Table Of ContentAMPHIOXUS IMMUNITY
Tracing the Origins of Human
Immunity
Edited by
ANLONG XU
Sun Yat-sen University, Guangzhou, China
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DEDICATION
This book is dedicated to my PhD mentor Dr Harris Lewin and postdoctoral mentor
Dr Helen M. Ranney.
LIST OF CONTRIBUTORS
Xingsheng Cai
South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
Xiangru Dong
Thermo Fisher Scientific, Shanghai, China
Yuchao Feng
Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
Guangrui Huang
Beijing University of Chinese Medicine, Beijing, China
Shengfeng Huang
Sun Yat-sen University, Guangzhou, China
Jun Li
Liaocheng University, Shandong, China
Rui Li
Beijing Sinobioway Group Co., Ltd., Beijing, China
Yuxin Li
Sun Yat-sen University, Guangzhou, China
Jian Peng
Guizhou Medical University, Guizhou, China
Jie Ruan
Sun Yat-sen University, Guangzhou, China
Xin Tao
Sun Yat-sen University, Guangzhou, China
Ruihua Wang
Guangdong Provincial Hospital of Traditional Chinese Medicine
Anlong Xu
Sun Yat-sen University, Guangzhou, China
Ping Yang
GenStar Biosolutions Co., Ltd., Beijing, China
Rirong Yang
Guangxi Medical University, Guangxi, China
Dongjuan Yuan
Sun Yat-sen University, Guangzhou, China
xi
xii List of Contributors
Shaochun Yuan
Sun Yat-sen University, Guangzhou, China
Jie Zhang
DiaSys Diagnostic Systems Greater China, Shanghai, China
Tingting Zheng
Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine,
Shanghai, China
ABOUT THE AUTHOR
Anlong Xu was awarded a government scholarship
to study in the United States after his BS degree
in Biology from Zhongshan University in 1985.
He attended the University of Illinois at Urbana-
Champaign (UIUC) in September 1986 to pursue
graduate studies in immunogenetics under Dr Har-
ris Lewin’s (member of the US National Academy
of Science) supervision, and he obtained his PhD
from UIUC in 1992. Dr Xu then did his postdoc-
toral research for 2 years under the supervision of
Dr Helen M. Ranney, a professor in Medicine at the
University of California, San Diego, and member of
the US National Academy of Science and Institute
of Medicine. Dr Xu worked at the San Diego–based
Alliance Pharmaceutical Corporation from 1994 to
1996 researching new drugs. In 1996, after 10 years
of study and research work in the United States, he
joined the faculty of the Department of Biochemistry at the College of Life Sciences,
Sun Yat-sen (Zhongshan) University, his alma mater. He served as Director of the State
Key Laboratory of Biocontrol and Director of the National Engineering Center for
Marine Biotechnology, South China Sea. Dr Xu was appointed as Vice President for
Research and Development at Sun Yat-sen University in 2008 after serving as Dean of
the College of Life Sciences for 8 years. He currently is a professor of Molecular Biology
and Immunology and President of Beijing University of Chinese Medicine.
Dr Xu has published more than 150 papers in peer-reviewed international journals,
such as the New England Journal of Medicine, Nature, Nature Immunology, Nature Commu-
nications, Science Signaling, Genome Research, Journal of Human Genetics, Proceedings of the
National Academy of Sciences, Cell Research, Journal of Immunology, International Society of
Microbial Ecology Journal, Journal of Biological Chemistry, Free Radical Biology and Medicine,
European Journal of Immunology, Molecular Immunology Developmental and Comparative Im-
munology, Human Immunology, Immunogenetics, and Fish and Shellfish Immunology.
Dr Xu is currently a member of the American Association of Immunologists,
American Society for Biochemistry and Molecular Biology, American Association for
the Advancement of Science, Chinese Society of Biochemistry and Molecular Biology
and Chinese Society of Immunology. He is currently President of the Guangdong
Society of Biochemistry and Molecular Biology and Vice President of International
xiii
xiv About the Author
Society for Developmental and Comparative Immunology. He currently serves on the
Editorial Board for the following international journals: Annual Review of Animal Biosci-
ences, BMC Genomics, and Animal Biotechnology. His main research focus is the study of
the origin and evolution of the vertebrate immune system.
