Genome-wide identification of cancer/testis genes and their association with prognosis in a pan-cancer analysis

Silva, Vandeclécio Lira da; Fonseca, André; Fonseca, Maira Christina Marques; Silva, Thayna Emilia da; Coelho, Ana Carolina; Kroll, José Eduardo; Souza, Jorge Estefano Santana de; Stransky, Beatriz; Souza, Gustavo; Souza, Sandro J. de

doi:10.18632/oncotarget.21715

Cited by 50 publications

(53 citation statements)

References 52 publications

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“…Expression of some CTAs in transformed cells may represent an epiphenomenon of altered genomic methylation or acquisition of stem‐like properties, but in general, CTAs are thought to contribute to oncogenesis, presumably to a degree sufficient to offset the increased immunogenicity and susceptibility to immunoediting (expression of CTAs can be associated with CD8+ T‐cell signatures in tumors …”

Section: Discussionmentioning

confidence: 99%

“…65,66 Expression of some CTAs in transformed cells may represent an epiphenomenon of altered genomic methylation or acquisition of stem-like properties, but in general, CTAs are thought to contribute to oncogenesis, 67 presumably to a degree sufficient to offset the increased immunogenicity and susceptibility to immunoediting (expression of CTAs can be associated with CD8+ T-cell signatures in tumors. 68,69 ) The role of many autosomal CTAs in oncogenesis is generally better established than for their X-linked counterparts, increasing their relative worth as therapeutic targets. Even if their less-well-restricted tissue expression rules out use in immunotherapy, inhibiting the function of these oncogenic proteins in hematologic malignancies by pharmacologic means may be an important, underinvestigated treatment approach.…”

Section: Discussionmentioning

confidence: 99%

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Cancer‐testis antigens in canine histiocytic sarcoma and other malignancies

Nemec

Kapatos

Holmes

et al. 2019

Vet Comparative Oncology

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Cancer‐testis antigens (CTAs) are a category of self proteins aberrantly expressed in diverse malignancies, mostly solid tumours, due to epigenetic de‐repression. Normally expressed only in fetal or gametogenic tissues, CTAs are tantalizing immunotherapy targets, since autoimmunity risks appear minimal. Few prevalent CTAs have been identified in human hematologic cancers, and just two in their veterinary counterparts. We sought to discover new CTAs in canine hematologic cancers such as histiocytic sarcoma (HS) and lymphoma to foster immunotherapy development. To accomplish this, the ligandome binding the dog leukocyte antigen (DLA)‐88*508:01 class I allele overexpressed in an HS line was searched by mass spectrometry to identify possible CTA‐derived peptides, which could serve as CD8+ T‐cell epitopes. Twenty‐two peptides mapped to 5 human CTAs and 12 additional proteins with CTA characteristics. Expression of five promising candidates was then evaluated in tumour and normal tissue by quantitative and end‐point RT‐PCR. The ortholog of an established CTA, IGF2BP3, had unexpectedly high expression in peripheral blood mononuclear cells (PBMCs). Four other testis‐enhanced proteins were also assessed. AKR1E2, SPECC1 and TPX2 were expressed variably in HS and T‐cell lymphoma biopsies, but also at high levels in critical tissues, including kidney, brain and marrow, diminishing their utility. A more tissue‐restricted candidate, NT5C1B, was detected in T‐cell lymphomas, but also at low levels in some normal dog tissues. These results illustrate the feasibility of discovering canine CTAs by a reverse approach, proceeding from identification of MHC class I‐presented peptides to a comparative RNA expression survey of tumours and normal tissues.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Cancer‐testis antigens in canine histiocytic sarcoma and other malignancies

Nemec

Kapatos

Holmes

et al. 2019

Vet Comparative Oncology

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“…Due to their restricted expression pattern, CT antigens are frequently recognized by the immune system of cancer patients. Interestingly, 4 SNPs in chr 17 that had suggestive cross-associations with three immune traits associated with T cell subsets mapped in proximity to the SPATA22 gene, which is also a CT antigen (da Silva et al, 2017;Wang et al, 2016).…”

Section: Tcga Only Includes Common Variant Germline Data and Not Wholmentioning

confidence: 99%

Germline genetic contribution to the immune landscape of cancer

Sayaman

Saad

Thórsson

et al. 2020

Preprint

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SummaryThe role of germline genetics in shaping the tumor immune landscape is largely unknown. Using genotypes from >9,000 individuals in The Cancer Genome Atlas, we investigated the association of common and rare variants with 139 well-defined immune traits. Our analysis of common variants identified 10 immune traits with significant heritability estimates, and an additional 23 with suggestive heritability, including estimates of T-cell subset abundance and interferon signaling. We performed genome-wide association on the 33 heritable traits and identified 23 genome-wide significant loci associated with at least one immune trait, including SNPs in the IFIH1 locus previously associated with several autoimmune diseases. We also found significant associations between immune traits and pathogenic or likely-pathogenic rare variants in BRCA1 and in genes functionally linked to telomere stabilization, and Wnt/Beta-catenin signaling. We conclude that germline genetic variants significantly impact the composition and functional orientation of the tumor immune microenvironment.

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“…The CT study was published by our group in (da Silva et al 2017), in which the integration of gene expression and clinical data guided us to detect some CT genes that are associated to prognosis in different types of cancer. This study executed a genome-wide screen for CT genes using data from several databases; hence, we reproduced the original pipeline ( Figure 4A It starts accessing 3 databases using <data> tags (lines 2, 3 and 4 for HBM, GTEX and HPA databases respectively).…”

Section: Case 3: Cancer/testis (Ct) Projectmentioning

confidence: 99%

Bio-DIA: A web-based tool for data and algorithms integration

Soares¹,

Silva²,

Faustino³

et al. 2019

Preprint

Self Cite

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Data science is historically a complex field, not only because of the huge amount of data and its variety of formats, but also because the necessity of collaboration between several specialists to retrieve valuable information. In this context, we created Bio-DIA, an online software to build data science workflow process focused in the integration of data and algorithms. Bio-DIA also facilitates the reusability of information/results obtained in previous process without the need of specific skills from the computer science field. The software was created with Angular at the front-end, Django at the back-end together with Spark to handle and process a variety of big data formats. The workflow/project is specified through XML file. Bio-DIA application facilitated the collaboration among users, allowing researcher ś groups to share data, scripts and information.Availability: https://ucrania.imd.ufrn.br/biodia-app/. Login: bioguest, password: welcome123.

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Genome-wide identification of cancer/testis genes and their association with prognosis in a pan-cancer analysis

Cited by 50 publications

References 52 publications

Cancer‐testis antigens in canine histiocytic sarcoma and other malignancies

Cancer‐testis antigens in canine histiocytic sarcoma and other malignancies

Germline genetic contribution to the immune landscape of cancer

Bio-DIA: A web-based tool for data and algorithms integration

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