Research

Immunogenetics

Every individual harbours a vast and unique repertoire of immune receptors (T-cell receptors and B-cell receptors) which discriminate, at the molecular level, self from non-self. The structural diversity of the T-cell receptor (TCR) that is necessary for recognizing diverse antigens is generated mainly by stochastic shuffling of the large number of short DNA segments that comprise TCR genes.  Although the central importance of T cells in adaptive immunity has been well established for decades,  the actual number and diversity of T cells that exist in an individual (i.e. the T-cell repertoire), how this changes in response to immune challenge, and how it varies from one individual to the next has remained unknown, and subject to much speculation.  We applied deep sequencing to T-cell repertoire analysis to obtain a first glimpse of repertoire diversity at the ultimate resolution of individual clonotypes (Freeman et al., Genome Res. 2009).  Currently, we are using these methods to explore the role of T cells in cancer, and how to enhance the anti-cancer immune response. We are particularly focussed on developing new sequence based approaches to T cell antigen discovery and characterization.

Synthetic immunology

Cancer immunotherapies using engineered autologous T-cells have shown remarkable efficacy against some cancer. We are engineering T cells to selectively deliver modified cytotoxic payloads and pro-drug activators, for the purpose of enhanced tumor cell killing and overcoming immune resistance.

Metagenomics - Infectious agents in Cancer

A substantial proportion (at least 15%) of the global cancer burden is attributable to known infectious agents, such as HPV, HBV and H.pylori.  It is possible that infectious agents may have a still greater role in cancer etiology, but traditional methods for finding them have limited sensitivity.  We find pathogens by their sequence signatures in human tissues, using genomic methods. Our application of these methods to colorectal carcinoma identified a strong link to the emerging pathogen Fusobacterium nucleatum.  Cancer-associated infectious agents are of potential utility as targets for vaccination, treatment and prevention.  

Cancer Genomes

We are using deep sequencing and novel computational methods to identify the spectrum of somatic mutations in various cancers, with a particular focus on tumor evolution and the identification of antigens for cancer vaccines.  

While most tumor mutations are sporadic, some hotspot mutations at seen in certain cancers at high frequency.  We are systematically assessing the most highly recurrent cancer mutations for their immunogenicity using a combination of mass spectrometry, flow cytometry and cellular immunoassays. We are optimizing procedures of isolating, expanding, activating, and redelivering these mutation-reactive T cells as targeted immunotherapies.

Holt Research Lab

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Selected Publications

189 total publications 1996-2019 | 78,229 total citations | Web of Science H-Index 69, Google scholar H-index 80 as of January 24, 2019 | Clarivate Analytics 2018 Highly Cited Researchers list (top 1% of Web of Science cited researchers for field & year)

The Cancer Genome Atlas Research Network. Genomic Classification of Cutaneous Melanoma. Cell. 2015 Jun 18;161(7):1681-96

Gibb EA, Warren RL, Wilson GE, Brown SD, Robertson G, Morin GB and Holt RA.  Activation of an endogenous retrovirus-associated long non-coding RNA in human adenocarcinoma.  Genome Medicine.  2015 Mar 5;7(1):22.

Sharma G and Holt RA. T-cell epitope discovery technologies. Human Immunology. 2014 Jun;75(6):514-519.

Brown SD, Warren RL, Gibb E, Martin SD, Nelson BH, Holt RA.  Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival.  Genome Research. 2014 May;24(5):743-50.

Wick D, Webb JR, Nielsen JS, Martin S, Kroeger DR, Milne K, Castellarin M, Twumasi-Boating K, Watson PH, Holt RA, Nelson BH.  Surveillance of the tumor mutanome by T cells during progression from primary to recurrent ovarian cancer.  Clinical Cancer Research. 2014 Mar 1;20(5):1125-34.

Woodsworth DJ, Castellarin M, Holt RA.  Sequence analysis of T-cell repertoires in health and disease.  Genome Medicine. 2013 Oct 30;5(10):98.

Watson CT, Steinberg KM, Huddleston J, Sudmant P, Warren RL, Malig M, Schein J, Willsey JA, Joy JB, Scott JK, Graves, Wilson RK, Holt RA, Eichler EE, Breden F.  Complete haplotype sequence of the human immunoglobulin heavy-chain variable, diversity, and joining genes and characterization of allelic and copy-number variation.  American Journal of Human Genetics.  2013 Apr 4;92(4):530-46.

Warren RL, Choe G, Freeman DJ, Castellarin M, Munro S, Moore R, Holt RA.  Derivation of HLA types from shotgun sequence datasets.  Genome Medicine. 2012 Dec 10;4(12):95.

Castellarin M, Milne K, Zeng T, Tse K, Mayo M, Zhao YJ, Webb JR, Watson PH, Nelson BH, Holt RA.  Clonal evolution of high-grade serous ovarian carcinoma from primary to recurrent disease.  Journal of Pathology. Epub ahead of print, 21 September 2012

The Cancer Genome Atlast Network.  Comprehensive molecular characterization of human colon and rectal cancer.  Nature.  2012 Jul 18; 478(7407):330-7.

Castellarin M, Warren RL, Freeman JD, Dreolini L, Krzywinski M, Strauss J, Barnes R, Watson P, Allen-Vercoe E, Moore RA, Holt RA.  Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Research. 2012 Feb;22(2):299-306.

Moore RA, Warren RL, Freeman JD, Gustavsen JA, Chenard C, Friedman JM, Suttle CA, Zhao Y, Holt RA. The sensitivity of massively parallel sequencing for detecting candidate infectious agents associated with human tissues.  PLoS One. 2011;6(5):e19838.

Warren RL, Freeman JD, Zeng T, Choe G, Munro S, Moore R, Webb JR, Holt RA. Exhaustive T- cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes. Genome Research. 21(5):790-7. 2011

Gardy JL et al. Whole Genome Sequencing and Social Network Analysis of a Tuberculosis Outbreak. New England Journal of Medicine. 364(8):730-9. 2010

Jones SJM et al. Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biology. 9;11(8):R82. 2010

Mead CL, Kuzyk MA, Moradian A, Wilson GM, Holt RA, Morin GB. Cytosolic protein interactions of the schizophrenia susceptibility gene dysbindin. Journal of Neurochemistry. 113(6):1491-1503. 2010

Freeman JD, Warren RL, Webb JR, Nelson BH, Holt RA. Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. Genome Research. 19(10):1817-18124. 2009.

Horspool DR, Coope RJ and Holt RA. Efficient assembly of very short oligonucleotides using T4 DNA Ligase. BMC Research Notes. 3(1):291. 2010

Holt RA et al. Rebuilding microbial genomes. Bioessays. 29: 580-590. 2007.

Warren RL, Sutton GG, Jones SJM and Holt RA. Assembling millions of short DNA sequences using SSAKE. Bioinformatics. 23: 500-501. 2007.

Wilson GE, Flibotte S, Missirlis PI, Marra MA, Jones S, Thornton K, Clark AG and Holt RA. Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla.  Genome Research. 16:173-181. 2006.

Marra MA, Jones SJ, Astell CR, Holt RA  et al., The Genome Sequence of the SARS-Associated Coronavirus.  Science. 300:1399-1404. 2003.

Holt RA et al.,The Genome Sequence of the Malaria Mosquito Anopheles gambiae. Science. 298:129-149. 2002.

Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA et al., The Sequence of the Human Genome. Science. 291:1304-1351. 2001.

Adams MD, Celniker SE, Holt RA et al. The Genome Sequence of Drosophila melanogaster.  Science. 287(5461):2185-2195. 2000

Robert Holt's complete publications list including selected links to full text articles.