is critical for treatment. Patient-derived human induced pluripotent stem cells (hiPSCs) are a promising tool for drug discovery. Here, we report an in vitro evaluation system for a DMD therapy using hiPSCs that recapitulate the primary pathology and can be used for DMD drug screening. Skeletal myotubes generated from hiPSCs are intact, which allows them to be used to model the initial pathology of DMD in vitro. Induced control and DMD myotubes were morphologically and physiologically comparable. However, electric stimulation of these myotubes for in vitro contraction caused pronounced calcium ion (Ca2+) influx only in DMD myocytes. Restoration of dystrophin by the exon-skipping technique suppressed this Ca2+ overflow and reduced the secretion of creatine kinase (CK) in DMD myotubes. These results suggest that the early pathogenesis of DMD can be effectively modelled in skeletal myotubes induced from patient-derived iPSCs, thereby enabling the development and evaluation of novel drugs.

Duchenne muscular dystrophy (DMD) is characterised by progressive muscle atrophy and weakness that eventually leads to ambulatory and respiratory deficiency from early childhood1. It is an X-linked recessive inherited disease with a relatively high frequency of 1 in 3500 males1,2.DMD, which is responsible for DMD, encodes 79 exons and produces dystrophin, which is one of the largest known cytoskeletal structural proteins3. Most DMD patients have various types of deletions or mutations in DMD that create premature terminations, resulting in a loss of protein expression4. Several promising approaches could be used to treat this devastating disease, such as mutation-specific drug exon-skipping5,6, cell therapy7, and gene therapy1,2.

Myoblasts from patients are the most common cell sources for assessing the disease phenotypes of DMD11,12. …Previous reports have shown that muscle cell differentiation from DMD patient myoblasts is delayed and that these cells have poor proliferation capacity compared to those of healthy individuals11,12. Our study revealed that control and DMD myoblasts obtained by activating tetracycline-dependent MyoD transfected into iPS cells (iPStet-MyoD cells) have comparable growth and differentiation potential and can produce a large number of intact and homogeneous myotubes repeatedly.

The pathogenesis of DMD is initiated and progresses with muscle contraction. The degree of muscle cell damage at the early stage of DMD can be evaluated by measuring the leakage of creatine kinase (CK) into the extracellular space15. Excess calcium ion (Ca2+) influx into skeletal muscle cells, together with increased susceptibility to plasma membrane injury, is regarded as the initial trigger of muscle damage in DMD19,20,21,22,23,24. Targeting these early pathogenic events is considered essential for developing therapeutics for DMD.

In this study, we established a novel evaluation system to analyse the cellular basis of early DMD pathogenesis by comparing DMD myotubes with the same clone but with truncated dystrophin-expressing DMD myotubes, using the exon-skipping technique. We demonstrated through in vitro contraction that excessive Ca2+ influx is one of the earliest events to occur in intact dystrophin-deficient muscle leading to extracellular leakage of CK in DMD myotubes.

Generation of tetracycline-inducible MyoD-transfected DMD patient-derived iPSCs (iPStet-MyoD cells)

Figure 1: Generation and characterization of control and DMD patient-derived Tet-MyoD-transfected hiPS cells.   Full size image

Morphologically and physiologically comparable intact myotubes differentiated from control and DMD-derived hiPSCs

Figure 2: Morphologically and physiologically comparable skeletal muscle cells differentiated from Control-iPStet-MyoD and DMD-iPStet-MyoD.   Full size image

Exon-skipping with AO88 restored expression of Dystrophin in DMD myotubes differentiated from DMD-iPStet-MyoD cells

 

Figure 3: Restoration of dystrophin protein expression by AO88.   Full size image

 
Restored dystrophin expression attenuates Ca2+ overflow in DMD-Myocytes

 

Figure 4: Restored expression of dystrophin diminishes Ca2+ influx in DMD muscle in response to electric stimulation.   Full size image


