Translational Research - A Basic Science
Perspective
• Translational research: translates basic science
discoveries into clinical applications, and/or uses clinical
observations to generate new research topics.
• Focus is on the integration of activities from bench to
bedside.
• Translational research is increasingly a focus of funding
agencies
• Makes it possible to expand your funding base
• Makes you eligible for new types of federal and, especially
private, grants
• Often involves new collaborations with clinical colleagues
• Can involve prospective clinical trials, or extensive use of
patient samples or information
Translational Projects
• Identify a translational opportunity - this can be a
project that involves clinical specimens
• Identify a clinical colleague with whom to work
• This can be on-site or off-site
• On-site is better for grantsmanship purposes easier to integrate. Needs to be a two-way street
• Better if the basic research plays some role in
selecting patient samples to be used - what types
of clinical specimens? Are specimens analyzed in
some way so as to rule them in or out of the
study?
• How does your research feed back into clinical
practice and the understanding of disease?
Basic Grantsmanship
• PI and a Co-PI - a joint R01
• Both individuals need to benefit and play an
active role
• Take IRB issues seriously - NIH spells out
specific pieces of information that you must
include regarding patient enrollment
• Seek advice from senior colleagues
• Prepare your grant sufficiently in advance
so that you can show it to colleagues - no
excuse for not doing this!
Expanding your funding base
• Funding diversity when starting your lab
– Get your first R01, but plan for your second
– Have someone else read your grants
– Joint R01 grants, with you as Co-PI. Generally,
you can’t get your second R01 until you
demonstrate productivity on your first. Joining
with someone on an R01 is a way to get around
this, to bring in an additional source of funding
before you obtain your second grant. It also
makes it much easier to write!
– Program projects
– Private awards and career development awards
Career Development (K) Awards
• A series of grant programs, most designed
to help young investigators, or mid career
investigators
• Many are appropriate for translational
research
• Specific requirements and guidelines may
vary from institute to institute. This can be
easily determined via web pages.
• Competition for these is not as intense as it
is for R01 and R21 grants
• Many people do not know about these
awards
K22 - NIH Career Transition Awards
• The primary objective of the K22 program is to help the
awardee develop a strong, independent research career.
This will be accomplished by supporting outstanding
postdoctoral scientists as they move to their first
academic position as assistant professors. The award
will ease the transition so the recipient can concentrate
on establishing a viable research laboratory prior to
applying for research grant support. The award is for
two years; you apply as a postdoc. If the grant is
awarded, you have 12 months to start an academic
position, at which point the grant begins. So, you take
this grant with you.
K23 - Mentored Patient-Oriented Research
• The purpose of the Mentored Patient-oriented Research
Career Development Award (K23) is to support the career
development of investigators who have made a commitment
to focus their research endeavors on patient-oriented
research. This mechanism provides support for three to five
years of supervised study and research for clinically trained
professionals who have the potential to develop into
productive, clinical investigators focusing on patient-oriented
research. Clinically trained professionals or individuals with a
clinical degree who are interested in further career
development in biomedical research that is not patientoriented, should apply for a Mentored Clinical Scientist
Career Development (K08) Award
K24 - Midcareer Investigator Award in
Patient-Oriented Research
• The purpose of the K24 is to provide support for clinicians to
allow them protected time (75%) to devote to patient-oriented
research and to act as mentors for beginning clinical
investigators. The target candidates are outstanding clinical
scientists who are actively engaged in patient-oriented
research. Candidates are generally within 15 years of their
specialty training. Candidates must be able to demonstrate
the need for a period of intensive research focus as a means
of enhancing their clinical research careers and must be
committed to mentoring the next generation of patientoriented researchers.
K25 Mentored Quantitative Research
• The K25 is meant to support investigators whose quantitative
science and engineering research has thus far not been
focused primarily on questions of health and disease.
Examples of quantitative scientific and technical backgrounds
considered appropriate for this award include, but are not
limited to: mathematics, statistics, economics, computer
science, imaging science, informatics, physics, chemistry,
and engineering. The K25 Award supports the career
development of such investigators who make a commitment
to basic or clinical biomedicine, bioengineering, bioimaging or
behavioral research. This award provides support for a period
of supervised study and research for productive professionals
with quantitative backgrounds. It is intended for investigators
from the postdoctoral level to the level of senior faculty.
