Altered somatic hypermutation patterns in COVID-19 patients classifies disease severity

被引：8

作者：

Safra, Modi ^{[1
,2
]}

Tamari, Zvi ^{[1
,2
]}

Polak, Pazit ^{[1
,2
]}

Shiber, Shachaf ^{[3
,4
]}

Matan, Moshe ^{[5
]}

Karameh, Hani ^{[6
]}

Helviz, Yigal ^{[7
]}

Levy-Barda, Adva ^{[8
]}

Yahalom, Vered ^{[9
]}

Peretz, Avi ^{[5
,10
]}

Ben-Chetrit, Eli ^{[11
]}

Brenner, Baruch ^{[4
,12
]}

Tuller, Tamir ^{[13
]}

Gal-Tanamy, Meital ^{[10
]}

Yaari, Gur ^{[1
,2
]}

机构：

[1] Bar Ilan Univ, Fac Engn, Bioengn, Ramat Gan, Israel

[2] Bar Ilan Univ, Bar Ilan Inst Nanotechnol & Adv Mat, Ramat Gan, Israel

[3] Rabin Med Ctr, Emergency Dept, Belinson Campus, Petah Tiqwa, Israel

[4] Tel Aviv Univ, Sackler Fac Med, Tel Aviv, Israel

[5] Baruch Padeh Med Ctr, Clin Microbiol Lab, Poriya, Israel

[6] Hebrew Univ Jerusalem, Sch Med, Jesselson Integrated Heart Ctr, Shaare Zedek Med Ctr, Jerusalem, Israel

[7] Hebrew Univ Jerusalem, Sch Med, Shaare Zedek Med Ctr, Intens Care Unit, Jerusalem, Israel

[8] Rabin Med Ctr, Dept Pathol, Biobank, Belinson Campus, Petah Tiqwa, Israel

[9] Rabin Med Ctr, Blood Serv & Apheresis Inst, Petah Tiqwa, Israel

[10] Bar Ilan Univ, Azrieli Fac Med, Safed, Israel

[11] Hebrew Univ Jerusalem, Sch Med, Shaare Zedek Med Ctr, Infect Dis Unit, Jerusalem, Israel

[12] Rabin Med Ctr, Inst Oncol, Belinson Campus, Petah Tiqwa, Israel

[13] Tel Aviv Univ, Sagol Sch Neurosci, Dept Biomed Engn, Tel Aviv, Israel

来源：

FRONTIERS IN IMMUNOLOGY | 2023年 / 14卷

关键词：

machine learning; BCR; AIRR-seq; COVID-19; somatic hypermutation; B cell; RECEPTOR REPERTOIRES; ANTIBODY-RESPONSES; CELL; SIGNATURES; TOOLKIT;

D O I：

10.3389/fimmu.2023.1031914

中图分类号：

R392 [医学免疫学]; Q939.91 [免疫学];

学科分类号：

100102 ;

摘要：

IntroductionThe success of the human body in fighting SARS-CoV2 infection relies on lymphocytes and their antigen receptors. Identifying and characterizing clinically relevant receptors is of utmost importance. MethodsWe report here the application of a machine learning approach, utilizing B cell receptor repertoire sequencing data from severely and mildly infected individuals with SARS-CoV2 compared with uninfected controls. ResultsIn contrast to previous studies, our approach successfully stratifies non-infected from infected individuals, as well as disease level of severity. The features that drive this classification are based on somatic hypermutation patterns, and point to alterations in the somatic hypermutation process in COVID-19 patients. DiscussionThese features may be used to build and adapt therapeutic strategies to COVID-19, in particular to quantitatively assess potential diagnostic and therapeutic antibodies. These results constitute a proof of concept for future epidemiological challenges.

