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Category Archives: Stem Cells

Yamanaka: 'Rejected, Slow and Clumsy'


This week's announcement of the Nobel
Prize for Shinya Yamanaka brought along some interesting
tidbits, including who was “snubbed” as well as recollections
from the recipient.

Jon Bardin of the Los Angeles Times
wrote the “snubbed” piece and quoted Christopher Scott of
Stanford and Paul Knoepfler of UC Davis about the selection issues.
Bardin's piece mentioned Jamie Thomson and Ian Wilmut as scientists
who also could have been considered for the award but were not named.
Ultimately, Bardin wrote that the award committee was looking for a
“singular, paradigm shifting discovery,” which he concluded was
not the case with Thomson or Wilmut.
How Yamanaka arrived at his research
was another topic in the news coverage, much of it dry as dust.
However, Lisa Krieger of the San Jose Mercury News began her story
with Yamanaka's travails some 20 years ago. At the time, no one was returning his phone
calls as he looked for work, and he was rejected by
50 apparently not-so-farsighted American labs.
But that job search in 1993 came only after Yamanaka
decided he was less than successful as an orthopedic surgeon,
according to an account in JapanRealTime. “Slow and clumsy” was
how Yamanaka described himself.
And so he moved on to research. But
again he reported stumbling. In this case, he found a way to reduce
“bad cholesterol” but with a tiny complication – liver cancer.
That in turn sent him on a journey to learn how cells proliferate and
develop, which led him to the work that won the Nobel Prize.
Yamanaka said his original interest in
orthopedic medicine was stimulated by his father along with the treatments
for injuries young Yamanaka received while playing rugby and learning judo. The JapanRealTime account continued,

“'My father probably still thinks in
heaven that I’m a doctor,' he said in the interview(with Asahi
Shimbun last April). 'IPS cells are still at a research phase and
have not treated a single patient. I hope to link it to actual
treatment soon so I will be not embarrassed when I meet my father
someday.'”

And then there was, of course, the much-repeated story from the researcher who shared the Nobel with Yamanaka, John Gurdon. He has preserved to this day a
report from a high school biology teacher that said the 15-year-old
Gurdon's desire to become a scientist was “quite ridiculous.”
The teacher, who is unnamed, wrote,

“If he can’t learn simple
biological facts he would have no chance of doing the work of a
specialist, and it would be a sheer waste of time, both on his part
and of those who would have to teach him.”

Source:
http://feedproxy.google.com/~r/blogspot/uqpFc/~3/7J31SRIukpg/yamanaka-rejected-slow-and-clumsy.html

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Tighter Controls on Stem Cell Grant Budgets Hits Quorum Bump


SAN FRANCISCO – A move to tighten
budget controls on grants from the $3 billion California stem cell
agency stalled Monday, but it appears that the plan is headed for
ultimate approval.

The proposal was up for consideration
by the agency's directors' Science Subcommittee, which could not act
on it after it lost its quorum.
Members of the panel generally favored
the stronger budget controls, but had questions about the specifics
of implementing the plan during closed-door reviews of grant
applications. The proposal is likely to be altered to respond to
those concerns. It would then either come back to the Science
Subcommittee or go to the full board.
The plan would make it clear to
recipients of large grants that approval of an application by the
agency's governing board does not provide a carte blanche to
researchers. Ellen Feigal, senior vice president for research and
development, said it can be “extremely difficult” for CIRM staff
to deal with budget problems in grants following board approval.
The committee also approved a plan to
speed the application process on its next disease team round, which
is aimed at driving research into the clinic. The concept proposal
for that round is scheduled to come before directors later this
month. The round will be limited to “more mature stage” research
that is close to a clinical trial, if not in one. Feigal said 10 to
15 applications are expected.
Another proposal to add more millions
to CIRM's strategic partnership program was also approved.

Source:
http://feedproxy.google.com/~r/blogspot/uqpFc/~3/EqLIk55mLu4/tighter-controls-on-stem-cell-grant.html

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Yamanaka and the Golden State


The iPierian biopharmaceutical company
in South San Francisco was quick to make a change in its web site
this morning after the Nobel Prize for medicine was announced.