Ca2+ influx provokes skeletal muscle cellular damage in DMD muscle

 

Figure 5: Ca2+ influx induces prominent skeletal muscle cellular damage in DMD-Myocytes.   Full size image

 

Skeletal muscle differentiation in myoblasts from DMD patients is generally delayed compared to that in healthy individuals11,36,37.  Our differentiation system successfully induced the formation of myotubes from DMD patients, and the myotubes displayed analogous morphology and maturity compared with control myotubes (Fig. 2a–c).  Comparing myotubes generated from patient-derived iPS cells with those derived from the same DMD clones but expressing dystrophin by application of the exon-skipping technique enabled us to demonstrate the primary cellular phenotypes in skeletal muscle solely resulting from the loss of the dystrophin protein (Fig. 4b).  Our results demonstrate that truncated but functional dystrophin protein expression improved the cellular phenotype of DMD myotubes.

In DMD, the lack of dystrophin induces an excess influx of Ca2+ , leading to pathological dystrophic changes22. We consistently observed excess Ca2+ influx in DMD-Myocytes compared to Control-Myocytes (Supplementary Figure S3a and S3b) in response to electric stimulation. TRP channels, which are mechanical stimuli-activated Ca2+ channels40that are expressed in skeletal muscle cells41, can account for this pathogenic Ca2+ influx…

In conclusion, our study revealed that the absence of dystrophin protein induces skeletal muscle damage by allowing excess Ca2+ influx in DMD myotubes. Our experimental system recapitulated the early phase of DMD pathology as demonstrated by visualisation and quantification of Ca2+ influx using intact myotubes differentiated from hiPS cells.  This evaluation system significantly expands prospective applications with regard to assessing the effectiveness of exon-skipping drugs and also enables the discovery of drugs that regulate the initial events in DMD.

Duchenne muscular dystrophy affects stem cells, University of Ottawa study finds  

New treatments could one day be available for the most common form of muscular dystrophy after a study suggests the debilitating genetic disease affects the stem cells that produce healthy muscle fibres.

The findings are based on research from the University of Ottawa and The Ottawa Hospital, published Monday in the journal Nature Medicine.

For nearly two decades, doctors had thought the muscular weakness that is the hallmark of the disease was due to problems with human muscle fibers, said Dr. Michael Rudnicki, the study’s senior author.

The new research shows the specific protein characterized by its absence in Duchenne muscular dystrophy normally exists in stem cells.

Dystrophin protein found in stem cells

“The prevailing notion was that the protein that’s missing in Duchenne muscular dystrophy — a protein called dystrophin — was not involved at all in the function of the stem cells.”

http://soundcloud.com/cbcottawa1

When the genetic mutations caused by Duchenne muscular dystrophy inhibit the production of dystrophin in stem cells, those stem cells produce significantly fewer precursor cells — and thus fewer properly functioning muscle fibres.  Further, stem cells need dystrophin to sense their environment to figure out if they need to divide to produce more stem cells or perform muscle repair work.

Genetic repair might treat Duchenne muscular dystrophy

July 25, 2011|By Thomas H. Maugh II, Los Angeles Times
 

A genetic technique that allows the body to work around a crucial mutation that causes Duchenne muscular dystrophy increased the mass and function of muscles in a small group of patients with the devastating disease, paving the way for larger clinical trials of the drug. The study in a handful of boys age 5 to 15 showed that patients receiving the highest level of the drug, called AVI-4658 or eteplirsen, had a significant increase in production of a missing protein and increases in muscle fibers. The study demonstrated that the drug is safe in the short term. Results were reported Sunday in the journal Lancet.

Duchenne muscular dystrophy affects about one in every 3,500 males worldwide. It is caused by any one of several different mutations that affect production of a protein called dystrophin, which is important for the production and maintenance of muscle fibers. Affected patients become unable to walk and must use a wheelchair by age 8 to 12. Deterioration continues through their teens and 20s, and the condition typically proves fatal as muscle failure impairs their ability to breathe.

