The STAP paper sage continues – the Knoepfler post

Stem cell scientist and blogger Paul Knoepfler (from my alma mater, UC Davis), has written a nice summary of the STAP situation as it sits.  See his very useful post here.  He points out the ironic truth that Obokata and her co-authors agreed to retract the Nature STAP cell letter, but not the Nature article even though the Nature letter is not the one found by the RIKEN Center to contain figures that were manipulated.   Dr. Knoepfler wrote an editorial to the journal Nature in which he called for the journal to retract BOTH papers.  This is pretty much the view of the scientific community in general, at least from where I sit.  

Once the STAP papers came out, a host of labs tried to recapitulate the experiments described in the papers.  These are some very successful stem cell labs with very talented people.  They pretty universally had trouble recapitulating the results of Obokata and others.  Now that’s not definitive proof that something’s wrong.  Some experiments are really hard to do and it takes time to learn how to do them even if you are really good.  However, even after the detailed STAP protocol was made available, people still had trouble getting it to work.  Now things started to look hinkey.  Further mining of the papers began to show some really deep problems – things that did not make sense.  When clarification was asked for, the problems began to look even bigger.  This is the point at which the RIKEN Center became involved.

I think we should give the RIKEN Center some credit.  After all, looking into a signature publication from your own institute and the workings of one of your own is not easy.  But investigate they did, and the results were not pretty.  They did not sugar-coat their findings, but reported them forthrightly.  According to Dr. Knoepfler, RIKEN is currently determining a punishment for what it called “Dr. Obokata’s misconduct.”  If misconduct produced the Nature article then it should be retracted.  If there is some good science in that paper, then let the authors re-do it and resubmit it.  But as it stands, I think Dr. Knoepfler is completely correct when he writes, “the whole STAP story is fundamentally flawed.”

Nature should request and then demand a retraction from the authors.  If they do not get this approval, it seems to me that they are well within their rights to either retract the papers on their own pending further review or take legal action to get the papers retracted.  Most of the stem cell community, bloggers included, just want to put this whole affair behind us.

Polymer Nanoflower Encapsulates Two Cancer Drugs to Hit Tumors with More Punch

Get a load of this!!

Lyra Nara Blog

Many existing anti-cancer drugs can be disappointingly ineffective in clinical practice, but often it is the delivery method and not the medication itself that limits effectiveness. Being able to deliver multiple drugs together, each with a different mechanism of action, to their target can be considerably more powerful than separate administrations. Researchers at North Carolina State University and the University of North Carolina at Chapel Hill have developed a “nanoflower” made out of a hydrophilic polymer that carries camptothecin and doxorubicin directly into cancer cells.

nanoflower Polymer Nanoflower Encapsulates Two Cancer Drugs to Hit Tumors with More Punch

The hydrophobic drugs are encapsulated within the polyethylene glycol structure similarly to how proteins fold in on themselves. At about 50 nanometers in diameter, the nanoflowers can be injected into the bloodstream to seek out cancer cells. In an animal study, the structures stayed together until they penetrated lung cancer cells by taking advantage of “lipid raft and clathrin-mediated endocytotic pathway without premature leakage,” according…

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Human Infra-patellar Fat Pad-Derived Stromal Cells Show Great Cartilage-Making Potential, Which is Enhanced By Connective Tissue Components

With age and overuse, our knees wear out and we sometimes need an artificial one. The cartilage shock absorber at the ends of our bones simply does not regenerate very well, and this results in large problems when we get older.

Is there an effective way to regenerate cartilage? Stem cells do have the ability to make cartilage, but finding the right stem cell and delivering enough of them to make a difference remains a challenge.

To that end, Tang-Yuan Chu and his colleagues from Tzu Chi University and the Buddhist Tzu Chi General Hospital in Hualien, Taiwan have discovered that stem cells from the fat pad that surrounds the knee appear to be one of the best sources of cartilage-making cells for the knee.

The infra-patellar fat pad or IFP contains a stem cell population called infra-patellar fat pad-derived stromal cells or IFPSCs. These IFPSCs were isolated by Chu and his colleagues from patients who were undergoing arthroscopic surgery. When Chu and others grew these cells in culture, the IFPSCs grew robustly for two weeks. The culture protocol was a standard one and no special requirements were required. In fact, after two weeks, the IFPSCs grew to more than 10 million cells on the third passage.

