SUMMARY STATEMENT 

PROGRAM CONTACT: ( Privileged Communication ) Release Date: 10/25/2010 

Application Number: 1 R21 AI094009-01 

Principal Investigator 

MCCUNE, JOSEPH M MD, PHD 

Applicant Organization: UNIVERSITY OF CALIFORNIA SAN FRANCISCO 

Review Group: IHD 

Immunity and Host Defense Study Section 

Meeting Date: 10/14/2010 RFA/PA: PA10-069 

Council: JAN 2011 PCC: I2H 

Requested Start: 04/01/2011 

Project Title: Human immune system layering and the neonatal response to vaccines 

SRG Action: Impact/Priority Score: 

Human Subjects: 30-Human subjects involved - Certified, no SRG concerns 

Animal Subjects: 10-No live vertebrate animals involved for competingappl. 

Gender: 

Minority: 

Children: 

Project

Year 

1 

2 

TOTAL 

1A-Both genders, scientifically acceptable

1A-Minorities and non-minorities, scientifically acceptable 

1A-Both Children and Adults, scientifically acceptable 

Clinical Research - not NIH-defined Phase III Trial 

Direct Costs 

Requested 

_ 

Estimated 

Total Cost 

_ 

ADMINISTRATIVE BUDGET NOTE: The budget shown is the requested budget and has not been 

adjusted to reflect any recommendations made by reviewers. If an award is planned, the costs will be 

calculated by Institute grants management staff based on the recommendations outlined below in the 

COMMITTEE BUDGET RECOMMENDATIONS section. 

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1 R21 AI094009-01 2 IHD 

MCCUNE, J 

1R21AI094009-01 MCCUNE, JOSEPH 

RESUME AND SUMMARY OF DISCUSSION: The investigator proposes in this application to test his 

hypothesis that human fetal and adult hematopoietic stem/progenitor cells (HSPC) give distinct 

lymphocyte lineages to yield a range of fetal/adult T cells ratio at birth. Neonates with a high ratio will 

generate predominant Th2 responses to routine childhood immunizations. To test this hypothesis, the 

investigator will analyze cord blood from infants and correlate this profile with vaccine response to 

hepatitis B virus (HBV). The Committee felt that the proposed work will provide new information on 

neonatal immune regulation. Although high risk, the work can provide the foundation to identify those 

newborns at risk to serious infections and to develop personalized immunization strategies relevant to 

the immune maturity status. Other strengths include the outstanding investigator; his accomplished 

collaborators; the excellent research environment and resource; the well laid-out system; the innovative 

techniques; and, the intriguing supporting data. Despite of minor issues with some approaches, the 

enthusiasm of the Committee for this application is outstanding because of its feasibility. 

DESCRIPTION (provided by applicant): The development of the mammalian immune system is 

typically thought to occur in a linear fashion, from immaturity to maturity as a function of antigen 

exposure. Previous findings in birds and in mice, however, indicate that this view is oversimplified. 

Thus, in these species, the developing immune system appears to be "layered" in a manner that is 

independent of antigen exposure, beginning as a multilineage fetal system that is replaced by an 

anatomically and biologically distinct multilineage system after birth. If so, then developmentally ordered 

and unique hematopoietic stem/progenitor cells (HSPC) could give rise to distinct lymphocyte lineages 

at different stages of development. In ongoing experiments, we have found that such immune system 