This study is designed to assess the efficacy, safety, tolerability, and pharmacokinetics (PK) of AVI-4658 (eteplirsen) in both 50.0 mg/kg and 30.0 mg/kg doses administered over 24 weeks in subjects diagnosed with Duchenne muscular dystrophy (DMD).

 

Condition Intervention Phase
Duchenne Muscular Dystrophy Drug: AVI-4658 (Eteplirsen)
Other: Placebo
Phase 2
Study Type:Interventional
Study Design:Allocation: Randomized
Endpoint Classification: Safety/Efficacy Study
Intervention Model: Parallel Assignment
Masking: Double Blind (Subject, Caregiver, Investigator, Outcomes Assessor)
Primary Purpose: Treatment
Official Title:A Randomized, Double-Blind, Placebo-Controlled, Multiple Dose Efficacy, Safety, Tolerability and Pharmacokinetics Study of AVI-4658(Eteplirsen),in the Treatment of Ambulant Subjects With Duchenne Muscular Dystrophy
 
 
Resource links provided by NLM:
 
 
Dystrophin expression in muscle stem cells regulates their polarity and asymmetric division

Nature Medicine(2015)   http://dx.doi.org:/10.1038/nm.3990

Dystrophin is expressed in differentiated myofibers, in which it is required for sarcolemmal integrity, and loss-of-function mutations in the gene that encodes it result in Duchenne muscular dystrophy (DMD), a disease characterized by progressive and severe skeletal muscle degeneration. Here we found that dystrophin is also highly expressed in activated muscle stem cells (also known as satellite cells), in which it associates with the serine-threonine kinase Mark2 (also known as Par1b), an important regulator of cell polarity. In the absence of dystrophin, expression of Mark2 protein is downregulated, resulting in the inability to localize the cell polarity regulator Pard3 to the opposite side of the cell. Consequently, the number of asymmetric divisions is strikingly reduced in dystrophin-deficient satellite cells, which also display a loss of polarity, abnormal division patterns (including centrosome amplification), impaired mitotic spindle orientation and prolonged cell divisions. Altogether, these intrinsic defects strongly reduce the generation of myogenic progenitors that are needed for proper muscle regeneration. Therefore, we conclude that dystrophin has an essential role in the regulation of satellite cell polarity and asymmetric division. Our findings indicate that muscle wasting in DMD not only is caused by myofiber fragility, but also is exacerbated by impaired regeneration owing to intrinsic satellite cell dysfunction.

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What about Theranos?

Curator: Larry H. Bernstein, MD, FCAP

Is Theranos Situation False Crowdfunding Claims at Scale or ‘Outsider’ Naivety?

http://www.mdtmag.com/blog/2015/11/theranos-situation-false-crowdfunding-claims-scale-or-outsider-naivety

If you’ve been following the Theranos situation that involves several damning articles from the Wall Street Journal on the company (see sidebar below video), you know that “something is rotten in the state of Denmark.” That is to say, regardless of whether or not you believe the WSJ articles 100%, believe Theranos 100%, or land somewhere in between, it’s hard not to see that something at the company is definitely creating questions about their original claims. In fact, the company has apparently even tempered some language with regard to its capabilities while “debating” the accuracy of the WSJ articles. It’s really a big mess for a company that was supposedly making significant changes in the way we’d conduct blood testing and the way patients controlled and accessed their own health data (although, I think the idea behind that specific aspect is a very good one).

Due to FDA inspections and findings of concern with Thernos practices, the company is currently only collecting blood for one test using its revolutionary proprietary technology. While the company’s CEO Elizabeth Holmes continues to assure the public that the problems are tied to FDA related procedures and not an issue with the technology itself, stakeholders such as Walgreens put any further interactions with the company on hold.