引用

页数：12

共 49 条

[1] Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage
Aran, Dvir
Looney, Agnieszka P.
Liu, Leqian
Wu, Esther
Fong, Valerie
Hsu, Austin
Chak, Suzanna
Naikawadi, Ram P.
Wolters, Paul J.
Abate, Adam R.
Butte, Atul J.
Bhattacharya, Mallar
[J]. NATURE IMMUNOLOGY, 2019, 20 (02) : 163 - +
[2] The Future of Blood Testing Is the Immunome
Arnaout, Ramy A.
Prak, Eline T. Luning
Schwab, Nicholas
Rubelt, Florian
[J]. FRONTIERS IN IMMUNOLOGY, 2021, 12
[3] CONTROLLING THE FALSE DISCOVERY RATE - A PRACTICAL AND POWERFUL APPROACH TO MULTIPLE TESTING
BENJAMINI, Y
HOCHBERG, Y
[J]. JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY, 1995, 57 (01) : 289 - 300
[4] IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis
Brochet, Xavier
Lefranc, Marie-Paule
Giudicelli, Veronique
[J]. NUCLEIC ACIDS RESEARCH, 2008, 36 : W503 - W508
[5] Single T Cell Sequencing Demonstrates the Functional Role αβ TCR Pairing in Cell Lineage and Antigen Specificity
Carter, Jason A.
Preall, Jonathan B.
Grigaityte, Kristina
Goldfless, Stephen J.
Jeffery, Eric
Briggs, Adrian W.
Vigneault, Francois
Atwal, Gurinder S.
[J]. FRONTIERS IN IMMUNOLOGY, 2019, 10
[6] Cascella M, 2020, Statpearls
[7] V(D)J recombination, somatic hypermutation and class switch recombination of immunoglobulins: mechanism and regulation
Chi, Xiying
Li, Yue
Qiu, Xiaoyan
[J]. IMMUNOLOGY, 2020, 160 (03) : 233 - 247
[8] iReceptor: A platform for querying and analyzing antibody/B-cell and T-cell receptor repertoire data across federated repositories
Corrie, Brian D.
Marthandan, Nishanth
Zimonja, Bojan
Jaglale, Jerome
Zhou, Yang
Barr, Emily
Knoetze, Nicole
Breden, Frances M. W.
Christley, Scott
Scott, Jamie K.
Cowell, Lindsay G.
Breden, Felix
[J]. IMMUNOLOGICAL REVIEWS, 2018, 284 (01) : 24 - 41
[9] Clinical Validation of a Novel T-Cell Receptor Sequencing Assay for Identification of Recent or Prior Severe Acute Respiratory Syndrome Coronavirus 2 Infection
Dalai, Sudeb C.
Dines, Jennifer N.
Snyder, Thomas M.
Gittelman, Rachel M.
Eerkes, Tera
Vaney, Pashmi
Howard, Sally
Akers, Kipp
Skewis, Lynell
Monteforte, Anthony
Witte, Pamela R.
Wolf, Cristina
Nesse, Hans
Herndon, Megan
Qadeer, Jia
Duffy, Sarah
Svejnoha, Emily
Taromino, Caroline
Kaplan, Ian M.
Alsobrook, John
Manley, Thomas
Baldo, Lance
[J]. CLINICAL INFECTIOUS DISEASES, 2022, 75 (12) : 2079 - 2087
[10] SARS-CoV-2 reactive and neutralizing antibodies discovered by single-cell sequencing of plasma cells and mammalian display
Ehling, Roy A.
Weber, Cedric R.
Mason, Derek M.
Friedensohn, Simon
Wagner, Bastian
Bieberich, Florian
Kapetanovic, Edo
Vazquez-Lombardi, Rodrigo
Di Roberto, Raphael B.
Hong, Kai-Lin
Wagner, Camille
Pataia, Michele
Overath, Max D.
Sheward, Daniel J.
Murrell, Ben
Yermanos, Alexander
Cuny, Andreas P.
Savic, Miodrag
Rudolf, Fabian
Reddy, Sai T.
[J]. CELL REPORTS, 2022, 38 (03):

← 1 2 3 4 5 →