Single Cell Sequencing and Systems Immunology

184 Pages·2015·4.772 MB·English

by  Xiangdong Wang (eds.)

Translational Bioinformatics 5
Series Editor: Xiangdong Wang, MD, PhD, Prof
Xiangdong Wang Editor
Single Cell
Sequencing
and Systems
Immunology
Translational Bioinformatics
Volume 5
Serieseditor
XiangdongWang,MD,Ph.D.
Professor of Medicine, Zhongshan Hospital, Fudan University Medical School,
China
DirectorofShanghaiInstituteofClinicalBioinformatics,(www.fuccb.org)
ProfessorofClinicalBioinformatics,LundUniversity,Sweden
AimsandScope
The Book Series in Translational Bioinformatics is a powerful and integrative resource for
understanding and translating discoveries and advances of genomic, transcriptomic, proteomic
andbioinformatic technologies intothestudy ofhuman diseases. TheSeries represents leading
global opinions on the translation of bioinformatics sciences into both the clinical setting and
descriptions to medical informatics. It presents the critical evidence to further understand the
molecular mechanisms underlying organ or cell dysfunctions in human diseases, the results of
genomic,transcriptomic,proteomicandbioinformaticstudiesfromhumantissuesdedicatedtothe
discovery andvalidationof diagnosticand prognostic disease biomarkers, essential information
ontheidentificationandvalidationofnoveldrugtargetsandtheapplicationoftissuegenomics,
transcriptomics,proteomicsandbioinformaticsindrugefficacyandtoxicityinclinicalresearch.
The Book Series in Translational Bioinformatics focuses on outstanding articles/chapters
presenting significant recent works in genomic, transcriptomic, proteomic and bioinformatic
profiles related to human organ or cell dysfunctions and clinical findings. The Series includes
bioinformatics-driven molecular and cellular disease mechanisms, the understanding of human
diseasesandtheimprovementofpatientprognoses.Additionally,itprovidespracticalanduseful
studyinsightsintoandprotocolsofdesignandmethodology.
SeriesDescription
Translational bioinformatics is defined as the development of storage-related, analytic, and
interpretivemethodstooptimizethetransformationofincreasinglyvoluminousbiomedicaldata,
and genomic data in particular, into proactive, predictive, preventive, and participatory health.
Translational bioinformatics includes research on the development of novel techniques for the
integrationofbiologicalandclinicaldataandtheevolutionofclinicalinformaticsmethodologyto
encompassbiologicalobservations. Theendproductoftranslationalbioinformaticsisthenewly
foundknowledgefromtheseintegrativeeffortsthatcanbedisseminatedtoavarietyofstakeholders
includingbiomedical scientists,clinicians,andpatients.Issues relatedtodatabase management,
administration, or policy will be coordinated through the clinical research informatics domain.
Analytic,storage-related, andinterpretivemethodsshouldbeusedtoimprovepredictions, early
diagnostics,severitymonitoring,therapeuticeffects,andtheprognosisofhumandiseases.
RecentlyPublishedandForthcomingVolumes
AppliedComputationalGenomics PediatricBiomedicalInformatics
Editor:YinYaoShugart Editor:JohnHutton
Volume1 Volume2
BioinformaticsofHumanProteomics BioinformaticsforDiagnosis,Prognosis
Editor:XiangdongWang andTreatmentofComplexDiseases
Volume3 Editor:BairongShen
Volume4
Moreinformationaboutthisseriesathttp://www.springer.com/series/11057
Xiangdong Wang
Editor
Single Cell Sequencing and
Systems Immunology
Honor editors
Xiaoming Chen
Zhihong Sun
Jinglin Xia
123
Editor
XiangdongWang
ZhongshanHospital
FudanUniversity
China
ShanghaiInstituteofClinicalBioinformatics
China
ISSN2213-2775 ISSN2213-2783 (electronic)
TranslationalBioinformatics
ISBN978-94-017-9752-8 ISBN978-94-017-9753-5 (eBook)
DOI10.1007/978-94-017-9753-5
LibraryofCongressControlNumber:2015936190
SpringerDordrechtHeidelbergNewYorkLondon
©SpringerScience+BusinessMediaDordrecht2015
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Preface
TheVolumeofSingleCellSequencingandSystemsImmunologyhastakenmore
than a year to prepare and write, due to the rapid development of science and
discovery.Thisparticularvolumebringsaspecialattentiononpracticalapplication
of single cellsequencingandsystems immunologyforclinicalresearch or human
materials-basedstudies.Ithasbeenatruelabourofprotocoldevelopment,includ-
ing methodological design and collection, practical repeatability, and handling
experience. It has been a hard time of concept definition and clarification of
systems immunology. We hope that the readers can find the link between single
cell sequencing and systems immunology, apply single cell sequencing for the
understandingofsystemsimmunology,andintegratebothtodiscovernewdisease-
specific biomarkers and therapeutic targets. The most important feature of the
Volume is to emphasize the potential of single cell biology and function in the
pathogenesis of diseases. It is a time to explore alterations of human single
cell biological function, epigenetics, metabolisms, or gene/protein networks and
interactions.The Volumeis particularlysuitable forbiomedicalstudents, practical
junior researchers, and principle investigators who are working and planning to
perform studies on single cell sequencing and systems immunology. One of the
greatestjoysincreatingthisVolumehasbeenworkingwithalloutstandingexperts,
especiallythoseyoungresearchersandscientistswhogavethisprojectnotjusttheir
timeandeffort,buttheirheartsandsouls.Theirseriousnessandhardworkdeserved
thehighestrespectandcongratulation.Idonotbelievewecancreatesuchexciting
andstimulatingVolumewithouttheirdedicationandcontributions.
China XiangdongWang
v