In the following video from Fortune’s Global Forum, you can see Ms. Holmes discussing the situation over the FDA inspections and the changes that are currently in place with regard to the testing that’s happening at the company.

https://youtu.be/A8qgmGtRMsY

So what’s the story behind this story? Is this a deliberate attempt to deceive on the part of Theranos or is it an example of what can happen when an “outsider” gets involved in the highly regulated medical device industry and faces off with the FDA without the proper experience in place to address potential areas of concern?

In a recent blog, I looked at the crowdfunding of medical devices and what can happen when claims made don’t live up to the reality of the product that’s actually developed. Once enthusiastic investors can quickly (and loudly) turn on a company or project, venting their frustration even directly on the crowdfunding page for all to see. Unfortunately, with the way these sites seem to be set-up, the money is still provided to the company that produces a product, albeit one that does not live up to the initial concept.

Is that what Theranos ultimately is? Were the technology claims taken at face value by significant investment backers? It would seem very unlikely, but given some of the accusations of former Theranos employees in the WSJ articles, it wouldn’t be the only instance of Theranos trying to manipulate testing protocols for the sake of appearing more impressive. Theranos counters those claims by saying the former employees were actually unfamiliar with the actual testing the company performs. Whether or not you believe that is entirely up to you.

Another alternative to blatant deceit on the part of Theranos is the possibility that the company was simply playing in an industry it wasn’t truly experienced enough to handle. In other words, how many FDA savy employees work for Theranos? Did they seek consultants to help with the regulatory processes? Or were they simply naïve to the ways of the regulated industry in which they were entering?

Again, this scenario too seems unlikely, but it also brings in the debate over lab-developed tests and the FDA’s regulation of them. If Theranos testing protocols fall under the realm of LDTs, then they aren’t necessary under the oversight of the FDA. Sure, the blood collection device is (and that’s why changes are currently occurring at the company), but does the FDA have the authority to inspect the company’s tests if they are LDTs?

Ultimately, I think everyone (with the exception of competitors to Theranos perhaps) wants the company to be successful. The ideas and hope embedded within the original claims the company made will only enhance the quality of care that we are able to achieve within our healthcare system. Further, empowering patients to make decisions and get involved with their own healthcare management would likely improve their overall health.

Unfortunately, before any of that will be possible, Theranos is going to have an uphill battle in defending itself, its technology, and its CEO in this very public debate over the realistic capabilities it can provide. Hopefully, it learns from this experience and if the technology truly functions the way they’ve claimed, they’ll bring on the necessary regulatory experts and better navigate the troubled waters in which they currently find themselves.

Single Blood Drop Diagnostics Key to Resolving Healthcare Challenges

At TEDMED 2014, President and CEO of Theranos, Elizabeth Holmes, talked about the importance of enabling early detection of disease through new diagnostic tools and empowering individuals to make educated decisions about their healthcare.

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stand-alone software systems

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

Optimization of a Coherent OMA Acquisition System

Sophisticated testing instruments, as well as integrated calibration and error correction software (or stand-alone software systems), can evaluate today’s complex designs. Such tools position designers to successfully tackle challenges in the even faster data environment of the future.

CHRIS LOBERG, TEKTRONIX INC.             http://www.photonics.com/Article.aspx?AID=57878

The demand for optical network data has soared, with rates of 100 Gb/s evolving into 400 Gb/s, 1 Tb/s and beyond, pushing designers to explore inventive and even unconventional modulation schemes in order to encode data more efficiently for faster throughput. In this context, it can pay off for designers to think about how to optimize their testing environment to quickly and accurately evaluate design progress.

When considering a coherent optical modulation analysis system, it’s important to consider the signal fidelity of its acquisition system. This typically includes an optical modulation analyzer (OMA) or coherent receiver, as well as a digitizer (usually an oscilloscope), and some form of algorithmic processing.

When purchasing a coherent optical acquisition system, users must look beyond obvious performance parameters, such as coherent receiver bandwidth and oscilloscope sample rate. Consider also these vital questions:

• Does this OMA achieve the lowest possible error vector magnitude (EVM) value for the acquisition system? And is this oscilloscope the most effective digitizer available? These two considerations have an obvious impact on measured signal quality.

