CC BY
0БИОЛОГИЯ, ХИМИЯ
DOI 10.24412/cl-37235-2024-1-74-79
PAN-CANCER SCREENING FOR TERT AND ATRX MUTATION-ASSOCIATED CHANGES IN TELOMERE MAINTENANCE
MECHANISMS
M. Hakobyan1
1Bioinformatics Group, Institute of Molecular Biology NAS RA anilem.hakobyan@gmail.com
ABSTRACT
Telomeres, located at the linear chromosome ends in eukaryotic cells, are essential for preserving chromosome stability, regulating genome replication, and influencing cell longevity. Cells with unlimited replicative potential utilize telomere maintenance to ensure the length of telomeres remains intact. Currently, two primary mechanisms are recognized: telomer-ase-dependent (TEL) and an alternative lengthening of telomeres (ALT). The TEL pathway described by the telomerase enzyme consists of two key parts: the telomerase reverse transcriptase (TERT) the catalytic component and the TERC internal telomerase RNA template. Additionally, ATRX gene mutations are frequently observed in several ALT tumor types, such as adult lower-grade gliomas and pediatric glioblastomas. To assess the impact of ALT and TEL pathway gene mutations on pathway activity, we conducted an analysis comparing altered and unaltered samples across 33 cancer types in The Cancer Genome Atlas (TCGA). Our study aimed to evaluate the influence of TERT and ATRX mutations on pathway activity. We found no significant differences in telomere maintenance pathway activities between the mutated and non-mutated samples in pan-cancer settings. However, for individual-level comparisons, we observed significant differences for Testicular Germ Cell Tumors in the TEL pathway and Breast invasive carcinoma, Colon adenocarcinoma, Lung adenocarci-noma, and Uterine Corpus Endometrial Carcinoma for the ALT. Keywords: cancer; telomere maintenance mechanisms; alternative lengthening of telomeres; TERT; ATRX.
Introduction
Telomeres are specialized structures consisting of nucleoproteins found at the terminal ends of linear chromosomes [1]. They serve as protective caps, shielding chromosomes from fusion, preventing degradation, and mitigating chromosomal instability [2]. During cell division, the "end replication problem" results in the gradual shortening of the DNA in the terminal regions [3, 4]. To address this issue, cells that can continuously divide employ the Telomere Maintenance Mechanism
(TMM). This cellular process involves various mechanisms aimed at conserving telomere length. One key method involves the action of an enzyme called telomer-ase (TEL), which elongates telomeres by adding repetitive DNA sequences to the ends of chromosomes [5]. Another mechanism involves alternative lengthening of telomeres (ALT), a process utilizing recombination and DNA repair mechanisms to maintain or lengthen telomeres without telomerase activity [6]. Key components of the telomerase enzyme are: telomerase reverse transcriptase (TERT) which plays a crucial role in cancer development by maintaining telomere length and the telomer-ase RNA component (TERC) which provides the template sequence necessary for telomere elongation through the action of telomerase [7]. Transcriptional modifications within the TERT component represent a common occurrence across various cancer types [8]. On the other hand, mutations in the ATRX gene are commonly found in various tumor types that utilize the ALT mechanism [9,10]. This underscores the necessity for pan-cancer investigation of TERT and ATRX gene mutations on the TMM pathways activity. In our study, we aimed to examine the impact of TERT mutations and ATRX mutations on pathway activity by comparing samples with TERT mutations to those without mutations, as well as samples with ATRX mutations to those without mutations.
Materials and Methods
The methodology involving data preprocessing, TMM signatures [11], and the PSF [12,13] algorithm has been extensively described in our prior study [14]. In this study, we utilized the previously derived PSF scores for the ALT and TEL pathways. The comprehensive description of these methodologies and analyses can be referenced in our earlier work [14].
Mutations in TMM pathways
TEL and ALT pathway-related gene mutation datasets were obtained from the cBioPortal [15] for the corresponding TCGA projects. Samples were classified as "mutated" if at least one gene in the pathway exhibited a mutation, while samples lacking mutations in all pathway genes were labeled as "non-mutated". A unified dataset was created by combining the data from different cancer types.
Results
To assess the implications of ALT and TEL pathway gene mutations on pathway activity, we analyzed altered versus unaltered samples across all 33 cancer types. We retrieved data for the ALT and TEL pathway genes from the cBioPortal for various cancer types. The ALT and TEL pathways activity are comparably
higher in mutated samples than in non-mutated samples for the ALT (p = 5.3 x 1012, Wilcoxon rank-sum test) and TEL (p = 1.5 x 10-5, Wilcoxon rank-sum test) pathways genes overall (Figure 1 A, B).
Figure 1. Activity plots of ALT and TEL pathways for TEL ALT pathway genes mutated\non-mutated and TERTATRXmutated\non-mutatedgenes samples (A) TEL and (B) ALT pathway genes mutated\non-mutated sample plots for 33 cancer types. (C) TERT mutated/TERT non-mutated samples
TEL pathway activity patterns across all cancer types. (D) ATRX mu-tated/ATRX non-mutated samples ALT pathway activity patterns across all
cancer types.