Specific Aims
• One page maximum
• Should be self explanatory - tells a story,
not just bare bones specific aims
• 3-5 Specific Aims
• Straight forwards Aims with best prelim
data go first, put risky aims at the end
• Aims should talk to and build on one
another
Specific Aims - provide enough information to make
aims understandable
D1. Explore the role of the bridging sheet region in receptor binding and
virus infection. Does this region represent a conserved coreceptor binding site,
does it govern coreceptor binding affinity, and is it involved in triggering the
fusion-inducing conformational changes?
D2. Examine the relationships between Env-coreceptor affinity and virus
tropism, pathogenesis, and receptor density. We have developed technologies
needed to rigorously measure Env-coreceptor binding constants, and can now
study the relationship between this and viral tropism and pathogenicity using a
panel of well characterized primary HIV, SIV, and SHIV Env proteins.
D3. Determine how many receptor binding events are needed to activate
HIV and SIV Env trimers, and explore the consequences this has for
synergistic neutralization of HIV by different classes of entry inhibitors.
Our preliminary studies indicate that multiple receptor binding events are
needed, which in turn led us to hypothesize and subsequently demonstrate that
HIV can be synergistically inhibited by different classes of entry inhibitors.
Background and Significance
• Three page maximum
• Don’t forget Significance; I usually end this
section with a specific paragraph on
significance
• Tell what is known, what is not known, why
it is important to study what is not known,
and how your Aims will address this
• Refer to each Specific Aim, in bold face.
Background and Significance
Refer to your Specific Aims
Significance for vertical transmission. Vertical transmission of HIV results in the
infection of thousands of children every year. Although vertical transmission
frequently occurs during birth, a substantial proportion also occurs in utero. The
presence of DC-SIGN and DC-SIGNR on specific cell types in the placenta (both
maternal and fetal sides of the circulation) raises the possibility that these attachment
factors could impact this process. We do not plan to directly test this possibility in
vivo at the present time, concentrating instead on the potential role of DC-SIGN in
sexual transmission as described above. However, our in vitro studies and detailed
examination of DC-SIGN and DC-SIGNR expression may help guide future in vivo
experiments or determine if they are even warranted. For example, which specific
cell types in the placenta express DC-SIGN and DC-SIGNR (Specific Aim #4)? At
what levels are these attachment factors expressed (Specific Aim #4); and are there
differences in how viruses interact with these attachment factors (Specific Aim #2)?
If there are differences, do these correlate with specific virus types (Specific Aim
#2)? We feel that the studies proposed in this grant will provide important baseline
information that will be needed to consider this question in the future.
Preliminary Results
• 5-10 pages, in my opinion
• A critical section - B/S should convince reviewers
that you are proposing something that is worth
doing, Prelim Results should convince them that you
can actually do it
• Refer to Spec Aims, noting how specific preliminary
findings will make it possible to achieve your goals
• Identify key technologies, reagents and
collaborations; can list in Section C1
(reagents/assays)
Prelim Results - Provide a roadmap
Anticipate reveiwer’s concerns
We have generated or obtained many of reagents that will be needed to accomplish the
Specific Aims of this proposal. In addition, our long standing interests in HIV and SIV Env
structure and function, virus entry, and the humoral response to virus infection means that we
already have many of the ancillary reagents and techniques that will be required to fully
understand DC-SIGN and DC-SIGNR function and their potential roles in virus transmission
and infection in vitro and in vivo. Finally, the close-knit collaborations between our labs, other
labs at Penn, and our interest and long track-record in establishing collaborations with scientists
at other institutions means that some real synergy should be obtained in these studies. Also,
please note that the five papers on DC-SIGN and DC-SIGNR we have submitted for publication
in the last 6 months (listed in Section C11) are included as Appendix material and include much
of our Preliminary data. The Preliminary Results contains the following sections:
C1. Cloning of DC-SIGN, establishment of cell lines, and preliminary functional studies.
C2. Generation of rabbit sera and monoclonal antibodies to DC-SIGN and DC-SIGNR.
C3. Relationship between expression levels and function.
C4. Expression of DC-SIGN in vitro, detected biochemically.
C5. Expression of DC-SIGN on PBDCs, detected by FACS.
C6. DC-SIGN structure-function studies.
C7. Binding and transmission functions are dissociable.
C8. Binding to DC-SIGN alters HIV-1 Env structure.
C9. DC SIGNR expression and function.
C10. General virological and receptor reagents and assays.
C11. DC-SIGN and DC-SIGNR related publications.