• Is the analysis software that comes with the OMA adequate for testing the complexities of the design or research?

• Do these instruments meet not only present acquisition needs, but also anticipated needs in one year, two years or even longer?

 

Achieving low EVM and high ENOB

Signal quality is obviously critical to testing success. EVM is often seen as a representation of the overall signal quality — the lower the better. An EVM is simply the vector that points from the actual measured symbol to where that symbol was intended in the signal constellation diagram.

The manufacturing process can introduce a wide range of system impairment and configuration issues into the OMA, which can adversely impact the receiver EVM. These include IQ (in-phase and quadrature) phase angle errors, IQ gain imbalance, IQ skew errors, and XY polarization skew errors. The good news is that some OMAs are able to precisely measure these manufacturing errors and calibrate their impacts in the algorithmic processing that typically follows coherent detection.

With these OMAs, each receiver is tested at the time of manufacture, and a unique calibration file is created. It is later automatically used by the optical modulation analyzer software that comes with the receiver to remove the impacts discussed above during acquisition.

Figure 1 offers an example of the software that accompanies a Tektronix OM4245 45-GHz OMA. Unique calibration files are created for all Tektronix OMAs at the time of manufacture, so that the software can remove any impacts. Once the signal is received by the OMA, the next step is to digitize it on the electrical signal paths using a multichannel oscilloscope. This can introduce a number of factors that can affect the EVM, the most fundamental being the oscilloscope’s bandwidth and sample rate.

 

An example of the software that accompanies optical modulation analyzer (OMA) systems; here, a Tektronix OM4245 45-GHz OMA

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Figure 1. An example of the software that accompanies optical modulation analyzer (OMA) systems; here, a Tektronix OM4245 45-GHz OMA is shown.

 

Assuming an oscilloscope with the appropriate bandwidth and sample rate is utilized, and that all OMA impairments are being corrected algorithmically as described above, achieving the lowest measurable EVM comes down to a function of the effective number of bits (ENOB) of the oscilloscope. The ENOB is measurably impacted by the way the oscilloscope handles interleaved sampling. Some real-time oscilloscopes use frequency interleaving techniques in order to extend bandwidth, but they do so at the cost of increasing the noise in the measurement channel.

The limitation of the frequency interleaving approach lies in how the various frequency ranges are added together to reconstruct the final waveform, a step that compromises noise performance. In traditional frequency interleaving, each analog-to-digital converter (ADC) in the signal acquisition system only “sees” part of the input spectrum. But other oscilloscopes, such as the one shown in Figure 2, use a time-based interleaving approach, where all the ADCs see the full spectrum with full signal path symmetry. This approach preserves signal fidelity and ensures the highest possible ENOB.

 

Some oscilloscopes, such as this one, provide signal acquisition up to 70-GHz bandwidth.

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Figure 2. Some oscilloscopes, such as this one, provide signal acquisition up to 70-GHz bandwidth. Its asynchronous time interleaving (ATI) architecture provides a low-noise, real-time signal acquisition and high effective number of bits (ENOB).

 

Analysis for conclusive evaluation

Any test and measurement coherent receiver comes with some sort of analysis and visualization software package. But will that software have the particular types of measurement and visualization tools needed for evaluating specific designs or research?

For example, when evaluating the quality of a new phase recovery algorithm, OMA software may be needed. This type of software can provide not only the basic building blocks for measurements but also allows the complete customization of the signal processing. Stand-alone optical analysis software packages of high quality are on the market. Some include features such as a library of analysis algorithms designed specifically for coherent optical analysis and executed in a customer-supplied MATLAB installation, with an applications programmatic interface (API) to these algorithms. Some provide a graphical user interface with optical tools that analyze complex modulated optical signals without needing to know any MATLAB, analysis algorithms or software programming, as shown in Figure 3.