When the ability of IFPSCs to form cartilage-making cells (chondrocytes) were compared with mesenchymal stem cells from bone marrow, fat and umbilical cord connective tissue (Wharton’s jelly), the IFPSCs showed a clear superiority to these other cells types, and differentiated into chondrocytes quite effectively.

Next, Chu and his crew cultured the IFPSCs on a material called hyaluronic acid (HA). HA is a common component of the synovial fluid that helps lubricate our larger joints and in connective tissue, and basement membranes upon which epithelial cells sit.

Hyaluronic Acid

When grown on 25% HA, the IFPSCs were better at making bone or fat than IFPSCs grown on no HA. Furthermore, when grown on 25% HA, IFPSCs showed a four-fold increase in their ability to form chondrocytes. The HA also did not affect the ability of the cells to divide.

In conclusions, these IFPSCs seem to possess a strong potential to differentiate into chondrocytes and regenerate cartilage. Also, this ability is augmented in a growth environment of 25% HA. Certainly some preclinical trials with laboratory animal are due. Wouldn’t you say?

Source: Dah-Ching Ding; Kun-Chi Wu; Hsiang-Lan Chou; Wei-Ting Hung; Hwan-Wun Liu; Tang-Yuan Chu. Human infra-patellar fat pad-derived stromal cells have more potent differentiation capacity than other mesenchymal cells and can be enhanced by hyaluronan.  Cell Transplantation,

Using Patient Stem Cells to Make “Heart-Disease-on-a-Chip”

Personalized medicine is a new but quickly advancing innovation in medicine that tailors the diagnosis and treatment of a particular patient according to their specific genetic and physiological idiosyncrasies. As an example, if a patient has high blood pressure, which treatment would work the best? If the patient is an African-American, it is unlikely that a group of drugs called ACE inhibitor or another group called ARBs would work terribly well because African-American patients tend to lack sufficient quantities of the targets of these two type of drugs for them to work properly. Therefore, diuretics or beta blockers are better drugs to lower the blood pressure of such patients.

Other examples include the enzymes that chemically modify drugs are they circulate throughout our bodies. Some patients have excessive amounts of a liver enzyme called CYP2D6, and this enzyme modifies the painkiller codeine.  Codeine, you see, is not given in an active form.  It only becomes active after the liver enzyme CYP2D6 modifies it.  People with large amounts of CYP2D6, which includes about 10% of Arabs, over-activate codeine, which causes side effects like profound sedation and stomach cramps (codeine or hydrocodone is a form of morphine).  Therefore, before the patient is prescribed codeine, which is present in several different types of prescription painkillers (e.g., Norco, Lortab, Tusnel-HC, Canges-HC, Drocon-CS, Excof-SF, TriVent-HC, etc.), it would be immensely useful to know if your patient had this condition in order to cut their codeine dose or prescribe an altogether different pain-killer.

Now that you have, hopefully been convinced that personalized medicine can potentially save lives, I hope to tell you about a new advance that brings stem cells into the personalized medicine arena.  Kevin Kit Parker and William Pu have used stem cell and “organ-on-a-chip” technologies to grow functioning heart tissue that carries an inherited cardiovascular disease.  This research appears to be a big step forward for personalized medicine.

Parker and Pu modeled a cardiovascular disease called Barth Syndrome, which is caused by mutations on a gene that resides on the X chromosome called TAZ, which encodes the Tafazzin protein.  Barth Syndrome is also affects heart and skeletal muscle function.  Skin biopsies were taken from two male patients who suffer from Barth Syndrome.  These cells were de-differentiated into induced pluripotent stem cells (iPSCs) that were further differentiated into heart muscle cells.  To differentiate the iPSCs into heart muscle cells , the cells were grown on small slides known as chips lined with human extracellular matrix proteins that mimicked the environment of the human heart.  The cells were tricked into thinking that they were in a heart and they differentiated into heart tissue.  Not surprisingly, the heart tissue made on a chip contracted very weakly compared to normal heart tissue.

To confirm that they were not barking up the wrong tree, Parker and Pu used normal cells that had been genetically engineered to possess mutations in the TAZ gene.  When these engineered cells were used to make heart tissue on a chip, they too contracted very weakly.  This told Parker and Pu that they were definitely on the right track.

“You don’t relay understand the meaning of a single cell’s genetic mutation until you build a huge function,” said Parker, who has spent over a decade working on “organs-on-a-chip” technology.  “In the case of the cells grown out of patients with Barth Syndrome, we saw much weaker contractions and irregular tissue assembly.  Being able to model the disease from a single cell all the way up to heart tissue, I think that’s a big advance.”.

