Plantaginaceae, consisting of 12 tribes, is a diverse, cosmopolitan family. To date, the inter-tribal relationships of this family have been unresolved, and the plastome structure and composition within Plantaginaceae have seldom been comprehensively investigated. In this study, we compared the plastomes from 41 Plantaginaceae species (including 6 newly sequenced samples and 35 publicly representative species) representing 11 tribes. To clarify the inter-tribal relationships of Plantaginaceae, we inferred phylogenic relationships based on the concatenated and coalescent analyses of 68 plastid protein-coding genes. PhyParts analysis was performed to assess the level of concordance and conflict among gene trees across the species tree. The results indicate that most plastomes of Plantaginaceae are largely conserved in terms of genome structure and gene content. In contrast to most previous studies, a robust phylogeny was recovered using plastome data, providing new insights for better understanding the inter-tribal relationships of Plantaginaceae. Both concatenated and coalescent phylogenies favored the sister relationship between Plantagineae and Digitalideae, as well as between Veroniceae and Hemiphragmeae. Sibthorpieae diverged into a separate branch which was sister to a clade comprising the four tribes mentioned above. Furthermore, the sister relationship between Russelieae and Cheloneae is strongly supported. The results of PhyParts showed gene tree congruence and conflict to varying degrees, but most plastid genes were uninformative for phylogenetic nodes, revealing the defects of previous studies using single or multiple plastid DNA sequences to infer the phylogeny of Plantaginaceae.
Purpose
About 30–40% of patients with diffuse large B-cell lymphoma (DLBCL) relapse or fail to respond to first-line treatment. The molecular heterogeneity is considered to be the main factor affecting the therapeutic response of DLBCL. The existing classification methods can not fully explain these heterogeneity, so we try to explain DLBCL heterogeneity by defining DLBCL subtypes from the perspective of metabolism.
Methods
In this study, we integrated five DLBCL data sets (GSE10846, GSE11318, GSE53786, GSE87371 and GSE23501) (n = 742) from geo database, screened 106 metabolic related genes (MAD > 0.5, Cox P < 0.001), and identified dlbcl2 subclasses (nmftype1, nmftype2) by non-negative matrix factorization clustering (NMF).
Results
nmftype1 showed low metabolic activity ,while nmftype2 showed high metabolic activity. Compared with the two subtypes of immune infiltration, it was found that nmftype1 was mainly infiltrated by B cells, and nmftype2 was mainly infiltrated by T cells and macrophages, and the high expression of nmftype2 was more in immune checkpoint. The difference of metabolic subtype OS was statistically significant, and the overall survival (OS) of nfmtype1 was worse than that of nmftype2. The combination of metabolic subtypes and ABCGCB subtypes can predict the prognosis of DLBCL patients better than the existing ABCGCB subtypes. Finally, 34 gene classifiers were identified. The consistency results were verified by GSE31312 (n = 470), and a new classification of DLBCL based on metabolic gene expression profile was established.
Conclusions
We have obtained a new DLBCL typing method, which has prognostic significance. It has a certain correlation with immune escape and can guide individualization application of immunotherapy and metabolic therapy.
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