Altered was the bio for one of its
scientific advisors, Shinya Yamanaka, to note that he had won the
Nobel. The bio is tucked away on the site, but it is likely that the
company, which specializes in iPS work, will figure out how to put
the news out front on its home page as well as issue a press release.
It was all part of the reaction today
in California to the Nobel for Yamanaka, who has substantial links to
the Golden State, including UCSF and the Gladstone Institutes.
Both enterprises moved with greater
deftness than iPierian. Yamanaka is a professor at UCSF and a senior
investigator at Gladstone, and the organizations quickly put together a news conference this morning that featured Yamanaka on a video
hook-up from Japan.
UCSF, which is allied with Gladstone,
issued a press release that quoted the president of Gladstone, R.
Sanders Williams, who also mentioned the California stem cell agency.
Williams said,

“Dr. Yamanaka’s story is a
thrilling tale of creative genius, focused dedication and successful
cross-disciplinary science. These traits, nurtured during Dr.
Yamanaka’s postdoctoral training at Gladstone, have led to a
breakthrough that has helped propel the San Francisco Bay Area to the
forefront of stem cell research. Dozens of labs — often supported
by organizations such as the California Institute for Regenerative
Medicine (CIRM) and the Roddenberry Foundation–have adopted his
technology.” 

CIRM, which is the state's $3 billion
stem cell effort, published an item on its blog quoting CIRM
President Alan Trounson. He said,

"There are few moments in science
that are undisputed as genuine elegant creativity and simplicity.
Shinya Yamanaka is responsible for one of those. The induced
pluripotent stem cells he created will allow us to interrogate and
understand the full extent and variation of human disease, will
enable us to develop new medicines and will forever change the way
science and medicine will be conducted for the benefit of mankind. An
extraordinary accomplishment by a genuinely modest and brilliant
scientist. He absolutely deserves a Nobel award.”

The CIRM item by Amy Adams, the
agency's communications manager, said that just five years after
Yamanaka's research,

“CIRM alone is funding almost $190
million in awards developing better ways of creating iPS cells and
using those cells to develop new therapies (the
full list of iPS grants is on our website).”

One of the recipients of CIRM's iPS
cash is the well-connected iPierian, which has taken in $7.1 million.
Yamanaka, however, has never received a grant from the agency, and
it is not known whether he ever applied since CIRM releases only the
names of researchers whose applications were approved.

Source:
http://feedproxy.google.com/~r/blogspot/uqpFc/~3/RbQ09EsO8Qc/yamanaka-and-golden-state.html

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Stem Cell Orthodoxy and Peer Review


Going against the grain can be
difficult as UC Davis stem cell scientist Paul Knoepfler learned
again in connection with his research that dealt with similarities
between cancer and iPS cells.

His “unsettling” findings troubled
some scientists who reviewed his paper prior to its publication in
September in Stem Cells and Development. (See here and here.)
As many readers know, iPS or
reprogrammed adult cells are currently a hot research avenue in stem
cell research because they avoid many of the ticklish ethical and
political problems connected with human embryonic stem cells.
Knoepfler shared his thoughts on the
publication and peer review process on his blog last week. He wrote,

“Not surprisingly...there are certain
members of the stem cell field who would rather focus away from the
ideas that iPS cells are similar in some respects to cancer.”

Knoepfler, whose research was financed
in part by the California stem cell agency, wrote,

“Once we had a manuscript together
comparing iPS cells to cancer cells, we sent it to several high
profile journals without much luck. We thought that the fact that our
data indicated that iPS cells are similar to cancer cells might make
reviewers and editors excited. We thought that the paper was novel
and thought provoking in a number of ways. At the same time I
realized the theme of the paper would be controversial. 

“I would say two general things about
the review process at the two journals that turned down the paper.
First, the reviewers at these journals were enormously helpful with
their suggestions and helped us improve the paper substantially.
Second, they were clearly very uncomfortable with the notion that iPS
cells are related in some ways to cancer so unsettled in fact that I
believe it influenced their reviews.”

At one journal, a reviewer said the
findings were either “not sufficiently novel” or “trivial.”
“Little useful insights” said another. And a third said, “many
unsettling results....”
Knoepfler commented on this blog,

“Yeah, it may be unsettling that iPS
cells share traits with cancer cells, but if that is the reality,
isn’t it important that people know that and think about it, talk
about it, and address the issue with eyes open?”

