Specific TCR V–J gene segment recombinations leading to the identification pan-V–J CDR3s associated with survival distinctions: diffuse large B-cell lymphoma

Cios, Konrad J.; Huda, Taha I.; Eakins, Rachel A.; Mihyu, Moody M.; Blanck, George

doi:10.1080/10428194.2021.2020781

Cited by 7 publications

(3 citation statements)

References 42 publications

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“…Multivariate analyses were conducted as described [27]. Briefly, the analysis was conducted using the IBM Statistical Package for the Social Sciences (version 27).…”

Section: Methodsmentioning

confidence: 99%

“…The process of isolating the productive adaptive IR recombination reads, that is, with in-frame CDR3 reading frames, from the TCGA-SKCM and Moffitt Cancer Center WXS files has been extensively described and benchmarked, for example, with regard to concordance with T-and B-cell gene expression markers [6][7][8]24]; and with regard to overlapping CDR3 AA sequences from WXS and RNAseq files [24]. The original python script for mining the IR receptors is freely available at https:// github.com/bchobrut-USF/blanck_group, with readme files; recent refinements are available at the following web link and represent refinements used in reference [27]. https://github.com/kcios/2021; and a dockerized version is at https://hub.docker.com/r/bchobrut/vdj, also including a readme file.…”

Section: Isolation Of the Trg Recombination Readsmentioning

confidence: 99%

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Chemical features of melanoma tumor resident TRG CDR3s associated with better survival probabilities

Agnila,

Huda,

Eakins

et al. 2023

Melanoma Research

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We assessed the T-cell receptor gamma (TRG) recombination reads from the cancer genome atlas melanoma tumor exome files and the TRG recombination reads from an independent, melanoma exome file dataset, from the Moffitt Cancer Center. TRG complementarity determining region-3 (CDR3) amino acid (AA) sequences were assessed for chemical complementarity to cancer testis antigens, with such complementarity for FAM133A and CRISP2 associated with better survival probabilities for both datasets. These results, along with related TRG CDR3 AA chemical feature assessments provided in this report, have indicated opportunities for melanoma patient stratifications based on the recovery of TRG recombination reads from both tumor and blood samples, and the results may point towards novel, effective melanoma antigens.

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“…Multivariate analyses were conducted as described [27]. Briefly, the analysis was conducted using the IBM Statistical Package for the Social Sciences (version 27).…”

Section: Methodsmentioning

confidence: 99%

Section: Isolation Of the Trg Recombination Readsmentioning

confidence: 99%

Chemical features of melanoma tumor resident TRG CDR3s associated with better survival probabilities

Agnila,

Huda,

Eakins

et al. 2023

Melanoma Research

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“…And, for particular autoimmune and infectious diseases, certain combinations of TCR gene segment usage and HLA alleles predominate (Miles et al., 2010; Miles et al., 2011; Quandt et al., 2012). Recently, this has been shown to be the case for certain cancer survival probability distinctions as well (Arndt et al., 2020; Callahan, Tong, et al., 2018; Callahan, Yavorski, et al., 2018; Cios et al., 2022; Clark et al., 2019; Huda et al., 2021; Roca et al., 2019; Tong et al., 2019). Presumably or possibly, the association of specific TCR gene segment usage, HLA allele combinations with cancer outcomes is due to certain combinations representing either a better or worse opportunity to present cancer antigens, reflecting analogous presumptions for autoimmunity and infectious diseases.…”

Section: Introductionmentioning

confidence: 95%

TCR gene segment usage and HLA alleles that are associated with cancer survival rates also represent racial disparities

Angelakakis

Serraneau

Barker

et al. 2022

Int J Immunogenetics

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Understanding racial disparities in cancer outcomes continues to be a challenge, with likely many factors at play, including socioeconomic factors and genetic polymorphisms impacting basic cellular and molecular functions. Additionally, it is possible that specific combinations of environment and genetics have specific impacts. T‐cell receptor (TCR) gene segment usage, HLA allele combinations have been associated with autoimmune and infectious disease courses, and more recently, TCR gene segment usage, HLA allele combinations have been associated with distinct survival outcomes in cancer as well. We examined several such, previously reported cancer‐related TCR gene segment usage, HLA allele combinations for evidence of racial disparities, with regard to the prevalence of the combination in different racial groups. Results indicated that TCR gene segment usage, potentially reflecting environmental factors related to previous pathogen exposure, in combination with certain HLA alleles or independently, may represent a novel explanation for racial disparities in cancer outcomes. Overall, at this point, a genetic connection to racial disparities in cancer outcomes is detectable but remains modest, suggesting that other factors, such as socioeconomic factors, remain as important considerations.

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Specific Intratumor Bacteria Genera and TRG Recombinations Associated with Greater Survival Probability in Alimentary Tract Cancers

Zaman

Chobrutskiy

Quach

et al. 2023

J Gastrointest Canc

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Specific TCR V–J gene segment recombinations leading to the identification pan-V–J CDR3s associated with survival distinctions: diffuse large B-cell lymphoma

Cited by 7 publications

References 42 publications

Chemical features of melanoma tumor resident TRG CDR3s associated with better survival probabilities

Chemical features of melanoma tumor resident TRG CDR3s associated with better survival probabilities

TCR gene segment usage and HLA alleles that are associated with cancer survival rates also represent racial disparities

Specific Intratumor Bacteria Genera and TRG Recombinations Associated with Greater Survival Probability in Alimentary Tract Cancers

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