A Stem Cell Clash: Silva Comments on MBD3/NuRD Debate with Hanna

Researchers probing how to reprogram cells into powerful stem cells (induced pluripotent stem cells or IPSCs) and what the molecular mechanisms are behind this process have become entangled in a conflict.

Of course over the years scientists including stem cell scientists have had their share of disagreements and debates in the past including heated ones, but this reprogramming clash has taken it up a notch beyond past ones and has some unique elements to it.

For example, this scientific clash is unfolding largely in the public domain and involves post-publication review such as on PubPeer.

Looking under the “hood” of cells so to speak, their reprogramming involves a molecule called MBD3 and a corepressor complex called “NuRD” ( for more on NuRD see my review with my postdoc mentor Bob Eisenman on NuRD here in Cell). It seems that most everyone agrees that MBD3 and NuRD play some role in reprogramming.

However, what the exact roles of MBD3 and NuRD might be in this area are very unclear at this time and there are quite distinct views.

Jacob Hanna

On one side we have Jacob Hanna, a well-known stem cell scientist who was previously a postdoc in the lab of Rudy Jaenisch. Hanna (pictured at right) has had a number of very high profile papers including on induced pluripotency.

One major assertion from the Hanna Lab is that a repressive chromatin complex including MBD3 and NuRD proteins is inhibitory for pluripotency (e.g. in their Rais et al. paper that I discussed on this blog when it came out in 2013). I also had a chance hear Hanna talk at the 2013 Till & McCulloch meeting, where I asked him some questions from the audience (see here).

On the other side we have José Silva, another top stem cell investigator. Silva did his post-doctoral work in the lab of Austin Smith. Of course Jaenisch and Smith are two of the top scholars in the stem cell field. The Silva lab has published a Cell Stem Cell paper coming to pretty much the opposite conclusion of Hanna.

Jose SilvaThis stem cell conundrum has been the subject of vigorous discussion on PubPeer. Now this MBD3 disagreement has also spilled over to bioRxiv where further back and forth is ongoing. On Silva’s side of the MBD3/NuRD fence are also well-known researchers Brian Hendrich and Paul Bertone.

In an effort to get to the bottom of this and build a bridge for constructive discussion, I have invited both Silva and Hanna to comment here on this situation.

Hanna has indicated that he would prefer to wait a month or so until additional work is published and then will provide comment. Stay tuned for that as my invitation to him stays open.

Silva has provided comments now, which are included verbatim below:

“Please find below the key elements (in no particular order) being discussed on the ongoing debate on MBD3/NuRD and reprogramming and my view on these:

1- Levels of Mbd3 expression and its relation to reprogramming.

Rais et al. evaluated the potential of Mbd3 depletion primarily in the Mbd3fl/- heterozygous background. Dr Hanna claimed that these cells express hypomorphic levels of Mbd3, corresponding to 20% that observed from wild type cells. Dr Hanna also claimed that these cells could reprogram with near 100% efficiency. However, our analysis of Dr Hanna’s data revealed that Mbd3fl/- cells express instead nearly wild type levels of Mbd3. This is also in line with the quantification of Mbd3 levels in Mbd3fl/- cells assessed in Dr Hendrich’s lab and mine. This evidence led us to question the effective depletion of Mbd3/NuRD function as having been a significant factor in the reported increase in reprogramming efficiency. (Please note that Dr Hanna’s Mbd3fl/- cells used in the Rais et al. study were generated by Dr Hendrich’s lab.)

2- Use of elevated copy number of Oct4-GFP reporter transgenes to assess ongoing reprogramming efficiency

The high copy number of randomly integrated Oct4-GFP reporter transgenes may lead to spurious GFP expression in non-reprogrammed cells.

3- Comparison of reprogramming efficiency to a control cell line harboring a deficient Oct4-GFP reporter transgene.

While Mbd3fl/- cells harbored an intact Oct4-GFP reporter known to be promiscuous for expression in a range of cell types, the control cells were transfected with an alternative Oct4-GFP reporter with much greater specificity for pluripotent cells. This finding indicates that key methodology was absent from the paper, and the comparison of reprogramming efficiency between cell lines representing compatible measurement conditions was potentially invalid.

4- Reproducibility of Dr Hanna’s claims. Rais et al. was regarded as a  landmark paper in stem cell biology and numerous labs around the world have tried to reproduce these results. Their attempts using independent systems have been unsuccessful. We do not dispute that Dr Hanna’s cells reprogram relatively efficiently. However, based on our own experimental work and on the detailed analysis led by Dr Bertone of genomic datasets published by Rais et al., we found no evidence to support the claim that depletion of Mbd3 leads to deterministic reprogramming.