"layering" occurs in humans. Our preliminary data show that a vigorous human fetal immune response 

to exogenous antigens can be actively suppressed by antigen-specific Tregs, that these fetal Tregs are 

derived from a fetal-specific lineage of T cells, and that this lineage is generated by an HSPC that is 

distinct from that found in adults. These data suggest that the human immune system is comprised of 

two distinct waves: one generated from a "fetal" HSPC that exists in utero in the fetal liver and bone 

marrow, and another generated from a superseding "adult" HSPC that resides in the bone marrow at 

later time points. The former gives rise to an immune system that is prone to deliver a tolerogenic 

response to foreign antigens. The latter gives rise to an immune system that is more likely to generate 

an immunoreactive response (e.g., one including cytotoxic T cells and neutralizing antibodies). Given 

these findings, we hypothesize that physiologic layering of immune system ontogeny leads to a normal 

range in the ratio of fetal- to adult-type T cells at birth, with some neonates exhibiting a higher fraction 

of fetal T cells than others; and that those with a high ratio of fetal/adult T cells will generate 

predominant Th2 responses to routine childhood immunizations. These hypotheses will be addressed 

in the experiments of the following Specific Aims: (1) to determine the normal range of fetal to adult T 

cells in the umbilical cord blood of the full term neonate; and (2) to determine whether those full term 

neonates with a high ratio of fetal/adult T cells are more likely to generate a Th2-polarized immune 

response to routine childhood vaccines. Should this exploratory study reveal normal variation in the 

ratio of fetal to adult T cells at birth and should such variation be directly related to a Th2 skew after 

childhood vaccination, modalities aimed at changing this ratio more towards the adult lineage at birth 

may provide benefit to a substantial number of newborns. 

PUBLIC HEALTH RELEVANCE: These exploratory studies are relevant to public health for two 

reasons. First, they may provide proof-of- concept evidence for the existence of a range in the extent of 

immune system "layering" in human neonates. Secondly, they may demonstrate that this range is itself 

related to (and possibly causal of) differences in the ability of neonates to withstand infections and to 

respond to vaccines. 

CRITIQUE 1: 

Significance: 2 

Investigator(s): 1 
 

 

 

 

 

 

 

 

 

 

1 R21 AI094009-01 3 IHD 

MCCUNE, J 

Innovation: 1 

Approach: 1 

Environment: 1 

Overall Impact: 

The research in this application should lead to a paradigm shift in our understanding of the 

development of the neonatal immune system, particularly the shift from a tolerogenic phenotype in 

utero to a highly responsive phenotype after birth. The hypothesis is clearly presented, and the 

experiments are expected to unequivocally prove or disprove the hypothesis. Either way, the results will 

be of great interest. If the hypothesis proves to be true, it may become possible to identify those 

newborns at the highest risk for serious or life-threatening infections, and to tailor immunization 

strategies to an individual’s immune maturity status. 

1. Significance: 

Strengths 

• The limited ability of the neonatal immune system to effectively resist infections is a major cause 

of morbidity and mortality. Understanding the reasons for this would allow us to identify infants 

at the highest risk for infections, might allow us to tailor organization approaches appropriately, 

and might ultimately lead to immune modulatory approaches. 

• The clear demonstration of layering in the human developing immune system would greatly alter 

the prevailing paradigms of immune system development. 

Weaknesses 

2. Investigator(s): 

Strengths 

• The PI has a long and highly accomplished record in this field, and is exceptionally well-suited 

for these studies. 

Weaknesses 

3. Innovation: 

Strengths 

• The application of the concept of layering to the developing human immune system is 

innovative. 

• The hypothesis that temporal differences in the layering process might lead to variations in the 

balance of Th1 vs Th2 type responses is highly innovative. 

• The development of a transcriptional signature for fetal versus adult lineage T cells is highly 

innovative. 

Weaknesses 

4. Approach: 

Strengths 

• The extensive preliminary data, all of which is highly relevant to this proposal, is a clear strength 

of the application. 
 

 

 

 

 

1 R21 AI094009-01 4 IHD 

MCCUNE, J 

• The extremely clear presentation of the experimental approach is another strength. 

• The inclusion of multiple collaborators at different sites as sources for cord blood is good. 

• The well-thought-out and clear data analysis plan is a strength. 

• The overall synergy between the aims and between the sub aims is remarkable. 

• The expected results and their interpretation are clearly presented. 