We performed individual-level comparisons between mutated and non-mutated samples for the TEL and ALT pathways across all 33 cancer types. Through this analysis, we observed significant differences in the TEL and ALT pathways PSF in the TEL pathway PSF levels in Head and Neck squamous cell carcinoma (HNSC), Lung squamous cell carcinoma (LUSC), Stomach adenocarcinoma (STAD), and Uterine Corpus Endometrial Carcinoma (UCEC) (p = 5.6 x 10-16, Kruskal-Wallis test) and for the ALT pathway in Bladder Urothelial Carcinoma (BLCA), Breast
invasive carcinoma (BRCA), Colon adenocarcinoma (COAD), Kidney renal papillary cell carcinoma (KIRP), Lung adenocarcinoma (LUAD), Ovarian serous cystad-enocarcinoma (OV), Skin Cutaneous Melanoma (SKCM), Stomach adenocarcinoma (STAD), and UCEC (p <2.2 x 10-16, Kruskal-Wallis test) (Figure 2 A, B).
Figure 2. Activity plots of ALT and TEL pathways for TEL/ALT pathway genes mutated/non-mutated, and TERT/ATRXmutated/non-mutated samples individual comparison. (A) TEL and (B) ALT pathway activity plots for mutated and non-mutated samples. (C) TEL pathway activity patterns in TERT mutated and non-mutated samples. For CHOL, LAML, PCPG, THYM, and UVM cancer types TERT mutated samples were missing. (D) ALT pathway activity patterns in ATRX mutated and non-mutated samples across all cancer types. For CHOL, KIRP, LAML, TGCT, THYM, and UMV cancer types ATRXmutated samples were missing.
We further investigated the impact of TERT mutations and ATRX mutations on pathway activity by comparing TERT mutated versus TERT non-mutated samples and ATRX mutated versus ATRX non-mutated samples. Using the same approach as previously described for ALT and TEL pathway genes, we analyzed the altered and unaltered samples across all 33 cancer types in a combined dataset. However, no significant difference was observed in pathway activity (ALT/ ATRX: p = 0.22, Wilcoxon rank-sum test and TEL/TERT: p = 0.59, Wilcoxon rank-sum test)
(Figure 1 C, D). However, in our individual-level comparisons, we observed significant differences in the TERT and ATRX altered and unaltered samples in Testicular Germ Cell Tumors (TGCT) for the TEL and BRCA, COAD, LUAD, and UCEC for the ALT pathways. (Figure 2 C, D). Analysis of pathway gene mutations showed that mutated samples had higher pathway activity compared to non-mutated samples for both the ALT and TEL pathways for individual cancer types. The overall comparison between mutated and non-mutated samples indicates significantly heightened activity in mutated samples for both ALT and TEL pathways, implying a potential association between these mutations and increased pathway activation. While the overall analysis doesn't reveal stark differences in TERT and ATRX mutations' effect on pathway activity, the individual-level comparisons uncovered noteworthy differences.
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ПАН-РАКОВЫЙ СКРИНИНГ ИЗМЕНЕНИЙ В МЕХАНИЗМАХ ПОДДЕРЖАНИЯ ТЕЛОМЕР, СВЯЗАННЫХ С МУТАЦИЯМИ TERT И ATRX
М.А. Акопян1
'Группа биоинформатики, Институт молекулярной биологии НАН РА anilem.hakobyan@gmail.com
АННОТАЦИЯ
Теломеры, расположенные на линейных концах хромосом в эукарио-тических клетках, необходимы для сохранения стабильности хромосом, регуляции репликации генома и влияния на продолжительность жизни клетки. В клетках с неограниченным репликативным потенциалом для поддержания длины теломер используется механизм поддержания длины теломер. В настоящее время признаны два основных механизма: теломераз-зависимый (TEL) и альтернативное удлинение теломер (ALT). Путь TEL, описываемый ферментом теломеразой, состоит из двух ключевых частей: каталитического компонента -тело-меразной обратной транскриптазы (TERT) и внутреннего шаблона теломеразной РНК (TERC). Кроме того, мутации гена ATRX часто наблюдаются в некоторых типах опухолей ALT - таких, как глиомы и детские глиобластомы. Для оценки влияния мутаций генов ALT- и TEL-путей на активность путей мы провели сравнительный анализ измененных и неизмененных образцов по 33 типам рака в "The Cancer Genome Atlas" (TCGA). Наше исследование было направлено на оценку влияния мутаций TERT и ATRX на активность пути. Мы не обнаружили существенных различий в активности путей поддержания теломер между мутировавшими и немутировавшими образцами в пан-раковых условиях. Однако при сравнении на индивидуальном уровне мы наблюдали значимые различия для тестикулярного рака для пути TEL и для инвазивной карциномы молочной железы, адено-карциномы толстой кишки, аденокарциномы легкого и эндометри-альной карциномы тела матки для пути ALT.
Ключевые слова: рак, механизмы поддержания теломер, альтернативное удлинение теломер, ТЕРТ, АТРХ.
