Following two years working in clinical trials Dr Cocker started his PhD under the supervision of Professor Mark Johnson and Dr Nesrina Imami, studying the impact of HIV-1 infection on pregnancy related immunological changes using fluorescent cytometry and functional assays to explore natural killer, dendritic and T cell populations longitudinally.
Dr Cocker is continuing his work in HIV and other infectious diseases, and is especially focussed on how chronic infection can affect natural killer cell education, development and function.

Professional Education

  • Bachelor of Science, University Of Leeds (2012)
  • Doctor of Philosophy, Imperial College of Science, Technology & Medicine (2019)

Stanford Advisors

All Publications

  • Natural LILRB1 D1-D2 variants show frequency differences in populations and bind to HLA class I with various avidities. Immunogenetics Liu, F., Cocker, A. T., Pugh, J. L., Djaoud, Z., Parham, P., Guethlein, L. A. 2022


    Leukocyte immunoglobulin-like receptor B1 (LILRB1) is widely expressed on various immune cells and the engagement of LILRB1to HLA class I and pathogen-derived proteins can modulate the immune response. In the current study, 108 LILRB1 alleles were identified by screening the LILRB1 locus from the 1000 Genomes Phase 3 database. Forty-six alleles that occurred in three or more individuals encode 28 LILRB1 allotypes, and the inferred LILRB1 allotypes were then grouped into 9 LILRB1 D1-D2 variants for further analysis. We found that variants 1, 2, and 3 represent the three most frequent LILRB1 D1-D2 variants and the nine variants show frequency differences in populations. The binding assay demonstrated that variant 1 bound to HLA class I with the highest avidity, and all tested LILRB1 D1-D2 variants bound to HLA-C with lower avidity than to HLA-A and -B. Locus-specific polymorphisms at positions 183, 189, and 268 in HLA class I and dimorphisms in HLA-A (positions 207 and 253) and in HLA-B (position 194) affect their binding to LILRB1. Notably, the electrostatic interaction plays a critical role in the binding of LILRB1 to HLA class I as revealed by electrostatic analysis and by comparison of different binding avidities caused by polymorphisms at positions 72 and 103 of LILRB1. In this paper, we present a comprehensive study of the population genetics and binding abilities of LILRB1. The data will help us better understand the LILRB1-related diversity of the immune system and lay a foundation for functional studies.

    View details for DOI 10.1007/s00251-022-01264-7

    View details for PubMedID 35562487

  • Phosphoantigen-stimulated gammadelta T cells suppress natural killer cell-responses to missing-self. Cancer immunology research Walwyn-Brown, K., Pugh, J., Cocker, A. T., Beyzaie, N., Singer, B. B., Olive, D., Guethlein, L. A., Parham, P., Djaoud, Z. 2022


    gammadelta T cells stimulated by phosphoantigens (pAg) are potent effectors that secrete Th1 cytokines and kill tumor cells. Consequently, they are considered candidates for use in cancer immunotherapy. However, they have proven only moderately effective in several clinical trials. We studied the consequences of pAg-stimulated gammadelta T-cell interactions with Natural Killer (NK) cells and CD8+ T cells, major innate and adaptive effectors, respectively. We found that pAg-stimulated gammadelta T cells suppressed NK-cell responses to "missing-self" but had no effect on antigen-specific CD8+ T-cell responses. Extensive analysis of the secreted cytokines showed that pAg-stimulated gammadelta T cells had a pro-inflammatory profile. CMV-pp65-specific CD8+ T cells primed with pAg-stimulated gammadelta T cells showed little effect on responses to pp65-loaded target cells. By contrast, NK cells primed similarly with gammadelta T cells had impaired capacity to degranulate and produce IFNgamma in response to HLA class I-deficient targets. This effect depended on BTN3A1 and required direct contact between NK cells and gammadelta T cells. gammadelta T cell-priming of NK cells also led to a downregulation of NKG2D and NKp44 on NK cells. Every NK-cell subset was affected by gammadelta T cell-mediated immunosuppression, but the strongest effect was on KIR+NKG2A- NK cells. We therefore report a previously unknown function for gammadelta T cells, as brakes of NK-cell responses to "missing-self". This provides a new perspective for optimizing the use of gammadelta T cells in cancer immunotherapy and for assessing their role in immune responses to pAg-producing pathogens.