José Silva

This is your brain on diapers: new mindbogglingly cool imaging trick

Expansion microscopy brain

Swollen brain cells – Scientists modified the superabsorbant diaper compound, polyacrylate, to magnify brain tissue. Courtesy of Boyden lab, MIT, Cambridge, MA. NIH

In what NIH describes as “outside-the-box” thinking, an MIT team led by Edward Boyden has found a way to use a diaper ingredient to transform microscopy including brain imaging.

This is cool stuff.

Boyden’s group found that the super-absorbent diaper compound sodium polyacrylate, can be used in a very novel way for microscopy.

For any who have ever wished for a more powerful microscope (and isn’t that everyone?), Boyden’s team thought of something pretty revolutionary. Instead of pushing the microscope beyond the limits of optical physics, Boyden uses the diaper compound to make his samples bigger and hence they looked bigger under the scope under the same magnification. You can see a lot more.

I wish I had thought of that.

Even with the almost 5-fold acrylate-based expansion the tissues retained its general structure, but was just far easier to see.

NIH quoted Boyden:

“Our results show that we can scan large chunks of brain tissue with nanoscale precision. We think this can be applied to a variety of tissues and help answer a lot of different questions in science and medicine,” said Dr. Boyden.

In the future, Dr. Boyden and his team plan to test ways to combine the technique with other visualization methods and use it to study diseases in human brain tissue.

You can see an example of swollen brain cells imaged by the team above from the NIH website. Also from the NIH piece:

“Expansion microscopy is a potential game changer,” said Walter Koroshetz, M.D., acting director of NIH’s National Institute of Neurological Disorders and Stroke. “This is the kind of outside- the-box technical innovation that expands the capability of microscopes widely used in the scientific community to explore the fine structure of the nervous system in health and disease.”

All those years changing my kids’ diapers, then going off to look at samples on scopes, and this never occurred to me.

Stemedica reply on Olbermann interview regarding Gordie Howe

The stem cell company Stemedica along with Mexican partner Novastem conducted a stem cell intervention on hockey legend Gordie Howe, who had suffered strokes in 2014. This situation has sparked a lot of discussion and media attention including a recent interview with Stemedica leadership on the Keith Olbermann show on ESPN.

For balance and fairness I invited Stemedica to comment on this situation and below I have posted their January 23 response verbatim:

“As part of ipscell.com’s coverage of Gordie Howe’s participation in a stem cell trial for stroke, we believe several key facts have been missed, and certain circumstances have been misrepresented. Thank you for allowing us to set the record straight.

* Gordie was an accepted participant in a government authorized clinical trial in Mexico. That clinical trial meets all of their government’s requirements including: IRB/Ethics Committee oversight of an approved clinical trial protocol and the conduct of clinical trials; adherence to inclusion/exclusion criteria of the protocol; signing an informed consent; reporting adverse events; and, collecting other clinical data as outlined in the protocol.

* Gordie Howe, (as his family reported to the media), was not eligible for enrollment in Stemedica’s US-based stroke clinical trial due to certain inclusion criteria. The family did apply for enrollment in the stroke trial at Novastem’s Clinica Santa Clarita where the inclusion criteria are different. Stemedica’s stroke trial in the U.S. has a six-month wait period post-stroke and the family was concerned that Gordie might not live for six more months. The fact that the wait time for participation is different between these two clinical trials was the determining factor the family used in choosing the Novastem clinical trial at Clinica Santa Clarita.

* As a participant of a clinical trial, Gordie Howe’s involvement in that trial was confidential. There was no effort by Stemedica or our Geographic Distribution Partner in Mexico, Novastem, to breach that confidentiality. It was Gordie’s family, under constant requests from media and fans to know more about Gordie’s health, that they, (the Gordie Howe family), made a public pronouncement. Since then, we have professionally responded to approaches from the media after receiving a request from the Howe family to do so.

* It’s important to note that not all stem cells are manufactured the same way. Therefore, different stem cells manufactured by different companies exhibit different properties. There is still an honest and open debate about what role autologous adult stem cells, allogeneic adult stem cells, iPS cells and, embryonic stem cells are going to play in developing new medications for the treatment of various conditions in the future. The efficacy of adult allogeneic stem cells – as is the case with all stem cells – can only be evaluated based on data collected through well run and government-approved clinical trials.

* As was the case in Keith Olbermann’s interview with Stemedica’s Vice Chair/CEO, Dr. Maynard Howe, on January 21, 2015, whenever Stemedica has an opportunity to interact with the media, we make best efforts with that audience to emphasize the need to be cautious about: treatments which are unregulated; use of stem cells of unknown origin; and/or, promises or guarantees of positive outcomes. We work diligently to adhere to all laws, professional practices, and ethical standards. We encourage patients, like Gordie Howe and his family, to demand documentation of the clinical trial’s compliance with these guidelines before committing to any investigational treatment or trial opportunity.