Knoepfler's item and similar comments
from other researchers that can found elsewhere on the Internet
indirectly raise questions about the California stem cell agency's process
of peer review of applications for hundreds of millions of dollars in
funding, especially in the wake of this summer's unprecedented rash of appeals of decisions by grant reviewers.
The key question is whether the agency's closed-door process reinforces orthodoxy or, in fact, is all but controlled by what
amounts to scientific conventional wisdom. Obviously, no researcher
likes to see a paper rejected or a grant denied. But the record
number of appeals at CIRM and other private complaints could well indicate
that potentially profitable proposals are receiving a less than
welcome reception behind closed doors from agency reviewers.
The agency's board itself is
hard-pressed to make such determinations. It is hamstrung by
procedures that do not permit it to expand an application directly –
only a staff-written summary. Names of applicants and institutions
are censored, although the board is required by law to discuss in
public most aspects of a research proposal. Exceptions are permitted for proprietary information. Additionally, a handful of the 29 members of the governing board do participate in the reviews, which come before final action by the board. 
Currently the agency is pushing hard to
commercialize stem cell research and fulfill at least some of the
promises to voters that were made in 2004. To do that, the agency may
well have to step outside of the normal comfort zone of the good
burghers of stem cell science.

Source:
http://feedproxy.google.com/~r/blogspot/uqpFc/~3/LITB6cXS-ZM/stem-cell-orthodoxy-and-peer-review.html

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Researcher Alert: California Stem Cell Agency Tightening Budget Oversight on Grants


Some of California's top stem cell
researchers are going to have to sharpen their spreadsheets if they
want to win money from the state's $3 billion stem cell agency.

The agency is moving to beef up
scrutiny of the high-profile, big-ticket grant applications
that it will consider during the next several years. The effort may well extend to all grant programs. The move also makes
it clear to researchers that the CIRM staff is in the driver's seat
when it comes to budgeting on research projects.
The plan was laid out this week in a memo to directors of the California Institute for Regenerative Medicine (CIRM) by Ellen Feigal, the agency's senior vice
president for research and development. She said,

“Increasing the importance of
budgetary review will encourage applicants to propose rigorous,
realistic and vetted budgets, and will further our mission to be good
stewards of taxpayer dollars. These additions will not significantly
increase the workload burden on GWG members (grant reviewers) and
explicitly acknowledge that program goals, scientific plans, accurate budgeting and prudent spending are inextricably linked.”

The proposal comes before the CIRM
directors' Science Subcommittee next Monday and would alter the
closed-door grant review process in the following manner, according
to Feigal's memo.

• “To assist GWG review,
appropriate expertise on budget and financial matters (e.g., this
could be in the form of a specialist reviewer, or can also be
assigned to a GWG reviewer with the appropriate background and
expertise), will review applications for sound budgeting and provide
comments or questions to the GWG for consideration by the reviewers
before the reviewer’s final scores are entered.
• “If the financial/budgetary
matter potentially directly impacts on the design or feasibility of
conducting the project, the GWG may consider this issue in the
scoring; otherwise, budgetary and financial issues and questions will
not contribute to the scientific score.
• “As appropriate, review summaries
sent to the ICOC (the CIRM governing board) will identify scientific
as well as budget or other issues. To the extent endorsed by the
GWG, the review summaries will also identify potential resolution
should the ICOC approve a given award with budget issues.
• “CIRM officers should be provided
explicit discretion to consider the budget comments, as well as
budget or other issues. To the extent endorsed by the GWG, the
review summaries will also identify potential resolution should the
ICOC approve a given award with budget issues.”

