Macallan D, Borghans JAM, Asquith B (in print)

Human T cell memory: a dynamic view



De Wit J, Borghans JAM, Kesmir C, van Baarle D (2016)

Editorial: Role of HLA and KIR in viral infections.

Frontiers in Immunology 7, 286.


Drylewicz J, Vrisekoop N, Mugwagwa T, de Boer AB, Otto SA, Hazenberg MD,

Tesselaar K, de Boer RJ, Borghans JAM. (2016)

Reconciling Longitudinal Naive T-Cell and TREC Dynamics during HIV-1 Infection.

PLoS One 11(3):e0152513.


van den Broek T, Delemarre EM, Janssen WJ, Nievelstein RA, Broen JC, Tesselaar K,

Borghans JAM, Nieuwenhuis EE, Prakken BJ, Mokry M, Jansen NJ, van Wijk F (2016)

Neonatal thymectomy reveals differentiation and plasticity within human naive T cells.

J Clin Invest. 126(3):1126-36.


Spits HB, Mudrikova T, Schellens IM, Wensing AM, Prins JM, Feuth T, Spierings E,

Nijhuis M, van Baarle D, Borghans JAM (2016)

The presence of protective cytotoxic T lymphocytes does not correlate with shorter lifespans

of productively infected cells in HIV-1 infection.

AIDS 30, 9-17.


Ahmed R, Westera L, Drylewicz J, Elemans M, Zhang Y, Kelly E, Reljic R, Tesselaar K,

de Boer RJ, Macallan DC*, Borghans JAM*, Asquith B* (2015)

Reconciling Estimates of Cell Proliferation from Stable Isotope Labeling Experiments.

PLoS Comput Biol. 11(10):e1004355.


Vrisekoop N, Drylewicz J, Van Gent R, Mugwagwa T, Van Lelyveld SF, Veel E, Otto SA,

Ackermans MT, Vermeulen JN, Huidekoper HH, Prins JM, Miedema F, de Boer RJ,

Tesselaar K, Borghans JAM (2015)

Quantification of naive and memory T-cell turnover during HIV-1 infection.

AIDS 29, 2071-80.


Van Lelyveld SF, Drylewicz J, Krikke M, Veel EM, Otto SA, Richter C, Soetekouw R,

Prins JM, Brinkman K, Mulder JW, Kroon F, Middel A, Symons J, Wensing AM, Nijhuis M,

Borghans JAM, Tesselaar K, Hoepelman AI and the MIRS study group (2015)

Maraviroc Intensification of cART in Patients with Suboptimal Immunological Recovery: A 48-Week,

Placebo-Controlled Randomized Trial.

PLoS One 10(7):e0132430.


Spits HB, Grijsen ML, Steingrover R, Nanlohy NM, Kootstra N, Borghans JAM, van Baarle D,

Prins JM, Schellens IM (2015)

A lower viral set point but little immunological impact after early treatment during primary HIV infection.

Viral Immunol. 28,134-44.


Westera L, van Hoeven V, Drylewicz J, Spierenburg G, van Velzen JF, de Boer RJ,

Tesselaar K, Borghans JAM (2015)

Lymphocyte maintenance during healthy aging requires no substantial alterations in cellular turnover.

Aging Cell. 14, 219-27.


Costa AI, Koning D, Ladell K, McLaren JE, Grady BPX, Schellens IMM, van Ham P, Nijhuis M,

Borghans JAM, Kesmir C, Price DA, van Baarle D (2015)

Complex T-cell receptor repertoire dynamics underlie the CD8+ T-cell response to HIV-1.

J Virol. 89, 110-119.


Schellens IM, Spits HB, Navis M, Westerlaken GH, Nanlohy NM, Coffeng LE, Kootstra N,

Miedema F, Schuitemaker H, Borghans JAM*, van Baarle D* (2014)

Differential characteristics of cytotoxic T-lymphocytes restricted by the protective HLA alleles B*27 and

B*57 in HIV-1 infection.

J Acquir Immune Defic Syndr. 67, 236-245.