FOREWORD
In this book, Amphioxus Immunity, Anlong Xu covers a remarkable range of information
about this small fishlike organism and its evolutionary context. This compilation of what is
currently known about amphioxus, with a sharp focus on its immune system, is especially
timely for many reasons. The recent availability of the amphioxus genomic sequence and
its comparison with other metazoan genomes firmly establishes the phylogenetic position
of amphioxus as the representative head of the chordates. The new phylogeny tree thus
places amphioxus basal to the sister chordate lineages, tunicates, and vertebrates.
Amphioxus has single copies of the ancestral genes that originated through two
rounds of genome-wide duplication to up to four identifiable paralogous genes in jawed
vertebrates, including humans. There is still debate about whether the first round of
genome-wide duplication occurred before or after divergence of the jawless and jawed
vertebrate lineages. Nevertheless, the resultant gene redundancy undoubtedly facilitated
the evolutionary selection of new gene functions and more complicated biological sys-
tems, including those devoted to immune defense.
The competitive struggle for survival during the evolution of living forms on our planet
inevitably led to the development of a wide variety of mechanisms for recognizing and
repelling invasion by neighboring organisms. The diversity and complexity of the immune
defense systems that have been recognized in bacteria, plants, and animals defy simple clas-
sification, but they can be broadly categorized into innate and adaptive immune systems. An
important distinction between the two types of immunity is that for innate immunity, the
genes encoding recognition elements are inherited in a ready to use form by each individual
organism, whereas for adaptive immunity, the genes for the recognition receptors are inher-
ited in pieces that undergo combinatorial assembly during the differentiation of specialized
lymphoid cells. This combinatorial assembly strategy results in the generation of a very large
repertoire of clonally diverse lymphocytes, each of which has its own unique receptor as
the basis for recognition and response to a specific pathogen. Members of the lymphocyte
population are thus available to recognize and respond to specific pathogens at their first
encounter and give rise to long-lived progeny to provide specific immunological memory.
The diversity and constraints of presently known mechanisms for innate immunity is
described by Dr Xu, who also traces the evolution of the central genetic elements used
for these heritable defense systems. The unifying theme for innate immunity is the use of
germline-encoded pattern recognition receptors that can recognize molecular patterns
shared by many potential pathogens. The expression of a limited spectrum of cell surface
and intracellular pattern recognition receptors can thus be used to sense a wide variety
of potential pathogens and trigger cell-signaling cascades that lead to the activation of
genes responsible for effective defense responses.
xv
xvi Foreword
Innate immune systems are universal, but adaptive immune systems based on clon-
ally diverse lymphocytes have been defined only in vertebrates. Surprisingly, jawed and
jawless vertebrates use very different genes to encode their antigen-specific receptors,
although the lymphocytes that express them are very similar. In jawed vertebrates, com-
binatorial assembly of different immunoglobulin variable (V), diversity (D), and joining
(J) gene segments during lymphocyte differentiation in the thymus or hematopoietic tis-
sues results in the generation of highly diverse receptor repertoires for T and B lympho-
cytes. In jawless vertebrates, the combinatorial assembly of different leucine-rich-repeat
(LRR) gene segments to complete variable lymphocyte receptor (VLR) genes during
lymphocyte differentiation in thymus-equivalent or hematopoietic tissues results in the
generation of clonally diverse T- and B-like lymphocytes. The similarity between these
lymphocyte differentiation pathways in both vertebrate lineages suggests that bifurcated
lymphocyte differentiation evolved in a common vertebrate ancestor, before different
primordial genes were co-opted for modification to serve antigen recognition purposes
in the alternative adaptive immune systems of jawless and jawed vertebrates.
