# A combined computational and experimental approach to the evolution and role of the DNA sequence environment in targeting mutations to antibody V regions

> **NIH NIH R01** · ALBERT EINSTEIN COLLEGE OF MEDICINE · 2020 · $38,074

## Abstract

Project summary
There is a fundamental gap in our understanding of how mutations are preferentially targeted to the variable
(V) regions of the Immunoglobulin (Ig) loci during somatic hypermutation (SHM). The persistence of this gap
has limited our understanding of the mutagenic mechanisms involving activation-induced deaminase (AID)
in the immune response and in the role of AID in mis-targeting mutations leading to B-cell lymphomas and
other cancers. The long-term goal of the proposed research is to understand the global targeting of
mutations in immunity that are required to protect us from infections. As high-throughput data from human
antibody immune responses became available, it provided us with new opportunities to generate
hypotheses to explain the underlying mechanisms of SHM. We now propose to generate further hypotheses
using computational models applied to additional databases and to validate these hypotheses using cellular
and animal experiments. Our objective is to understand what directs SHM across the many human Ig heavy
chain V-regions. Our central hypothesis is that the V-region SHM process is highly dependent on a DNA
sequence signature(s) that drives mutations in a largely deterministic fashion. This hypothesis is supported
by our preliminary results using human in vivo data from a few human V region genes and has begun to be
validated using independent databases and experiments in human B cell lines. The rationale is that
evaluations of computational data based upon biological mechanisms, together with appropriate biological
experiments, will reveal the key differences between IGHV regions (IGHV 3-23, 4-34, 1-18, 1-02, etc.) that
lead to the dominance of each of those V regions in the responses to medically important antigens. Our
hypothesis will be tested by pursuing two specific aims: 1) identify the extent to which a DNA signature
determines the mutation process in four individual human IGHV genes that are important in disease
responses; 2) examine the relationship between AID hotspots and Polη hotspots across all the other human
V region genes, thus rigorously defining a mutation targeting signature. Both aims will also entail studying
human V region genes and modifications of them in human cell lines and in mice expressing a human V
region to further confirm the signature and identify molecular mechanisms in vivo. Our approach is
innovative because the computational models we are proposing will be mechanistically motivated focusing
on the interaction between AID and Polη hotspots, thus testing molecular mechanisms as opposed to
classic statistical models using whole V region sequences that ignore the underlying biology. In addition, to
focus on mechanisms we will leverage new high-throughput data from human V regions that have not
undergone antigen selection. Our results will be highly relevant to human IgV repertoire analyses from
immune responses that are currently hard to interpret and will help future vaccine and the...

## Key facts

- **NIH application ID:** 10090262
- **Project number:** 3R01AI132507-04S1
- **Recipient organization:** ALBERT EINSTEIN COLLEGE OF MEDICINE
- **Principal Investigator:** Thomas MacCarthy
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $38,074
- **Award type:** 3
- **Project period:** 2018-03-01 → 2020-10-19

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10090262

## Citation

> US National Institutes of Health, RePORTER application 10090262, A combined computational and experimental approach to the evolution and role of the DNA sequence environment in targeting mutations to antibody V regions (3R01AI132507-04S1). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10090262. Licensed CC0.

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