Drylewicz J, Tesselaar K, Borghans JAM (2014)

T-cell homeostasis. In: Encyclopedia of AIDS, Springer New York

DOI 10.1007/978-1-4614-9610-6_207-1


Miedema F, Hazenberg MD, Tesselaar K, van Baarle D, de Boer RJ, Borghans JAM (2013)

Immune activation and collateral damage in AIDS pathogenesis.

Front Immunol. 4, 298.


Westera L, Drylewicz J, den Braber I, Mugwagwa T, van der Maas I, Kwast L, Volman T,

van de Weg-Schrijver EH, Bartha I, Spierenburg G, Gaiser K, Ackermans MT, Asquith B, de Boer RJ,

Tesselaar K, Borghans JAM (2013)

Closing the gap between T-cell life span estimates from stable isotope-labeling studies in mice and humans.

Blood 122, 2205-12.


Tak T, Tesselaar K, Pillay J, Borghans JAM, Koenderman L (2013)

What's your age again? Determination of human neutrophil half-lives revisited.

J Leukoc Biol. 94, 595-601.


Westera L, Zhang Y, Tesselaar K, Borghans JAM, Macallan DC (2013)

Quantitating lymphocyte homeostasis in vivo in humans using stable isotope tracers.

Methods Mol Biol. 979,107-31.


Koning D, Costa AI, Hoof I, Miles JJ, Nanlohy NM, Ladell K, Matthews KK, Venturi V,

Schellens IM, Borghans JAM, Kesmir C, Price DA, van Baarle D (2013)

CD8+ TCR repertoire formation is guided primarily by the peptide component of the antigenic complex.

J. Immunol. 190, 931-939.


Baltcheva I, Veel E, Volman T, Koning D, Brouwer A, Le Boudec JY, Tesselaar K, de Boer RJ,

Borghans JAM (2012)

A generalized mathematical model to estimate T- and B-cell receptor diversities using AmpliCot.


Biophys J. 103, 999-1010.


Den Braber I*, Mugwagwa T*, Vrisekoop N*, Westera L, Mögling R, De Boer AB, Willems N,

Schrijver EHR, Spierenburg G, Gaiser K, Mul E, Otto SA, Ruiter AFC, Ackermans MT,

Miedema F, Borghans JAM*, De Boer RJ*, Tesselaar K* (2012)

Maintenance of peripheral naive T cells is sustained by thymus output in mice but not humans.

Immunity 36, 288-297.

* equal first or last authorship


Van Gent R, Schadenberg AW, Otto SA, Nievelstein RA, Sieswerda GT, Haas F, Miedema F,

Tesselaar K, Jansen NJ, Borghans JAM (2011)

Long-term restoration of the human T-cell compartment after thymectomy during infancy: a role for

thymic regeneration?

Blood 118, 627-34.


Schellens IMM, Navis M, van Deutekom HWM, Boeser-Nunnink B, Berkhout B, Kootstra N,

Miedema F, Keşmir C, Schuitemaker H, van Baarle D & Borghans JAM (2011)

Loss of HIV-1 derived CTL epitopes restricted by protective HLA-B alleles during the HIV-1 epidemic.

AIDS 25, 1691-1700.



Pillay J, den Braber I, Vrisekoop N, Kwast LM, de Boer RJ, Borghans JAM, Tesselaar K,

Koenderman L (2011)

Response: the in vivo half-life of human neutrophils.

Blood 117, 6053-4.


Bloemers BLP, Bont L, De Weger R, Otto SA, Borghans JAM, Tesselaar K (2011)

Decreased thymic output accounts for decreased naive T-cell numbers in children with Down syndrome.

J. Immunol. 186, 4500-7.


Van Tilburg CM, Van Gent R, Bierings MB, Otto SA, Sanders EAM, Nibbelke EE,

Gaiser JF, Janssens-Korpela PL, Wolfs TFW, Bloem AC, Borghans JAM, Tesselaar K (2011)

Immune reconstitution in children following chemotherapy for haematological malignancies:

a long-term follow-up.

Br. J. Haematology 152, 201-210.


Schellens IM, Pogany K, Westerlaken GH, Borghans JAM, Miedema F, van Valkengoed IG,

Kroon FP, Lange JM, Brinkman K, Prins JM, van Baarle D (2010)

Immunological analysis of treatment interruption after early highly active antiretroviral therapy.