The TAZ mutation disrupts the activity of the powerhouse of the cell, a small structure called the mitochondrion.  Even though the TAZ mutation did not affect the over all energy supply of the cells, it seems to affect the way the heart muscle constructs itself so that it can properly contract.

Since mitochondria use a process known as oxidative phosphorylation to make the lion share of their chemical energy in the form of the molecule ATP (adenosine triphosphate), mitochondria also generate toxic byproducts called reactive oxygen species or ROS.  Cells have mechanisms to squelch ROS, but these mechanisms can be overwhelmed if cells make excessive quantities of ROS.  Heart muscle that contains the TAZ mutation seems to make excessive quantities of ROS, and this affects the integrity of the heart muscle.

Can drugs that quench ROS be used to retreat patients with Barth Syndrome?  It is difficult to say, but this chip-on-a-dish is surely an excellent model system to determine if such an approach can work.  Already, Pu and his colleagues are testing drugs to treat this disorder by testing those drugs on heart tissue grown on chips.

“We tried to thread multiple needles at once and it certainly paid off,” said Parker.  “I feel that the technology that we’ve got arms industry and university-based researchers with the tools they need to go after this disease.”.

Authors Agree to Retract One STAP Paper

Embattled stem cell scientist Haruko Obokata from the Riken Center for Developmental Biology in Japan has agreed, albeit reluctantly, to retract one of the two Nature papers that describes a controversial technique for generating pluripotent stem cells by stressing adult cells with acid or pressure.

Obokata and her colleagues pioneered the STAP protocol that generates Stimulus-Triggered Acquisition of Pluripotency or STAP cells in two papers that were published in the international journal Nature in January, 2014. When these papers appeared, they were regarded as a revolutionary finding in the field of stem cells. Nevertheless, these papers also generated more than a fair share of suspicions, and rightly so. After all, these papers challenged many previous observations. Therefore, many laboratories tried to repeat Obokata’s results, without any success. While in and of itself this was not a definitive refutation of these papers, further mining of the data in these papers revealed discrepancies and inconsistencies. Again, while this is not a definitive refutation of the results in the paper, it was enough to implement further investigation. Therefore an internal investigation by the Riken Center was conducted.

In their investigation, Riken found evidence of misconduct.  According to the Riken report, two pictures of electrophroresis gels were spliced together, and that data from Obokata’s doctoral thesis was reused in two images despite that fact that these data came from experiments that had been conducted under different conditions.

Obokata apologized for her errors, but insisted that these mistakes were unintentional and that they did not detract from the validity of her work in general. She also said she would be appealing the findings. That appeal, however, was rejected earlier this month.

Now, Obokata has agreed to retract one, but not both, of two Nature papers. According to the Nature News Blog, which is editorially independent of the research editorial team, the “Bidirectional developmental potential in reprogrammed cells with acquired pluripotency” paper is to be retracted. Riken told the Nature News Blog that each co-author either agreed to the retraction or did not oppose it.  According to the Japan Times:

Of the three researchers, her lawyer said University of Yamanashi professor Teruhiko Wakayama is responsible for the paper Obokata has agreed to retract. He was engaged in all experiments, and Obokata wrote the paper under his guidance, lawyer Hideo Miki said.

She e-mailed the other main co-author, Yoshiki Sasai, deputy director of the Riken Center for Developmental Biology in Kobe, that she would have no problem if Wakayama wants to retract it, Miki said.

Both papers were published in the Jan. 30 edition of the journal, one as a “letter” and the other as an “article.”

However, the journal Nature couldn’t confirm the request. “Nature does not comment on corrections or retractions that may or may not be under consideration, nor does it comment on correspondence with authors, which is confidential,” a spokesperson tells the Nature News Blog. “We are currently conducting our own evaluation and we hope that we are close to reaching a conclusion and taking action.”

According to the Japan Times, Obokata has said that she will not retract the other paper.

Expanding Functional Cord Blood Stem Cells for Transplantation

Patients who suffer from blood-based diseases such as leukemia, lymphoma, and other blood-related diseases sometimes require bone marrow transplants in order to live. The paucity of available bone marrow necessitates the use of umbilical cord blood for these patients, but cord blood suffers from one flaw and that is small volumes of blood and low numbers of stem cells. Scientists have tried to grow cord blood stem cells in culture in order to beef up the numbers of stem cells, but cord blood stem cells sometimes lose their ability to repopulate the bone marrow while in culture.