Feigal's memo clearly indicates that
CIRM staff has experienced push-back from recalcitrant researchers
when efforts have been made to bring costs under control. She noted that
the agency's staff examines a research project's budget during the
“prefunding” review that follows board approval. However, Feigal
said, at that stage, “It is often challenging to make substantive
changes to the budget, based on appropriateness of study activities
and costs, given the ICOC approval at a given budget amount.”
The agency has already examined some
budgets prior to board approval. One grant review in a $200
million-plus round this summer, for example, declared that costs to
prepare regulation packages had “overlap” and were “excessive,”
along with costs dealing with manufacturing and per patient expenses.
That was for a high-scoring application by Antoni Ribas of UCLA, and
he was not alone.
In her memo, Feigal listed other cases
of budgetary shortcomings in recent applications:,

• “Budget does not align with the
program deliverables and milestones. For example, the budget
includes activities not relevant to project objective(s) or that are
out of scope.
•”Budget does not contain adequate
expenses for known costs. For example, an applicant may budget
$100,000 for a GMP manufacturing run of a biologic in which it is
generally accepted knowledge that the actual expenses are typically
much greater.
•“Budget item significantly exceeds
a known cost or seems excessive without adequate justification. For
example, an applicant may propose a surgical expense of $100,000 per
patient for a procedure with Medicare reimbursement set at $15,000.
•“Cost allocations are not done
properly. For example, an applicant is developing the same
therapeutic candidate for 3 indications, and is applying for CIRM
funding for 1 of the 3, but is charging CIRM for the cost of the
entire manufacturing run.”

Initially, the budgetary review would
be used in disease team, early translational, strategic partnership
rounds, and any new rounds “as deemed appropriate.” Feigal said,
however, that “all applications for CIRM awards should be
carefully examined for budgetary appropriateness.”
Our take: This seems to be a
well-advised move, albeit one that is not likely to find favor with
researchers accustomed to loose oversight. It moves budgetary review
to an earlier stage and gives the CIRM directors a chance to weigh in
on those matters prior to approval of grants, instead of creating a
sense of entitlement on the part of recipients that may pop up
following board approval of their applications. Indeed, the plan
makes such good sense that it raises the question why it was not in
place years ago.
A final note: Feigal's memo is an
excellent example of the type of information that clarifies issues
and helps CIRM directors make the best possible decisions. It
provides some history, good evidence for a change and an explanation
of benefits. Additionally, the memo is timely, having been posted on
the CIRM website sufficiently in advance of next week's meeting to give affected parties and others time to comment
and make constructive suggestions. The memo is also far superior to
the Power Point presentations that are often submitted to the board
minus any nuanced, written discussion of the issue at hand.
Next week's meeting will be based in
San Francisco but also has teleconference locations in Irvine (2), La
Jolla, Stanford, Pleasanton, Oakland and Los Angeles where the public
and researchers can participate. The specific addresses can be found on the agenda.

Source:
http://feedproxy.google.com/~r/blogspot/uqpFc/~3/30DY8fml4zE/researcher-alert-california-stem-cell.html

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UCD’s Knoepfler’s ‘Somewhat Provocative Paper’ on iPS


UC Davis researcher Paul Knoepfler is
the rare stem cell scientist who blogs about his work as well as
writing about issues in the field.

Over the weekend, he posted an item on
what he described as a “somewhat provocative paper” published by his lab in
“Stem Cells and Development.”  He said the paper argued
that iPS cells “are very similar in some ways to cancer cells.”
Most of his item deals with the
technical details and background of the research. But at the end of
this item, Knoepfler wrote,

“So what does this mean in the big
picture? 

“I believe that iPS cells and cancer
cells are, while not the same, close enough to be called siblings. As
such, the clinical use of iPS cells should wait for a lot more study.
Even if scientists do not use iPS cells themselves for transplants,
but instead use differentiated derivatives of iPS cells, the risk of
patients getting malignant cancers cannot be ignored. 

“At the same time, the studies
suggest possible ways to make iPS cells safer and support the notion
of reprogramming cancer cells as an innovative new cancer therapy. 

“Stay tuned in the next few days for
part 2 where I will discuss what this paper went through in terms of
review, etc. to get published. It wasn’t a popular story for some
folks.”

The UC Davis press release on the
research, which was financed by the California stem cell agency and the NIH,  was picked up by several online sites, including Redorbit,
Medicalexpress and geekosystem.

Source:
http://feedproxy.google.com/~r/blogspot/uqpFc/~3/eNPFE1TC2TI/ucds-knoepflers-somewhat-provocative.html

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