Prelim Results - Refer to Spec Aims
We have found that there is considerable variability in how avidly Env proteins
from different virus strains bind to their respective coreceptors. While we have
rigorously examined binding constants for only a handful of Env proteins, it is
clear that binding affinities can range from at least 4 nM to approximately 500
nM - a variance of two orders of magnitude . Do differences in how Env
proteins interact with their coreceptors have any impact on sensitivity to entry
inhibitors? A related question concerns mechanisms by which virus can acquire
resistance to entry inhibitors - a very real concern given that entry inhibitors are
now in clinical trials. Is there any cost associated with resistance to entry
inhibitors, and can entry inhibitors be used in various combinations to limit
virus evolution? These questions will be addressed in Specific Aim #3. In our
preliminary studies, we have begun to examine how differences in Envcoreceptor interactions impact sensitivity to T20 and how viruses develop
resistance to the CCR5 antagonist TAK779. We have also begun to survey
primary virus strains for their sensitivity to a panel of entry inhibitors used
singly and in combination. Finally, we have obtained sufficient quantities of
T20 and T1249 (a more potent derivative of T20) from Trimeris, AMD3100
from Anormed, and TAK779 for the experiments described in Specific Aim #3.
Experimental Design
• Many ways to do this; different reviewers
look for different things
• If you are a younger investigator, place
more emphasis on how you will do things,
have sections in possible outcomes and
pitfalls
• Don’t build a house of cards - i.e. entire
project, or much of it, rests on a reagent that
does not presently exist
• Refer back to Prelim Results
Specific Aims - Refer back to Prelim Results
D1a. Selection of mutations and choice of Env. Initially, we will introduce 13
single amino acid substitutions in the bridging sheet region of IIIB. As shown in
Section C3, we have already gotten a good start on this project, and the specific
mutations are listed in Table 1. A potential problem with our approach is that the
HxB gp120 binds to CXCR4 with poor affinity . By contrast, HxB-V3-BaL gp120
binds well to CCR5. Thus, while it is relatively trivial to study the impact of these
mutations on CXCR4-dependent membrane fusion activity, either in the context of
cell-cell fusion or virus entry assays, it is more difficult to measure their impact on
gp120-CXCR4 binding. As discussed below, we should be able to accomplish this
goal. However, it may prove desirable to place some of these mutations into an X4
Env protein that binds to CXCR4 with high affinity, though we have not yet
identified such a protein, at least for HIV-1. This is discussed in Section D1d.
Surviving and Thriving at Penn
“Hands”
Money
-Students
-Technicians
-Postdocs
- Start-up
- Grants
The Science
- Focus; getting papers out
- Resources at Penn
- Collaborations, affinity groups
Hands - Attracting Graduate Students
• Attracting students is an important part of
building a lab
• Your disadvantages: you are new and
relatively unknown; you may not have
students in your lab yet; high faculty to
student ratio
• Your advantages: students frequently
attracted to the labs of young faculty, who
are viewed as dynamic, more hands on, more
accessible, the student sees the PI more
• Teaching gives you an opportunity to meet
students - seminar courses are more
effective than lecture courses
Hands - Attracting Graduate Students
• Consider team-teaching a seminar course
with one or more faculty members; it spreads
the work around; and it also makes for a
more dynamic and interesting class
• Be sure to give chalk talks
• When you get rotation students, work with
them - go over papers with them, talk to them
frequently
• Get involved in recruiting; see if there are
T32 grants you can join
Technicians
• There is a great pool of technicians in the
Philadelphia area - lots of excellent colleges
and universities
• Many students want to work for 1-3 years
before going to grad school or med school,
and so have a reason to do well
• Get to know your personnel person; know
the rules; give your technician feedback,
both positive and negative
• If someone is not working out, you have to
cut them lose; pay attention to the
probationary period
Diversification through collaborations
• You need senior author papers - little else matters.
• Joint publications are OK, and are helpful, but
only if you have a sufficient number of senior
author papers
• Avoid publishing with your previous mentors
• Too many joint publications with a well known,
senior scientist, is a problem, unless if you have a
sufficient number of papers that do not involve
that individual.
• However, an effective collaboration can greatly
accelerate your research, and make it easier for
you to move into new areas, giving you both
scientific and funding diversity.
Other points in getting science done
• Find an affinity group - joint lab meetings
• Educate yourself about the resources available at
Penn; core facilities; other faculty
• You have to write quickly - don’t let things drag on,
don’t wait for the perfect paper
• Go to meetings - outside letters will be important
for tenure; stay in touch with people