Contents
1 SignificanceofSingleCellSequencinginFutureMedicine............ 1
MengjiaQian, DuojiaoWu, DingZhang, JianWang,
YunfengCheng,andXiangdongWang
2 UncoveringPhenotypeswithSupercells: Applications
toSingle-CellSequencing.................................................. 11
JuliánCandia,JayanthR.Banavar,andWolfgangLosert
3 Single-CellSequencingofMicroorganisms.............................. 31
YingChenandFengpingWang
4 TheApplicationofSingle-CellSequencinginDynamic
Transcriptomes ............................................................. 41
KenianChen,XiaominDong,andJiaqianWu
5 SystemImmunologyinMetabolicResearchofDendriticCells....... 65
DuojiaoWu
6 FOXP3+ TregCellsandSystemsBiologyApproaches
toStudyingTheirFunction................................................ 73
XueruiLuo,AndyTsun,JingYang,ZuojiaChen,YayiGao,
KongchenLi,MirandaPiccioni,andBinLi
7 ”•TCellsand’“TCells................................................... 95
LingyanWang,FupingWang,JieyiShi,andXiangdongWang
8 Prolymphocyte:LymphocytesandBioinformatics ..................... 111
MengjiaQian,ClaudioSpada,andXiangdongWang
9 LymphocytesinLiverCancer............................................. 123
XiaojingXu,WilliamC.S.Cho,andJinglinXia
10 EarlyBiomarkersofHepatocyteNecrosis............................... 143
MitchellR.McGillandHartmutJaeschke
vii
viii Contents
11 ProtocolforSingleCellIsolationbyFlowCytometry.................. 155
JianWang,ZhihuiMin,MeilingJin,andXiangdongWang
12 A Simple Protocol for Single Lung Cancer Cell
Isolation-Makingthe Single CellBasedLung Cancer
ResearchFeasibleforIndividualInvestigator........................... 165
DingZhangandXiangdongWang
13 CancerBioinformatics..................................................... 175
MingyanHe,LiFeng,andJinglinXia
About the Editors
Xiangdong Wang, M.D., Ph.D., is a Distinguished
Professor of Respiratory Medicine at Fudan Univer-
sity, Director of Fudan University Center of Clinical
Bioinformatics, Deputy Director of Shanghai Respira-
tory Research Institute, Adjunct Professor of Clinical
Bioinformatics at Lund University, and Visiting Pro-
fessor of King’s College of London. He serves as a
DirectorofBiomedicalResearchCenter,FudanUniver-
sity,ZhongshanHospital.Hismainresearchisfocused
on clinical bioinformatics, disease-specific biomark-
ers, cancer immunology, and molecular and cellular
therapies.
Hisgroupintegratesclinicalinformaticswithomicsscienceandbioinformatics
to identify and validate disease-specific biomarkers and therapeutic targets in
chronic lung diseases and lung cancer. His group initially developed the mirror-
butterfly chemical structure of phosphoinositide 3-kinase inhibitor to prevent and
treat chronic lung inflammation and injury, in combination of his pharmaceutical
experienceofdrugdiscoveryanddevelopment.
In addition, Dr Wang serves as the Executive Vice President of International
SocietyforTranslationalMedicine,ChairmanofExecutiveCommitteeofInterna-
tional Society for Translational Medicine, Deputy President of Chinese National
ProfessionalSocietyofInsurance&HealthandaSeniorAdvisorofChineseMedi-
calDoctorAssociation,andDirectorofNationalProgramofDoctor-Pharmaceutist
Communication.DrWangwasappointedasthePrincipalScientist,GlobalDisease
Advisor, Medical Monitor and Director, and Chairman of Director Board in
a number of pharmaceutical companies, e.g., Astra Draco, AstraZeneca, PPT,
and CatheWill. He worked on pharmacology profiles of target identification and
validation,drugscreeningandoptimization,drugPKandPDprofile,andtranslation
between discovery and development in areas of respiratory diseases, inflamma-
tion, and cancer. He acted as the Adjunct Professor of Molecular Bioscience at
ix