    View details for DOI 10.1158/2326-6066.CIR-21-0696

    View details for PubMedID 35263761

  • CD56-negative NK cells: Frequency in peripheral blood, expansion during HIV-1 infection, functional capacity, and KIR expression. Frontiers in immunology Cocker, A. T., Liu, F., Djaoud, Z., Guethlein, L. A., Parham, P. 2022; 13: 992723


    Human NK cells are usually defined as CD3-CD56+ lymphocytes. However, a CD56-CD16+ (CD56neg) lymphocyte population that displays NK-associated markers expands during chronic viral infections such as HIV-1 and HCV, and, to lesser extent, in herpesvirus infections. This CD56neg NK cell subset has been understudied because it requires the exclusion of other lymphocytes to accurately identify its presence. Many questions remain regarding the origin, development, phenotype, and function of the CD56neg NK cell population. Our objective was to determine the frequency of this NK subset in healthy controls and its alteration in viral infections by performing a meta-analysis. In addition to this, we analyzed deposited CyTOF and scRNAseq datasets to define the phenotype and subsets of the CD56neg NK cell population, as well as their functional variation. We found in 757 individuals, from a combined 28 studies and 6 datasets, that the CD56neg subset constitutes 5.67% of NK cells in healthy peripheral blood, while HIV-1 infection increases this population by a mean difference of 10.69%. Meta-analysis of surface marker expression between NK subsets showed no evidence of increased exhaustion or decreased proliferation within the CD56neg subset. CD56neg NK cells have a distinctive pattern of KIR expression, implying they have a unique potential for KIR-mediated education. A perforin-CD94-NKG2C-NKp30- CD56neg population exhibited different gene expression and degranulation responses against K562 cells compared to other CD56neg cells. This analysis distinguishes two functionally distinct subsets of CD56neg NK cells. They are phenotypically diverse and have differing capacity for education by HLA class-I interactions with KIRs.

    View details for DOI 10.3389/fimmu.2022.992723

    View details for PubMedID 36211403

  • Meta-analysis of the CD56-negative NK cell subset indicates altered functional responses and unique KIR regulation Cocker, A., Parham, P. AMER ASSOC IMMUNOLOGISTS. 2021
  • Pregnancy Gestation Impacts on HIV-1-Specific Granzyme B Response and Central Memory CD4 T Cells FRONTIERS IN IMMUNOLOGY Cocker, A. H., Shah, N. M., Raj, I., Dermont, S., Khan, W., Mandalia, S., Imami, N., Johnson, M. R. 2020; 11: 153


    Pregnancy induces alterations in peripheral T-cell populations with both changes in subset frequencies and anti-viral responses found to alter with gestation. In HIV-1 positive women anti-HIV-1 responses are associated with transmission risk, however detailed investigation into both HIV-1-specific memory responses associated with HIV-1 control and T-cell subset changes during pregnancy have not been undertaken. In this study we aimed to define pregnancy and gestation related changes to HIV-1-specific responses and T-cell phenotype in ART treated HIV-1 positive pregnant women. Eleven non-pregnant and 24 pregnant HIV-1 positive women were recruited, peripheral blood samples taken, fresh cells isolated, and compared using ELISpot assays and flow cytometry analysis. Clinical data were collected as part of standard care, and non-parametric statistics used. Alterations in induced IFNγ, IL-2, IL-10, and granzyme B secretion by peripheral blood mononuclear cells in response to HIV-1 Gag and Nef peptide pools and changes in T-cell subsets between pregnant and non-pregnant women were assessed, with data correlated with participant clinical parameters and longitudinal analysis performed. Cross-sectional comparison identified decreased IL-10 Nef response in HIV-1 positive pregnant women compared to non-pregnant, while correlations exhibited reversed Gag and Nef cytokine and protease response associations between groups. Longitudinal analysis of pregnant participants demonstrated transient increases in Gag granzyme B response and in the central memory CD4 T-cell subset frequency during their second trimester, with a decrease in CD4 effector memory T cells from their second to third trimester. Gag and Nef HIV-1-specific responses diverge with pregnancy time-point, coinciding with relevant T-cell phenotype, and gestation associated immunological adaptations. Decreased IL-10 Nef and both increased granzyme B Gag response and central memory CD4 T cells implies that amplified antigen production is occurring, which suggests a period of compromised HIV-1 control in pregnancy.

