Triple-negative breast cancer cells respond to T cells severely at the alternative splicing layer

BACKGROUND: Cross talk of tumor­immune cells at the gene expression level has been an area of intense research. However, it is largely unknown at the alternative splicing level which has been found to play important roles in the tumor­immune microenvironment. RESULTS: Here, we re-exploited one transcriptomic dataset to gain insight into tumor­immune interactions from the point of AS level. Our results showed that the AS profiles of triple-negative breast cancer cells co-cultured with activated T cells were significantly changed but not Estrogen receptor positive cells. We further suggested that the alteration in AS profiles in triple-negative breast cancer cells was largely caused by activated T cells rather than paracrine factors from activated T cells. Biological pathway analyses showed that translation initiation and tRNA aminoacylation pathways were most disturbed with T cell treatment. We also established an approach largely based on the AS factor­AS events associations and identified LSM7, an alternative splicing factor, may be responsible for the major altered events. CONCLUSIONS: Our study reveals the notable differences of response to T cells among breast cancer types which may facilitate the development or improvement of tumor immunotherapy.

CARACTERIZACIÓN DEL TALLO ACEPTOR DEL tARN MEDIANTE DESCRIPTORES LOCALES BASADOS EN CARGAS PARCIALES / tRNA ACCEPTOR STEM CHARACTERIZATION BY MEANS OF LOCAL DESCRIPTORS BASED ON PARTIAL CHARGES / CARACTERIZAÇÃO DO TALO ACEITADOR DO tRNA MEDIANTE DESCRITORES LOCAIS BASEADOS EM CARGAS PARCIAIS

En este trabajo se caracteriza la distribución de carga del tallo aceptor del tARN, considerando todas las posibles combinaciones de pares Watson-Crick. El estudio se realizó con 256 fragmentos moleculares de 10 nucleótidos que modelan los tres primeros pares del tallo aceptor, la base diferenciadora y el extremo CCA. Para caracterizar los nucleótidos se proponen dos descriptores locales basados en la distribución de carga de la base nitrogenada de cada nucleótido, los cuales se calculan a partir de las cargas parciales de Mulliken obtenidas de cálculos HF/6-31G. La caracterización y clasificación de los tallos según estos descriptores mostró cómo la base diferenciadora tiene un comportamiento particular respecto a los demás nucleótidos del tallo y una fuerte influencia sobre el extremo CCA. La clasificación de nueve variaciones del tallo aceptor del tARNAla mostró una buena relación estructura-actividad que pone en evidencia la bondad de los descriptores propuestos para caracterizar de manera local la distribución de carga de estas biomoléculas.

In this work the charge distribution of the tRNA acceptor stem is characterized, considering all the possible Watson- Crick base pair combinations. 256 RNA fragments modeled by 10 nucleotides were used in order to model the first three pairs of the acceptor stem, the discriminator base and the CCA end. We propose two local charge descriptors based on the charge distribution of the nitrogenated base to characterize each nucleotide. These descriptors were computed from atomic partial charges derived from HF/6-31G calculations. From the characterization and classification of the stems according to the proposed descriptors, we found a special behavior for the discriminator base (in contrast to the other positions) and a strong effect of this position on the CCA end. The classification of nine variations of the tRNAAla acceptor stem showed a good structure-activity relationship that makes evident the usefulness of the proposed descriptors to characterize the local charge distributions of these biomolecules.