Weaknesses 

5. Environment: 

Strengths 

• The environment at UCSF and the associated clinical sites is essentially perfect for this study. 

Weaknesses 

Protections for Human Subjects: 

Acceptable Risks and/or Adequate Protections 

• No concerns 

Data and Safety Monitoring Plan (Applicable for Clinical Trials Only): 

Inclusion of Women, Minorities and Children: 

G1A - Both Genders, Acceptable 

M1A - Minority and Non-minority, Acceptable 

C1A – Children Included, Acceptable 

• no concerns 

Vertebrate Animals: 

Not Applicable (No Vertebrate Animals) 

Biohazards: 

Acceptable 

• no concerns 

CRITIQUE 2: 

Significance: 1 

Investigator(s): 1 

Innovation: 1 

Approach: 2 

Environment: 1 

Overall Impact: 
 

 

 

 

 

 

 

 

 

 

 

1 R21 AI094009-01 5 IHD 

MCCUNE, J 

This is an interesting and highly translational study proposed by a seasoned investigator, proposing to 

comprehensively define the phenotypic, transcriptional and functional analyses of cord blood in 200 

infants of normal full term delivery, and to correlate this profile with vaccine response to HBV. The 

strength is the available resources and collaborators, a productive and accomplished PI as well as 

preliminary results that lend support to the proposed work. The proposed work will provide novel 

information about neonatal immune regulation that can then be correlated with vaccine response. One 

concern was the follow-up immune analysis using blood from neonates that may be difficult due to 

blood volume restrictions and parental consent. Further details in this regard would be helpful. 

1. Significance: 

Strengths 

• The proposed work is highly translational and may provide important new information regarding 

vaccine response and immune regulation in infants. 

Weaknesses 

2. Investigator(s): 

Strengths 

• Dr. McCune is a well-established and well-funded investigator in the fieldl of HIV immunology 

with a strong track record of productivity. Dr. McCune also has expertise in examining 

maternal/fetal immune regulation. Also somewhat related, he is RO-1 funded to study 

maternal/fetal transmission of HIV, relevant for this proposal. 

• There are active ongoing interactions with Drs Thyne and Burt in patient enrollment and sample 

collection. 

Weaknesses 

3. Innovation: 

Strengths 

• The approach to examine immune regulation (‘layering’) in neonates and to correlate it to 

vaccine response (and possibly other outcome in the future) is innovative. 

Weaknesses 

4. Approach: 

Strengths 

• The cord blood has been collected and most infants receive HBV immunization. There is an 

established collaboration with Dr. Thyne and involvement of Dr. Burt that facilitates the 

recruitment/sample collection process and the overall feasibility. 

• Certain transcriptional profiles for adult vs. fetal T cells have been defined based on preliminary 

results that can be applied. 

• Methods are largely established in the lab and state-of-the-art. 

Weaknesses 

• While standard phenotyping should be feasible with blood drawn from the babies at 6 and 12 

months, some estimation for overall cell need would be helpful for feasibility given that blood 

draw will be limited in neonates. As proposed, there will be standard phenotyping, proliferation 

assay with and without CD25+ T cell depletion stimulated with polyclonal activator, HepB 
 

 

 

 

 

 

 

 

 

1 R21 AI094009-01 6 IHD 

MCCUNE, J 

antigen and HepB peptides and intracellular cytokine staining for antigen-specific Th1/Th2 

cytokine response. 

• Would all parents agree to blood draws in their neonates? Would this be coordinated with other 

clinically indicated blood draws? Some feasibility and logistics consideration would be helpful in 

this regard, even if the investigators are experienced in this sort of work. 

5. Environment: 

Strengths 

• The scientific environment and resources at UCSF are outstanding. 