 

The user interface of software like this, Tektronix’s OM1106 Coherent Optical Analysis system, allows the user to conduct a detailed analysis of complex modulated optical signals without requiring knowledge of MATLAB, analysis algorithms or software programming.

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Figure 3. The user interface of software like this, Tektronix’s OM1106 Coherent Optical Analysis system, allows the user to conduct a detailed analysis of complex modulated optical signals without requiring knowledge of MATLAB, analysis algorithms or software programming.

 

Flexible measurement-taking software also is available. For instance, measurements can be made solely through the user interface, or via the programmatic interface to and from MATLAB for customized processing. Using both methods together is also an option, made possible by employing the user interface as a visualization and measurement framework, around which custom processing can be built.
Most software includes sophisticated core processing algorithms for analyzing coherent signals — estimating the signal phase, determining the signal clock frequency, performing ambiguity resolution, estimating the power spectral density, etc. — but some packages can customize the core processing algorithms. This provides an excellent method for conducting signal processing research. For instance, in order to speed up the development of signal processing routines, one user interface provides a dynamic MATLAB integration window (Figure 4).

 

A dynamic MATLAB integration window helps speed up the development of signal processing routines.

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Figure 4. A dynamic MATLAB integration window helps speed up the development of signal processing routines.

 

Any MATLAB code typed in this window is executed on every pass through the signal processing loop. This allows the “comment out” function calls, writing of specific values into data structures, or modification of signal processing parameters on the fly without having to stop the processing loop or modify the MATLAB source code.

Future-proofing an acquisition system

While the bulk of today’s coherent optical R&D activity is focused on 100-G signals, R&D with 400-G signals is already underway at many sites. Testing at 400 G may well be needed within the lifetime of many 100-G test instruments. Therefore, it makes sense to buy equipment at the right performance and price for 100 G now, but also to ensure that future expansion into 400 G is possible.

But how? Typically, four channels of 33-GHz real-time oscilloscope acquisition are used to test 100-G signals. In order to test 400-G signals in the future, bandwidths greater than 65 GHz will be needed, especially for a full dual-polarization system. But if testing at 100 G is all that’s needed now, it could be hard to justify the additional expense. One way around this problem is to purchase a system with a flexible, modular design, and one that uses distributed processing to allow for additional capacity for the system as needed.

For example, Figure 5 shows a system with four channels of 33-GHz acquisition that are distributed across two stand-alone oscilloscopes (left). The instruments are connected by a high speed bus, which not only provides a common external trigger between the two but also includes a common 12.5-GHz sample clock. The result is that the two oscilloscopes are combined to form, in effect, a single instrument whose acquisition-to-acquisition jitter across all channels delivers the same level of measurement precision as a stand-alone, monolithic oscilloscope.

 

Shown here is a modular way to build coherent optical testing systems from 100 to 400 G using an oscilloscope connected by cables.

Figure 5. Shown here is a modular way to build coherent optical testing systems from 100 to 400 G using an oscilloscope connected by cables. The processing is distributed and provides a common trigger without acquisition-to-acquisition jitter.

 

The system shown in Figure 5 also has two 70-GHz channels (one in each unit). Therefore, by simply switching from the 33-GHz channels to the 70-GHz channels, the oscilloscope bandwidth and sample rate can both be doubled. This permits a “peek” at single-polarization 400-G signals using the 100-G test system, as shown in the middle of the illustration. When the time comes to perform full 400-G testing, a second system can be added to the first with another high speed bus, providing two more channels of 70-GHz acquisition. This creates a system that is capable of full dual-polarization coherent optical acquisition (as demonstrated on the right). As the base units are stand-alone oscilloscopes, the systems can also be scaled down and redeployed to other projects as needed when a project comes to an end.

Meet the author

Chris Loberg is a senior technical marketing manager at Tektronix Inc., responsible for oscilloscopes in the Americas region; email: christopher.j.loberg@tektronix.com.

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