Viral Immunol. 23, 609-18.


Engram JC, Cervasi B, Borghans JAM, Klatt NR, Gordon SN, Chahroudi A, Else JG,

Mittler RS, Sodora DL, de Boer RJ, Brenchley JM, Silvestri G, Paiardini M (2010)

Lineage-specific T-cell reconstitution following in vivo CD4+ and CD8+ lymphocyte depletion

in nonhuman primates.

Blood 116, 748-58.


Pillay J, den Braber I, Vrisekoop N, Kwast LM, de Boer RJ, Borghans JAM, Tesselaar K,

Koenderman L (2010)

In vivo labeling with 2H2O reveals a human neutrophil lifespan of 5.4 days.

Blood 116, 625-7.


Ganusov VV, Borghans JAM & De Boer RJ (2010)

Explicit kinetic heterogeneity: mathematical models for interpretation of deuterium labeling of

heterogeneous cell populations.

PloS Comp Biology 6, e1000666


Van Gent R, Van Tilburg CM, Nibbelke EE, Otto SA, Gaiser JF, Janssens-Korpela PL, Sanders EAM,

Borghans JAM, Wulffraat NM, Bierings MB, Bloem AC & Tesselaar K (2009)

Refined characterization and reference values of the pediatric T- and B-cell compartments.

Clinical Immunology 133, 95-107.


Borghans JAM & Tesselaar K (2009) Be fruitful, multiply, and replenish.

Blood 113, 5369-70.


Asquith B, Borghans JAM, Ganusov VV & Macallan DC (2009)

Lymphocyte kinetics in health and disease.

Trends in Immunology 30, 182-189.


Van Gent R, Kater AP, Otto SA, Jaspers A, Borghans JAM, Vrisekoop N,  Ackermans MT,

Ruiter AFC, Wittebol S, Eldering E, van Oers MHJ,  Tesselaar K, Kersten MJ & Miedema F (2008) 

In vivo dynamics of stable chronic lymphocytic leukemia inversely correlate with somatic hypermutation

levels and suggest no major leukemic turnover in bone marrow.

Cancer Res. 68, 10137-10144.


Severins M, Borghans JAM & De Boer RJ (2008)

The role of Th1/Th2 phenotypes in T-cell vaccination: Insights from a mathematical model.

In: T-cell vaccination (J. Zhang & I.R. Cohen,  eds.), pp. 139-158.


Vrisekoop N, Van Gent R, De Boer AB, Otto SA, Borleffs JCC, Steingrover R, Prins JM, Kuijpers

TW, Wolfs TFW, Geelen SPM, Vulto I, Lansdorp P, Tesselaar K, Borghans JAM & Miedema F (2008)

Restoration of the CD4 T cell compartment after long-term highly active antiretroviral therapy without

phenotypical signs of accelerated immunological aging.

J. Immunol. 181, 1573-1581.


Schellens IMM, Borghans JAM, Jansen CA, de Cuyper IM, Geskus RB, van Baarle D &

Miedema F (2008)

Abundance of early functional HIV-specific CD8+ T cells does not predict AIDS-free survival time.

PLoS ONE 3, e2745.


Vrisekoop N, Den Braber I, De Boer AB, Ruiter AFC, Ackermans MT, Van der Crabben SN,

Schrijver EHR, Spierenburg G, Sauerwein HP, Hazenberg MD, De Boer RJ, Miedema F,

Borghans JAM & Tesselaar K (2008)

Sparse production but preferential incorporation of recently produced naive T cells in the human

peripheral pool.

Proc. Natl. Acad. Sci. USA 105, 6115-6120. 


Navis M, Schellens IMM, Van Swieten P, Borghans JAM, Miedema F, Kootstra NA, Van Baarle D

& Schuitemaker H (2008)

A nonprogressive clinical course in HIV-infected individuals expressing human leukocyte antigen B57/5801

is associated with preserved CD8+ T lymphocyte responsiveness to the HW9 epitope in Nef.