Weaknesses 

Protections for Human Subjects: 

Acceptable Risks and/or Adequate Protections 

Inclusion of Women, Minorities and Children: 

G1A - Both Genders, Acceptable 

M1A - Minority and Non-minority, Acceptable 

C1A – Children Included, Acceptable 

Vertebrate Animals: 

Not Applicable (No Vertebrate Animals) 

Biohazards: 

Not Applicable (No Biohazards) 

CRITIQUE 3: 

Significance: 1 

Investigator(s): 1 

Innovation: 1 

Approach: 2 

Environment: 1 

Overall Impact: 

The proposal is high risk but potentially outstanding in impact for understanding and manipulating 

immune response to childhood vaccination. Significance, investigative team, innovation and 

environment are outstanding. Minor issues with approach do not detract from overall Impact. 

1. Significance: 

Strengths 
 

 

 

 

 

 

 

 

 

 

 

1 R21 AI094009-01 7 IHD 

MCCUNE, J 

• Translating concept of “immune system layering” to evaluate the impact on immune responses 

of children to vaccination has potential long-term significance for human health. 

Weaknesses 

2. Investigator(s): 

Strengths 

• Outstanding PI and consultants. 

Weaknesses 

3. Innovation: 

Strengths 

• High risk, high reward project. 

• Identification of molecular signatures of fetal and adult HSPC derived T cells is promising. 

• Translational relevance to understanding and potentially manipulating vaccine response in 

children. 

Weaknesses 

4. Approach: 

Strengths 

• Intriguing preliminary data supporting concept, approach and feasibility. 

• Multiple sources of cord blood for analysis. 

• Well-described prospective study to track vaccine responses in context of fetal/adult T cell ratios 

in children. 

• Powered to provide sufficient evidence to support (or not) future efforts in this area. 

Weaknesses 

• Identification of a cell surface marker to evaluate along with selected gene markers would 

improve resolution. 

• The possibility that selected markers will not show co-ordinate restriction to T cells from fetal or 

adult HSPC between individuals is not discussed. 

5. Environment: 

Strengths 

• Outstanding 

Weaknesses 

Protections for Human Subjects: 

Acceptable Risks and/or Adequate Protections 

Inclusion of Women, Minorities and Children: 
 

 

 

1 R21 AI094009-01 8 IHD 

MCCUNE, J 

G1A - Both Genders, Acceptable 

M1A - Minority and Non-minority, Acceptable 

C1A - Children and Adults, Acceptable 

Vertebrate Animals: 

Not Applicable (No Vertebrate Animals) 

Biohazards: 

Acceptable 

• Human blood products, acceptable 

Budget and Period of Support: 

Recommend as Requested 

THE FOLLOWING RESUME SECTIONS WERE PREPARED BY THE SCIENTIFIC REVIEW 

OFFICER TO SUMMARIZE THE OUTCOME OF DISCUSSIONS OF THE REVIEW COMMITTEE ON 

THE FOLLOWING ISSUES: 

PROTECTION OF HUMAN SUBJECTS (Resume): ACCEPTABLE 

INCLUSION OF WOMEN PLAN (Resume): ACCEPTABLE 

INCLUSION OF MINORITIES PLAN (Resume): ACCEPTABLE 

INCLUSION OF CHILDREN PLAN (Resume): ACCEPTABLE 

COMMITTEE BUDGET RECOMMENDATIONS: The budget was recommended as requested. 

NIH has modified its policy regarding the receipt of resubmissions (amended applications). 

See Guide Notice NOT-OD-10-080 at http://grants.nih.gov/grants/guide/notice-files/NOT-OD10-080.html. 

The impact/priority score is calculated after discussion of an application by averaging the 

overall scores (1-9) given by all voting reviewers on the committee and multiplying by 10. The 

criterion scores are submitted prior to the meeting by the individual reviewers assigned to an 

application, and are not discussed specifically at the review meeting or calculated into the 

overall impact score. For details on the review process, see 

http://grants.nih.gov/grants/peer_review_process.htm#scoring.