Ten most frequent TCRs in the bulk 12TILs comprise >99% of the TIL population, and the neoantigens are shown to be the most dominant clones. Ten most frequent.

Slides:

Advertisements

Similar presentations

Deep sequencing of the human TCRγ and TCRβ repertoires provides evidence that TCRβ rearranges after αβ, γδ T cell commitment C.S. Carlson 1, A. Sherwood.

Advertisements

Immune profiling with high-throughput sequencing Harlan Robins 1,2 Cindy Desmarais 2, Chris Carlson 1,2 Fred Hutchinson Cancer Research Center, Seattle,

Eric S. Huseby et al, Cell (2005); Nature Immunol. (2007), compared the T cells of normal mice, with mice genetically engineered to present only one type.

Additional File 12. HeLa barcode passaging experimental results.

Socializing Individualized T-Cell Cancer Immunotherapy

GC TFH cells exhibit HIV antigen–driven clonal expansion and selection

Overview of next-generation sequencing, neoantigen prediction, and functional T-cell analyses. Overview of next-generation sequencing, neoantigen prediction,

Supplementary figure 1. Gating strategy used for FACS sorting of TIL subsets (CD3+, CD3+CD8+/-, CD3+CD8+PD-1+/-). Two representative fresh tumor samples.

Regional lymph nodes and distal extracranial metastases are not a reliable surrogate for actionable mutation in brain metastases. Regional lymph nodes.

Transcriptional activities of c-MYB and A-MYB fusion proteins.

Cytomegalovirus-specific T cells are primed early after cord blood transplant but fail to control virus in vivo by Suzanne M. McGoldrick, Marie E. Bleakley,

PD-1 and LAG-3 expression in MSI and MSS colorectal cancer specimens.

Emergence of resistance to immune checkpoint blockade is associated with elimination of mutation-associated neoantigens by LOH and a more diverse T-cell.

Applications of Immunogenomics to Cancer

Geographic distribution in situ of MSI and MSS colorectal cancer–infiltrating lymphocytes. Geographic distribution in situ of MSI and MSS colorectal cancer–infiltrating.

IHC staining of FFPE esophageal tissues in tissue microarrays (×20).

Potential clinical actionability.

Antigen-specific TCRβ clonotypes map to the TCRβ repertoire at markedly different frequencies. Antigen-specific TCRβ clonotypes map to the TCRβ repertoire.

Volume 38, Issue 2, Pages (February 2013)

Volume 4, Issue 1, Pages (January 1996)

A, relationship between weighted mean chromosome copy number and weighted Genome Instability Index (wGII). A, relationship between weighted mean chromosome.

Functions of myeloid cells.

Regions of sequence homology across dominant clones in TLR7tg animals.

CD8+ T cells from lupus-prone mice demonstrate substantial oligoclonality. CD8+ T cells from lupus-prone mice demonstrate substantial oligoclonality. (A–D)

Neoantigen-specific TCR expansion in stimulated T-cell cultures.

Peter A. Savage, Mark M. Davis Immunity

The summary page for cancer profiles.

Tetramer staining performed to determine frequencies of epitope-specific T cells after clearance of HPV16 infection but prior to isolation of T-cell clones.

Volume 12, Issue 5, Pages (May 2000)

Molecular Therapy - Oncolytics

High-throughput sequencing of the B-cell receptor in African Burkitt lymphoma reveals clues to pathogenesis by Katharine A. Lombardo, David G. Coffey,

Vaccine Adjuvants Alter TCR-Based Selection Thresholds

A B 12T Supplementary Figure 1: Characterization of the identified HLA peptides. (A) Logo of all HLA-I peptides of 8-13 amino acids in.

Sample details Number of non-synonymous mutations

Highly related T9 and T3 sarcoma cells show distinct tumor growth patterns but similar PD-L1 expression kinetics in vivo. Highly related T9 and T3 sarcoma.

Detection of neoantigen-specific T cell recognition in cancer.

Large pericentromeres colocalize more frequently with H3S10P foci than small pericentromeres. Large pericentromeres colocalize more frequently with H3S10P.

Volume 9, Issue 2, Pages (August 1998)

BRCA1 promoter methylation detected in the peripheral blood and corresponding tumor. BRCA1 promoter methylation detected in the peripheral blood and corresponding.