J. Infect. Dis. 197, 871-879.


Schellens IMM, Keşmir C, Miedema F, Van Baarle D & Borghans JAM (2008)

An unanticipated lack of consensus cytotoxic T lymphocyte epitopes in HIV-1 databases:

The contribution of prediction programs.

AIDS 22, 33-37.


Borghans JAM, Molgaard A, De Boer RJ & Keşmir C (2007)

HLA alleles associated with slow progression to AIDS truly prefer to present HIV-1 p24.

PLoS ONE 2, e920.


Navis M, Schellens IMM, Van Baarle D, Borghans JAM, Van Swieten P, Miedema F, Kootstra N &

Schuitemaker H (2007)

Viral replication capacity as a correlate of HLA B57/B5801-associated nonprogressive HIV-1 infection.

J. Immunol. 179, 3133-3143.


Borghans JAM & De Boer RJ (2007)

Quantification of T-cell dynamics: From telomeres to DNA labelling.

Imm. Rev. 216, 35-47.


Tsegaye A, Ran L, Wolday D, Petros B, Dorigo W, Piriou E, Messele T, Sanders E, Tilahun T,

Eshetu D, Schuitemaker H, Coutinho R, Miedema F, Borghans JAM & Van Baarle D (2007)

HIV-1 subtype C Gag-specific T-cell responses in relation to human leukocyte antigens in a diverse

population of HIV-infected Ethiopians.

J. Acquir. Immune Defic. Syndr. 45, 389-400.


Tsegaye A, Ran L, Wolday D, Petros B, Nanlohy NM, Meles H, Girma M, Hailu E, Borghans JAM,

Miedema F & Van Baarle D (2007)

Stable pattern of HIV-1 subtype C gag-specific T-cell responses coincides with slow rate of CD4+ T

cell decline in HIV-infected Ethiopians.

AIDS 21, 369-372.


Borghans JAM, Keşmir C & De Boer RJ (2007)

MHC diversity in individuals and populations

In: In Silico Immunology (Flower DR & Timmis J, editors), Springer, pp 177-195.


Borghans JAM, Bredius RG, Hazenberg MD, Roelofs H, Jol-van der Zijde EC, Heidt J, Otto SA,

Kuijpers TW, Fibbe WE, Vossen JM, Miedema F & van Tol MJ (2006)

Early determinants of long-term T-cell reconstitution after hematopoietic stem cell transplantation for

severe combined immunodeficiency

Blood 108, 763-9.


Vrisekoop N, Hazenberg MD, Miedema F & Borghans JAM (2006)

 T cell dynamics and the role of apoptosis in HIV infection.

In: Cell Death in HIV Infection (Badley AD, editor), CRC Press (Florida) pp 319-334.


Van Baarle D, Miedema F & Borghans JAM (2006)

Chronische immuunactivatie als verklaring voor CD4-T-cel-verlies bij HIV-infectie.

Tijdschrift voor Infectieziekten 3, 93-99.


Mekonnen Y, Geskus RB, Hendriks JCM, Messele T, Borghans JAM, Miedema F, Wolday D,

Coutinho RA & Dukers NHTM (2005)

Low CD4 T cell counts before HIV-1 seroconversion do not affect disease progression in Ethiopian

factory workers.

J. Inf. Dis. 192, 739-748.


Borghans JAM, Hazenberg MD & Miedema F (2005)

Limited role for the thymus in SIV pathogenesis.

Eur. J. Immunol. 35, 42-45.


Sanchez-Guajardo V, Borghans JAM, Marquez M-E, Garcia S & Freitas AA (2005)

Different competititve capacities of Stat4- and Stat6-deficient CD4+ T cells during lymphopenia-driven


J. Immunol. 174, 1178-1187.


Hazenberg MD, Otto SA, Van Rossum AMC, Scherpbier HJ, De Groot R, Kuijpers TW, Lange

JMA, Hamann D, De Boer RJ, Borghans JAM & Miedema F (2004)

Establishment of the CD4+ T-cell pool in healthy children and untreated children infected with HIV-1.

Blood 104, 3513-3519.


Van Asten L, Danisman F, Otto SA, Borghans JAM, Hazenberg MD, Coutinho RA, Prins M &

Miedema F (2004)

Pre-seroconversion immune status predicts the rate of CD4 T cell decline following HIV infection.

