The Popular Science of Stem Cells

Niles Interview Part 2

Earlier this year we published the first half of an interview with my longtime friend, colleague, and Etaluma Co-Founder, Dr. Walter (Lane) Niles. In the first half we discussed the recent paradigm shift in understanding the defects in neurodegenerative diseases and psychiatric disorders being much farther upstream than we may have previously believed. 

In Part 2 of the interview, I explore more popular science and politics of stem cell research.

Dr. Niles is a visiting researcher in Evan Snyder’s lab at the Sanford Burnham Prebys Medical Discovery Institute in La Jolla, CA where he focuses on regulation of chemosensitivity by neural stem cells during their migratory attraction toward loci of neuropathology. This interview marks the 5th anniversary of his publication entitled “Growth Dynamics of Fetal Human Neural Stem Cells” which discussed research that revealed critical factors and aspects of neural stem cell behavior during in vitro culture necessary for successful growth. Niles WD, Wakeman DR etc. and Snyder, EY (2013); Stem Cells Handbook, Sell, S (Ed), Springer Science+Business Media, New York, 75-89.

Me: As a person employed in the life sciences, I’m curious how this field has progressed since the California funding in response to the Bush administration regulations? How have the different stem cell types, i.e. fetal, umbilical, iPSC, etc. gained or lost popularity?

Dr. Niles: The field has progressed immensely. California voters approved an incredible impetus to move forward on all fronts. On a practical level, Prop 73 not only funded a substantial R&D program here in state, but also has spurred other states to enact their own grant programs – the New York Stem Cell Foundation immediately comes to mind. But Connecticut, Maryland, and New Jersey have set up their own state-level agencies.

At the clinical level – what was sold to the voters and what the voters expect – I think that a lot of basic research has been driven to produce clinical trial candidates. Locally, we are well aware through the news media of the various research programs surrounding Parkinson’s Disease that are aiming for and getting very close to full-scale (Phase III) human trials. And, it looks like UCSD has had some great success in addressing spinal cord injury. And Dr. Snyder has a research program focusing on ALS, others are working on various retinopathies, and, of course, our local company Viacyte has an established project to use stem-cell derived insulin secreting cells encapsulated in an immunologically resistant package to treat Type I diabetes. I have worked on projects attacking glioblastoma. While many would argue that these are essentially research programs still far away from the clinic – I would rejoin that it is impossible to plan science like a business project – many discoveries arise serendipitously in basic research that immediately offer clinical relevance. A few examples – discovery that some Herpes and Measles viruses kill cancer cells has opened a previously undiscovered avenue for cancer therapeutics. Similarly, Catriona Jamieson’s work on understanding stem cell mechanisms that sustain chronic myeloid leukemia by activating the blast crisis – work at the fundamental levels of receptor-mediated control of post-transcriptional modification of key metabolic regulators – has led to development of a small-molecule therapeutic in Phase I trials now.

I would like to emphasize that clinical trials here are extremely important to advancing therapy development. CIRM has enacted the Alpha Clinics to enable ordinary people to participate in clinical trials of these potential therapies. They can be found on the CIRM website, and I would encourage all who are in need to examine them.

Although CIRM has been tightly focused on therapeutic advancement, I think that the greatest advances have been in basic biology. For example, we are much further along in understanding how human babies develop from fertilized zygotes. In fact, we even understand a lot more about what happens at fertilization and how it progresses to the first cell division. We are much closer to unraveling the mysteries of how and when cells migrate around during development, and what can cause these processes to go wrong. And we are closing in on mechanisms of brain development that underlie mental disorders – which are often difficult to diagnose. I am especially impressed with how more and more is being discovered about how the brain develops, how cells become committed to various types of neurons and other brain cells, and how development is organized. It is important to realize that basic biology of stem cells will help in understanding how our brains work.

As for the Bush era prohibitions, they were relaxed a bit under Obama, but it appears as though the target of interest by opponents now is fetal tissue. All of biology has always operated under a moral/ethical cloud and it is no different now. While fetal tissue is a source of stem cells, it also provides the ability to prove that the artificial means of producing stem cells – such as induced pluripotent stem cells or transdifferentiated tissue cells – are, in fact, doing just that and not irrelevant. It has become fashionable to argue that scientists stating that they are apolitical or that their work has no political relevance are simply doing the bidding of the status quo. It may be the case, however, that scientists are just as or more than morally conflicted as the absolutists, but may simply be able to appreciate the arguments of both sides. This does not include the basic mercenaries who will adopt any position for its remuneration.

I think just about all types of toti-, pluri-, and multipotent cells are of interest. A very popular cell now is an end- or close-to-end stage tissue cell differentiated from either a traditional embryonic stem cell isolated from the blastula’s inner cell mass or an induced pluripotent cell derived from skin or blood. Differentiation procedures are an area that has been greatly improved by both the Yamanaka process of inducing pluripotency and its myriad forms (e.g., viral, plasmid, RNA) and the Jaenisch approach of transdifferentiating a fibroblast or leukocyte directly to a terminal or other desired cell type.

Me: What are the important landmarks in the IP landscape?