* While the correspondence between the FDA and a clinical trial sponsor is strictly confidential, including IND numbers, we do confirm that all clinical trials sponsored by Stemedica have FDA approval. These trials are listed on the governmental web site ClinicalTrials.gov under the following numbers:

STEM 101-M; NCT01297413 A Study of Allogeneic Mesenchymal Bone Marrow Cells in Subjects With Ischemic Stroke.

STEM 102-M; NCT01771679 Safety Study of Bone Marrow Derived Stem Cells on Patients With Cutaneous Photoaging.

STEM 103-M-STEMI; NCT01770613 A Study of Allogeneic Mesenchymal Bone Marrow Cells in Subjects With ST Segment Elevation Myocardial Infarction (STEMI)

STEM 104-M; NCT02123706 A Phase IIa, Single-blind, Placebo-controlled, Crossover, Multi-center, Randomized Study to Assess the Safety, Tolerability, and Preliminary Efficacy of a Single Intravenous Dose of Ischemia-tolerant Allogeneic Mesenchymal Bone Marrow Cells to Subjects With Heart Failure of Non-ischemic Etiology.

We, too, wish Gordie Howe the best of health in the future. We trust that Gordie’s participation in Novastem’s stroke study at Clinica Santa Clarita fulfills the time-honored purpose of clinical trials.

Thank You,

Stemedica Cell Technologies, Inc.”

TGIF: Biomedical weekend reading includes some cool papers

I’m working on an R01, but I still try to find time to read a wide variety of papers. Below are the ones I’m hoping to get to this weekend.

Less Myc, longer “health span” Cell paper from Sedivy Lab.

ESC Histone H3.3 nucleosomal functions Epigenetics & Chromatin paper from Keji Zhao Lab.

Human PGC specification Cell paper from Jacob Hanna Lab.

SETDB1 & hnRNP K tango to silence ERVs in ESCs PLOS Genetics paper from Matt Lorincz Lab.

Novel antibiotic isolated from dirt Nature paper from Kim Lewis Lab.

Olbermann Puff Interview on Stemedica & Gordie Howe

The stem cell company Stemedica has made a name for itself in the media lately through hockey legend Gordie Howe, who received a non-FDA approved stem cell “treatment” in Mexico via Stemedica and its partner, Novastem.

Howe, known as Mr. Hockey, had several strokes in late 2014 and his health was declining. Stemedica and Novastem gave Howe a free stem cell therapy. According to his family, Howe got a lot better.

I’m glad he’s feeling better.

What I’m less sure of is whether the stem cells or something else such as rehydration or simply some degree of natural recovery from the stroke helped Howe.

Science-based medicine examined this case in two pieces that I recommend (here and here).

Stemedica OlbermannA new  interview on this case–image above and video below–by Keith Olbermann in which he talked to Stemedica CEO Maynard Howe (no relation to Gordie Howe) sure seems like a big PR win for the company.

If you watch it, it basically feels like an ad for Stemedica.

I am a big fan of Olbermann, but he dropped the ball (err, puck) on this one.

I have no issue with Gordie Howe and I wish him the best. What makes me concerned is that this kind of interview is almost certain to drive many regular folks to get potentially risky, unproven stem cell “treatments”.

I asked internationally respected, translational stem cell scientist Jeanne Loring for her opinions on this Olbermann TV interview and here’s what she had to say:

“Since Stemedica is known to sue people who criticize them (I hope they don’t sue me for saying that), I will be very careful about how I present the facts.  There are two things that worry me.  First, the Stemedica representative did not say that in addition to the mesenchymal stem cells they used for treating Gordie Howe, they also used cells from aborted fetuses, which is one of the reasons that the treatment was done in Mexico. I would expect that to raise some ethical concerns.
The second is that there will soon be solid evidence about whether or not mesenchymal stem cells reduce the severity of stoke.  A company called Athersys is currently finishing a Phase 2 trial that has been specifically designed to determine whether mesenchymal stem cells have any effect on stroke  https://www.clinicaltrials.gov/ct2/show/NCT01436487?term=athersys&rank=2.
Stemedica’s trial in the US is essentially a repeat of what Athersys has already done- show safety  https://www.clinicaltrials.gov/ct2/show/NCT01297413?term=stemedica&rank=1.  This is a “safe” choice for a safety trial, since it’s already been done.
There is a third issue that I want people to understand, and this is personal.  If you’ve ever had a family member have a stroke, you know that there are often periods of great improvement in the months following the stroke.  It’s not a miracle. The recovery depends on the severity and the location of the stroke in the brain  I know that it is very traumatic for a family member to deal with stroke, and I think that it would be unfortunate if anyone would exploit that traumatic situation to sell a product.”

The bottom line is that the way it stands now the Olbermann interview has not helped provide clarity on this complicated issue, so a follow up piece from Olbermann with some depth and varying opinions is much needed for balance.Olbermann Knoepfler Twitter

I engaged Olbermann on Twitter on this. Perhaps he might do a broader, probing look at stem cells in pro sports? Let’s see. I suggested it.