AIDS 18, 1885-1893.


Nobile M, Correa R, Borghans JAM, D'Agostino C, Schneider P, De Boer RJ & Pantaleo G (2004)

De novo T cell generation in patients at different ages and stages of HIV-1 disease.

Blood 104, 470-477.


De Boer RJ, Borghans JAM, van Boven M, Keşmir C & Weissing FJ (2004)

Heterozygote advantage fails to explain the high degree of polymorphism of the MHC.

Immunogenetics 55, 725-731.


Borghans JAM, Beltman JB & De Boer RJ (2004)

MHC polymorphism under host-pathogen coevolution.

Immunogenetics 55, 732-739.


Borghans JAM & De Boer RJ (2004)

Diversiteit in het immuunsysteem.

In: De Wiskundige Kat, de Biologische Muis en de Jacht op Inzicht: Verkenningen op het Grensvlak

van Wiskunde en Biologie (Heesterbeek H, Diekmann O & Metz H, editors), Epsilon uitgaven

(Utrecht), pp 23-37.


Borghans JAM, Noest AJ & De Boer RJ (2003)

Thymic selection does not limit the individual MHC diversity.

Eur. J. Immunol. 33, 3353-3358.


Hazenberg MD, Borghans JAM, De Boer RJ & Miedema F (2003)

Thymic output: a bad TREC record.

Nat. Immunol. 4, 97-99.


Borghans JAM & De Boer RJ (2002)

Memorizing innate instructions requires a sufficiently specific adaptive immune system.

Int. Immunol. 14, 525-532.


Beltman J, Borghans JAM & De Boer RJ (2002)  

Major Histocompatibility Complex: Polymorphism from coevolution.

In: Adaptive Dynamics of Infectious Diseases (Dieckmann U, Metz JAJ, Sabelis MW & Sigmund K,

eds), Cambridge University Press, pp 185-197.


Almeida AR, Borghans JAM & Freitas AA (2001) 

T cell homeostasis: Thymus regeneration and peripheral T cell restoration in mice with a reduced

fraction of competent precursors.

J. Exp. Med. 194, 591-600.


Borghans JAM & De Boer RJ (2001)

Diversity in the immune system.

In: Design Principles for the Immune System and Other Distributed Autonomous Systems (Cohen IR &

Segel L, eds), Oxford University Press, 161-183.


Keşmir C, Borghans JAM & De Boer RJ (2000)  

Diversity of human ab T cell receptors.

Science 288, 1135a.


Borghans JAM, Taams LS, Wauben MHM & De Boer RJ (1999)

Competition for antigenic sites during T-cell proliferation: A mathematical interpretation of in vitro data.

Proc. Natl. Acad. Sci. USA 96, 10782-10787.


Borghans JAM, Noest AJ & De Boer RJ (1999)  

How specific should immunological memory be?

J. Immunol. 163, 569-575.


Borghans JAM & De Boer RJ (1998)  

Neonatal tolerance revisited by mathematical modelling.

Scand. J. Immunol. 48, 283-285.


Borghans JAM & De Boer RJ (1998)  

Crossreactivity of the T-cell receptor.

Immunol. Today 19, 428-429.


Borghans JAM, De Boer RJ, Sercarz E & Kumar V (1998)

T cell vaccination in Experimental Autoimmune Encephalomyelitis: A mathematical model.

J. Immunol. 161, 1087-1093.


Borghans JAM, Dupont G & Goldbeter A (1997)  

Complex intracellular calcium oscillations: A theoretical exploration of possible mechanisms.

BioPhys. Chem. 66, 25-41.


Borghans JAM, De Boer RJ & Segel LA (1996)  

Extending the quasi-steady state approximation by changing variables.

Bull. Math. Biol. 58, 43-63.


Borghans JAM & De Boer RJ (1995)  

A minimal model for T-cell vaccination.

Proc. R. Soc. Lond. B 259, 173-178.  


De Boer RJ & Borghans JAM (1995)  

Theoretical models for T-cell vaccination.

In: T Cell Vaccination and Autoimmune Disease

(J Zhang & Raus, JCM, eds) RG Landes Company, 61-82.