Dr. Niles: The IP landscape is very broad in biology. It is also illustrative of the many pitfalls of protecting intellectual property – classic Newton’s 3rd Law. For example, the WARF patents of Thompson’s human embryonic stem cells can be said to have spurred the discovery by Yamanaka of induced pluripotency, which is a convenient bypass of a difficult situation given the aggressiveness by which WARF – which technically is a non-profit alumni association – defended its exclusivity. The landscape also covers such issues as gene editing. CRISPR-Cas9 has been in the news lately. What the IP has done is set a lot of people off looking either for other Cas-like enzymes in nature (bacteria), mutating various Cas sequences to obtain a desired outcome, or revisiting some earlier methods, such as zinc-finger nucleases, and TALENs. Other areas of IP are growth media and supplements – but even here, the limitations of IP are apparent, in that even though a medium composition may be claimed, a lot of compositions remain undisclosed as “trade secrets”, with an uncertain relationship regarding the required extent of disclosure to regulatory authorities.

Me: What are some examples of approved stem cell therapies?

Dr. Niles: The approved stem cells therapies at present are fairly limited and in certain therapeutic areas. It is sort of illustrative of the state of clinical medicine, few actual areas, but lots of different options within each area.

I would say the major area is related to the old bone marrow transplant—which came online during the late 1950’s – as a therapy for replacing the blood system of patients whose blood cells have been wiped out by radiation or chemotherapy. Today, there is much more “fine structure” to marrow replacement. In other words, instead of replacing the whole bone marrow, what is done is to introduce a particular type of hematopoietic cell that can reconstitute the entire blood and immune system or just a part of it. Most of these products are derived from allogenic umbilical cord blood. I would say that hematopoietic stem cells are among the best understood multipotent cells precisely because of this clinical importance.

Dermatology is another therapeutic area benefitted by stem cells. Much of this work derives from some old US Army medical grants for better methods of skin grafting. These products have evolved from biocompatible 2-dimensional meshworks containing keratinocytes and fibroblasts, to understanding that many of the fibroblasts were actually mesenchymal stem cells capable of producing growth factors necessary to activate skin repair. Similar work is appearing for arthritis – chondrocytes (cartilage-producing cells) attached to collagen meshes are inserted into problem joints to reconstitute the synovial membrane. These products too probably contain chondrocyte progenitors to sustain the chondrocytes, and the advantage is they are autologous in origin, obviating the need for immunosuppression.

Me: What is the next big breakthrough on the horizon?

Dr. Niles: A big breakthrough will come in understanding how transcribed but untranslated RNAs appear to coordinate gene expression at multiple levels. This is just a glimpse into how we are just beginning to understand how the whole reductionist-derived understanding of bits and pieces of molecular and cellular biology fit together into an integrated system. My predictions for breakthroughs are:

(i) greater understanding the proteasome and its role in diseases leading to development of therapeutic approaches for diseases associated with abnormal protein expression or aggregation.

(ii) understanding Alzheimer’s disease (AD) biology more upstream at earlier intervention points – Larry Goldstein at UCSD has shown aberrant axonal transport in cultured neurons derived or engineered to have AD-suspected genotypes. Given the complete lack of understanding of how APP and axonal transport interact – and the abysmal clinical experience with targeting APP post-expression – this may be a way in. As axonal transport required microtubules, the tau-opathies found in AD and other neurodegenerative diseases, looking more upstream mechanistically may be the needed approach.

(iii) higher-resolution imaging of cell activity during behavior in living organisms.

(iv) computation of inherent disordered protein structures and rational design of specific kinase inhibitors

(v) mapping a human neural circuit

Me: How many passages are possible? Are stems cells a reagent in a bottle yet? and is there chemically defined media available for most?

Dr. Niles: I have found that the fetal human NSCs we use can be passaged a great many times (I have gone up to 63 passages) without entering senescence, beginning to differentiate, or dying, and the cells retain their original genotype, i.e., SNP profile. One of my goals is to develop NSCs as a reagent in a bottle, much like the hematopoietic and mesenchymal cells are today. In the clinical trials ongoing with NSCs, they have effectively been standardized such that a cryovial of cells is a standard dose.

We have been using chemically-defined (xeno-free) media for about 20 years. The original serum-free medium was DMEM containing double the typical amount of glucose with a supplement of 7 factors (such as insulin and transferrin) named N2, developed by Bottstein and Sato. Dr. Snyder developed the first serum-free medium for NSCs based on this work, and today, we use a special medium derived from his work, comprising Neurobasal medium with a retinoic acid-free B27 supplement. The Neurobasal is a minimal DMEM/F12 medium, missing excitotoxic amino acids such as glutamate and aspartate (which would kill cells acquiring neuron-like phenotypes), eliminating most of the trace metals (which are an increasing feature in many media designed for particular stem cells), and adding basic anabolites for nucleoside and lipid biosynthesis. This medium increases yields above serum-containing media by a factor of 2.

Me: Fluorescence seems to be off limits for patient autologous transplant?

Dr. Niles: Fluorescence and luminescence are generally regarded as unsuitable for autologous grafts because of the necessity to introduce a fluorophore into the cells, whether an organic molecule or fluorescent protein, or an exogenous luminophore, in the case of a chemiluminescent probe. However, I think the real issue is the inefficiency of fluorescence, luminescence or other light-based signals relative to other methods of detection. For example, a photon emitted at a red wavelength has 1/30-th the energy of the beta-ray electron emitted by a 14C atom. By contrast, stronger emitters along the electromagnetic spectrum seem much more conducive to in vivo monitoring. For example, thyroid tumor cells have been transduced with a gene for a sodium-iodide co-transporter in situ to induce uptake of toxic 125I into the tumor, and gamma-ray imaging has been used to follow both the incorporation of radionuclide into the tumor and subsequent elimination of the tumor as the localized radiation kills it. The more energetic signal simply means that fewer decay events are required for detection.