To solve this problem, researchers at the Icahn School of Medicine at Mount Sinai have designed a new technique to expand the number of cord blood stem cells without causing any loss of potency.

“Cord blood stem cells have always posed limitations for adult patients because of the small number of stem cells present in a single collection,” said Partita Chaurasia of the Tisch Cancer Institute at Mount Sinai. “These limitations have resulted in a high rate of graft failure and delayed engraftment in adult patients.”.

Chaurasia and coworkers used a technique called “epigenetic reprogramming” to reshape the structure of the genome of the stem cells. They used a combination of a drug called valproic acid and histone deacetylase inhibitors (HDACIs). The valproic acid-treated cells produced greater numbers of marrow repopulating stem cells in culture. These expanded cord blood stem cells were also able to reconstitute the bone marrow of immune-deficient mice, and when the reconstituted bone marrow of that mouse could be used to reconstitute the bone marrow of another immune-deficient mouse. Bone marrow from this second mouse could also reconstitute the bone marrow of a third immune deficient mouse.

These results have extremely important implications for patients who are in the midst of a battle with blood cancers, and might mean the difference between a successful cord blood transplant and one that fails.

Stem Cells Inc. Reports Additional Spinal Cord Injury Patients Transplanted with Neural Stem Cell Line Show Functional Improvements

StemCells, Inc. has developed a proprietary stem cell line called HuCNS-SC.  This stem cell line is a neural stem cell line, and neural stem cells can readily form neurons (the conducting cells of the nervous system), or glial cells (the support cells of the nervous system). In order to determine if these cells can regenerate spinal nerves in patients who have suffered a spinal cord injury, StemCells Inc. has commissioned a clinical trial to test their cells in human spinal cord injured patients.

Early indications showed that the HuCNS-SC cells were safe, but some patients have shows improvements in sensation.  Now StemCells Inc has issued an announcement that these initially reported improvements in only a few patients have also been confirmed in other patients.

According to Armin Curt, M.D., Professor and Chairman of the Spinal Cord Injury Center at Balgrist University Hospital, University of Zurich, and the principal investigator of their Phase I/II trial, the initial improvements that were observed in the first two patients treated with their HuCNS-SC neural stem cells have now been observed in two additional patients who have also been treated with these stem cells. These results come from an interim analysis of recent clinical data.

In a presentation to the Annual Meeting of the American Spinal Injury Association in San Antonio, Texas, Dr. Curt showed data on AIS B subjects who were transplanted with HuCNS-SC neural stem cells in the Phase I/II chronic spinal cord injury trial. This trial is different from the AIS A patients who have no mobility or sensory perception below the point of injury, since AIS B subjects are less severely injured, and are paralyzed but retain sensory perception below the point of injury. Two of the three AIS B patients who are participating in the study showed significant gains in sensory perception. The third patient remained stable.  These interim results confirm the favorable safety profile of these stem cells and the surgical implant procedure used to transplant them into the spinal cords of spinal cord injury patients.

Also included in Dr. Curt’s presentation was data from a total of five new subjects with a minimum six-month follow-up. In total, Stem Cells Inc. has now reported clinical updates on a total of eight of the twelve patients enrolled in its Phase I/II clinical trial that is testing this Company’s proprietary HuCNS-SC (purified human neural stem cells) platform technology for treating chronic thoracic spinal cord injury.

“Thoracic spinal cord injury was chosen as the indication in this first trial primarily to demonstrate safety. This patient population represents a form of spinal cord injury that has historically defied responses to experimental therapies and is associated with a very high hurdle to demonstrate any measurable clinical change. Because of the severity associated with thoracic injury, gains in multiple sensory modalities and segments are unexpected, and changes in motor function are even more unlikely,” said Dr. Curt. “In contrast, the cervical cord, which controls more motor function, may represent a patient population in which motor responses to transplant may be more readily anticipated.”

“We are seeing multi-segmental gains and a return of function in the cord in multiple patients. This indicates something that was not working in the spinal cord, now appears to be working following transplantation. This is even more significant because of the time that has elapsed from the date of injury, which ranges from 4 months to 24 months across the subjects with sensory gains,” said Stephen Huhn, M.D., FACS, FAAP, vice president, CNS clinical research at StemCells, Inc. “These results are exciting with respect to the expansion of this trial into patients with cervical injury because even a gain of one to two segments in cervical spinal cord injury patients can allow for additional function in the upper extremities.”