Nesse estudo é caracterizada a distribuição da carga do talo aceitador considerando- se todas as combinações possíveis dos pares Watson-Crick. O estudo realizouse com 256 fragmentos moleculares dos 10 nucleotídeos que modelam os três primeiros pares do talo aceitador, a base diferenciadora e o extremo CCA. Com o intuito de caracterizar cada nucleotídeo, foram propostos dois descritores locais baseados na distribuição de carga da base nitrogenada de cada nucleotídeo, os quais se calculam a partir das cargas parciais de Mulliken obtidas de cálculos HF/6-31G. A caracterização e classificação dos talos segundo esses descritores demonstrou um particular comportamento da base diferenciadora em relação aos demais nucleotídeos do talo e uma forte influência sobre o extremo CCA. A classificação de nove variações do talo aceitador do tRNA mostrou uma boa relação estrutura-atividade que colocam em evidência a utilidade dos descritores propostos para caracterizar de maneira local a distribuição de carga dessas bio-moléculas.

Qualitative and quantitative variation of tRNA in certain invertebrates.

Total tRNA was isolated, purified and quantitated from earthworm, cockroach, fresh water mussel and rat liver. The total tRNA content of invertebrates was found to be much lower than that of rat liver. When checked for aminoacylation capacity with homologous and heterologous enzymes and algal protein hydrolysate, the tRNA preparation from rat liver and fresh water mussel, a mollusc, were found to be active. On the other hand, the tRNAs from earthworm, an annelid, and cockroach, an arthropod, were completely inactive with the homologous enzymes but showed partial activity with heterologous enzymes. Similar results were obtained with individual amino acids also. The low activity or inactivity of earthworm and cockroach tRNAs appears to be due to certain endogenous aminoacylation inhibitors.

Conformational aspects and functions of tRNA.

In the process of protein biosynthesis, an aminoacyl-tRNA synthetase strictly recognizes the cognate amino acid and tRNA species. Spectroscopic and biochemical analyses have been made of a heterologous system of Thermus thermophilus glutamyl-tRNA synthetase and Escherichia coli tRNAGlu. The conformational difference between the initial complex and active complex has been observed, which is probably related with the strict recognition of aminoacyl-tRNA synthetase. tRNA species are post-transcriptionally modified at specific sites. Two types of modified uridine nucleosides have been found in the first position of anticodon, namely 5-hydroxyuridine derivatives (xo5U) and 5-methyl-2-thiouridine derivatives (xm5s2U). From the analyses of nuclear magnetic resonance spectra, the conformational characteristics of the two types of modified uridine nucleotides have been found to be remarkably different from each other. The conformational flexibility of xo5U nucleotides allow the multiple recognition of codons, whereas the conformational rigidity of xm5s2U nucleotides guarantees the recognition of correct codons. The modification of uridines in the first position of anticodon contributes to the correct and efficient translations of codons in protein biosynthesis.

Studies on the effects of in vitro methyiation on aminoacylation of transfer RNA.

In vitro methyiation of Escherichia coli transfer ribonucleic acid by cell free extracts of Mycobacterium smegmatis leads exclusively to the formation of 1-methyl adenine [Vani, B. R., Ramakrishnan, T., Taya, Y., Noguchi, S., Yamaiuzumi, Z. and Nishimura, S. (1978) J. Bact., 137,1085]. We have studied the effect of this modification on aminoacylation of Escherichia coli tRNA by mycobacterial enzymes. Aminoacylation with total algal protein hydrolysate as well as several individual aminoacids like methionine, valine, tyrosine, aspartic acid and lysine were monitored. In all the cases methyiation had a positive effect on the extent of aminoacylation by mycobacterial enzymes. Decreased aminoacylation in vitro was observed when hypomethylated transfer RNA from ethionine treated cells was used as the substrate for aminoacylation.

Age-related qualitative and quantitative changes in tRNA population of rat skeletal muscle.

Total tRNA was purified from skeletal muscle of young, adult and old female albino rats. Age-dependent variation of total tRNA was the same with respect to tRNA content and biological activity as measured by amino acid acceptor capacity. The tRNA content was more in young rats and showed a gradual decrease in the adult and old rats. The relative abundancy of eleven aminoacyl-tRNAs were checked at each age and during aging. Arginyl, glutamyl and tyrosyl-tRNAs do not show any quantitative or qualitative change with age.