    View details for DOI 10.3389/fimmu.2020.00153

    View details for Web of Science ID 000518026700001

    View details for PubMedID 32117291

    View details for PubMedCentralID PMC7027986

  • Short Communication: Therapeutic Immunization Benefits Mucosal-Associated Invariant T Cell Recovery in Contrast to Interleukin-2, Granulocyte-Macrophage Colony-Stimulating Factor, and Recombinant Human Growth Hormone Addition in HIV-1+Treated Patients: Individual Case Reports from Phase I Trial AIDS RESEARCH AND HUMAN RETROVIRUSES Cocker, A. H., Greathead, L., Herasimtschuk, A. A., Mandalia, S., Kelleher, P., Imami, N. 2019; 35 (3): 306–9


    Mucosal-associated invariant T (MAIT) cell populations are reduced in frequency in HIV-1+ patients, and this disruption is associated with systemic immune activation. Reconstitution of MAIT frequency may benefit HIV-1-infected individuals; however, only recently has in vivo work been endeavored. Treatment with interleukin (IL)-2, granulocyte-macrophage colony-stimulating factor (GM-CSF), and recombinant human growth hormone (rhGH) immunotherapy combined with an HIV-1 vaccine in the context of antiretroviral therapy (ART) has shown to reconstitute CD4 T cell population numbers and function. In this study cryopreserved peripheral blood mononuclear cells (PBMCs) from 12 HIV-1+ patients who were undergoing a combination of HIV-1 vaccine and/or IL-2, GM-CSF and rhGH immunotherapy in conjunction with ART were analyzed to assess the potential of this treatment to promote MAIT cell proliferation. PBMCs were thawed from study baseline, weeks 2 and 48 time points, fluorescently stained for MAIT cell markers, and assessed by flow cytometric analysis. Matched pairs and intergroup results were statistically compared using appropriate methods. MAIT cell frequency was increased from baseline at 48 weeks in participants who received vaccine only, whereas individuals receiving IL-2, GM-CSF, and rhGH immunotherapy with or without vaccine did not show additional benefit. Although IL-2, GM-CSF, and rhGH treatment promotes CD4 T cell reconstitution and HIV-1-specific T cell function, it does not support MAIT cell recovery in patients on suppressive ART. Therapeutic immunization however has a positive effect, highlighting the importance of aiming for balanced promotion of T cell population reconstitution to impact on HIV-1 transmission and pathogenesis.

    View details for DOI 10.1089/aid.2018.0176

    View details for Web of Science ID 000463903000012

    View details for PubMedID 30600702

  • Enrichment of HLA Types and Single-Nucleotide Polymorphism Associated With Non-progression in a Strictly Defined Cohort of HIV-1 Controllers. Frontiers in immunology Westrop, S. J., Cocker, A. T., Boasso, A. n., Sullivan, A. K., Nelson, M. R., Imami, N. n. 2017; 8: 746


    HIV-1 controllers (HIC) are extremely rare patients with the ability to control viral replication, maintain unchanging CD4 T-cell count, and evade disease progression for extensive periods of time, in the absence of antiretroviral therapy. In order to establish the representation of key genetic correlates of atypical disease progression within a cohort of HIV-1+ individuals who control viral replication, we examine four-digit resolution HLA type and single-nucleotide polymorphisms (SNP) previously identified to be correlated to non-progressive infection, in strictly defined HIC. Clinical histories were examined to identify patients exhibiting HIC status. Genomic DNA was extracted, and high definition HLA typing and genome-wide SNP analysis was performed. Data were compared with frequencies of SNP in European long-term non-progressors (LTNP) and primary infection cohorts. HLA-B alleles associated with atypical disease progression were at very high frequencies in the group of five HIC studied. All four HIC of European ancestry were HLA-B*57+ and half were also HLA-B*27+. All HIC, including one of self-reported African ethnicity, had the HLA-Cw*0602 allele, and the HLA-DQ9 allele was present only in HIC of European ancestry. A median 95% of the top 19 SNP known to be associated with LTNP status was observed in European HIC (range 78-100%); 17/19 of the SNP considered mapped to chromosome 6 in the HLA region, whereas 2/19 mapped to chromosome 8. The HIC investigated here demonstrated high enrichment of HLA types and SNP previously associated with long-term non-progression. These findings suggest that the extreme non-progressive phenotype considered here is associated with a genetic signature characterized by a single-genetic unit centered around the HLA-B*57 haplotype and the possible additive effect of HLA-B*27.

    View details for DOI 10.3389/fimmu.2017.00746

    View details for PubMedID 28702030

    View details for PubMedCentralID PMC5484768

  • A stepwise advance out of the shadows: leading HIV to its clearance FUTURE VIROLOGY Hardy, G. D., Cocker, A. H., Imami, N. 2015; 10 (12): 1263–66

    View details for DOI 10.2217/fvl.15.100

    View details for Web of Science ID 000366551800002