In this context, amphioxus is not only the best available model to gain insight into
the beginnings of vertebrate evolution, but it also provides a pivotal representative for
the study of how an adaptive immune system might have gradually emerged. Obsessed
with the daunting challenge of gaining insight into the evolutionary puzzle of how an
adaptive immune system evolved to augment pre-existing mechanisms for innate immu-
nity, Xu and his colleagues have sifted through the genomic sequences of two amphioxus
species, Branchiostoma floridae and Branchiostoma belcheri, which they sequenced, to find an
abundance of genes used in innate immunity. Although this exhaustive search does not
reveal orthologous genes for those used in the combinatorial generation of antigen-spe-
cific receptors in vertebrates, ancestral gene candidates were found for immunoglobulin
receptors and for many of the signaling elements used for activation of vertebrate lym-
phocytes. Most tantalizing is their identification of lymphocyte-like cells in the gill and
intestinal regions. These lymphocyte-like cells may be immobile and, indeed, blood in
the amphioxus circulatory system is acellular. Nevertheless, the tissue-based lymphocytes
of amphioxus respond to bacterial pathogens with an increase in size and the upregula-
tion of several genes characteristically used in vertebrate lymphocyte differentiation.
There are many interesting evolutionary principles yet to be learned from studies
in the amphioxus model, not least among them being the unfinished story about how
lymphocytes and their functions evolved. Amphioxus Immunity is filled with information
that will be useful for anyone who wishes to learn more about the origin of vertebrates
and adaptive immunity.
Max D. Cooper, MD
Georgia Research Alliance Eminent Scholar
Professor of Pathology and Laboratory Medicine
Emory University School of Medicine
Atlanta, GA, USA
PREFACE
I came to know the word immunity in Chinese for the first time when I was given a
shot of vaccine during my childhood in my hometown, a small town called Poyang
Town, named after the largest freshwater lake of China, Poyang Lake, near the middle of
Yangtze River, in Jiangxi province, China. After elementary school, middle school, and
high school in Poyang, I was admitted to Sun Yat-sen University (SYSU), my first alma
mater. At university, I had a chance to learn the basic terms of immunology, such as an-
tibody and antigen, with a major in biology. After graduating from SYSU, I was awarded
a government scholarship to study in the United States in 1985, and was eventually ad-
mitted to the PhD program of Immunogenetics at the University of Illinois at Urbana-
Champaign (UIUC) in 1986. Under Dr Harris Lewin’s supervision, I became fascinated
by the complexity and diversity of animal and human immunity, which prompted me to
question how this immunity originated and how it was formed during the evolution-
ary process. In addition to my scientific curiosity, my way of thinking about scientific
questions and conducting scientific experiments was completely established by my PhD
mentor’s hard training, which has influenced my scientific career ever since. After gradu-
ating from UIUC, my second alma mater, with both MS and PhD degrees, I was fortu-
nate to work with a world-famous physician scientist, Dr Helen M. Ranney, a professor
in the Department of Medicine, University of California San Diego (UCSD), in 1992
as her last postdoctoral student. I then went with Dr Ranney to work at a San Diego–
based pharmaceutical company, Alliance Pharmaceutical Corporation, after completing
my postdoctoral research. Dr Ranney has also had a great influence on my scientific
career, like Dr Lewin. In 1996, in consultation with these two important persons in my
scientific career, I decided to come back to China to join the faculty of the Department
of Biochemistry, College of Life Sciences.
The first thing I decided to do for my scientific research after returning to China
was to start something new that could use my scientific training in the United States and
explore new avenues in the field of immune research. I had many ideas about my new
research direction, and one of the most important for me was to understand the origin
and evolution of human immunity. However, I had no idea about which model species
to use in pursuit of this very important goal. It took me 1 year to figure out that am-
phioxus was the model organism to address my question best, and another 2 years to es-
tablish a laboratory-based aquaculture system of amphioxus and the infection model for
understanding the host immune response to infection. This made my laboratory a global
pioneer in the study of amphioxus immunity, although this species had been an iconic
model for evolutionary biology for more than 200 years. Instead of using conventional
immunological methods only, my laboratory combined traditional immune methods
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