Methylation status of IGFBPL1 in human breast cancer.

Specificity of HOM-MEL-40/SSX2 p stimulated CD8+ T-cells.

Integrated mRNA and microRNA expression and DNA methylation clusters.

Frequent alterations identified and potential actionability.

Antigen-specific CD8+ T cells express higher levels of PD-1 in animals that received the optimized SSX2 vaccine. Antigen-specific CD8+ T cells express.

KIT mutations in GISTs. A, amino acid sequence of KIT exon 11 mutations in clinical GIST biopsies. –, amino acids that are deleted; italicized amino acids,

The differential susceptibility to CTL-induced lysis does not involve Melan-A antigen expression. The differential susceptibility to CTL-induced lysis.

Increase in proliferation and activation of immune cells in peripheral blood after NKTR-214 treatment. Increase in proliferation and activation of immune.

CDN–treated MOC1 tumors demonstrate enhanced activation of innate and antigen-specific adaptive immunity. CDN–treated MOC1 tumors demonstrate enhanced.

Comparison of the frequency of nucleotide variation in the mtDNA D-loop region between stomach and other tumor cell lines. Comparison of the frequency.

Supplementary Figure 1 A B C D r2 = 0.15

Number of identical D-loop DNA clones detected in 10 DNA clones derived from liver tumor tissues. Number of identical D-loop DNA clones detected in 10.

Gene expression profiles of T cells.

Convergent expansion in less predominant B-lineage clones.

Activation status of CD8+ T cells.

Intratumoral changes in critical lymphocyte populations and numbers after NKTR-214 treatment. Intratumoral changes in critical lymphocyte populations and.

Frequently mutated genes in colorectal cancer.

Immune checkpoint molecule expression in primary and secondary tumors following radiotherapy. Immune checkpoint molecule expression in primary and secondary.

Strategies for personalized precision immunotherapy.

A, Schematic diagram of identified splice variants of PD-L1.

Enrichment of two rare SNPs among ABC DLBCL tumors.

Defining the eTME genes.

Correlations between APOBEC expression and immune cell markers across 22 cancer types. Correlations between APOBEC expression and immune cell markers across.

Interaction of cancer spheroids with mesothelium prompts mesothelial cell clearance. Interaction of cancer spheroids with mesothelium prompts mesothelial.

Moderate-affinity vaccine antigens elicited greatest antitumor response. Moderate-affinity vaccine antigens elicited greatest antitumor response. Wild-type.

Frequency and number of KLL-specific clonotypes in tumors from patients with KLL-specific T cells in PBMCs or cultured TILs. A wedge (the length of which.

Driver pathways and key genes in OSCC

CASP8 mutations are associated with fewer CNAs and RAS family mutations. CASP8 mutations are associated with fewer CNAs and RAS family mutations. A, number.

Integrated analysis of gene expression and copy number alterations.

Characteristic gene expression patterns distinguish LCH cells from other immune cells present in LCH lesions. Characteristic gene expression patterns distinguish.

IHC staining of FFPE esophageal tissues in tissue microarrays (×20).

Presentation transcript:

Ten most frequent TCRs in the bulk 12TILs comprise >99% of the TIL population, and the neoantigens are shown to be the most dominant clones. Ten most frequent TCRs in the bulk 12TILs comprise >99% of the TIL population, and the neoantigens are shown to be the most dominant clones. Bulk TILs and five different populations isolated from two different sorting experiments were analyzed using TCR sequencing to identify neoantigen-specific clones and reactive and nonreactive T-cell populations. A, Frequency of the top-10 abundant amino acid sequences found in the bulk TILs across the different samples and the second most abundant sequence from NCAPH2. As shown in the bars, these 11 TCRs comprise 90.75%–99.94% of the productive rearrangements in all the samples. B, The table indicates the 11 TCR sequences and their frequencies in the different samples. Clones 1 and 11 are against NCAPH2 and clones 3 and 4 are against MED15. Clone 2 is found in the tetramer-negative population and mostly negative to 4-1BB, and therefore probably represents a clone that expended in the tumor but its antigen was downpresented in the tumor cells as part of the immune-editing process. Shelly Kalaora et al. Cancer Discov 2018;8:1366-1375 ©2018 by American Association for Cancer Research