Predicting the Prognosis and Immunotherapeutic Response of Triple-Negative Breast Cancer by Constructing a Prognostic Model Based on CD8+ T Cell-Related Immune Genes.

Objective: Triple-negative breast cancer (TNBC) poses a significant challenge for treatment efficacy. CD8+ T cells, which are pivotal immune cells, can be effectively analyzed for differential gene expression across diverse cell populations owing to rapid advancements in sequencing technology. By leveraging these genes, our objective was to develop a prognostic model that accurately predicts the prognosis of patients with TNBC and their responsiveness to immunotherapy. Methods: Sample information and clinical data of TNBC were sourced from The Cancer Genome Atlas and METABRIC databases. In the initial stage, we identified 67 differentially expressed genes associated with immune response in CD8+ T cells. Subsequently, we narrowed our focus to three key genes, namely CXCL13, GBP2, and GZMB, which were used to construct a prognostic model. The accuracy of the model was assessed using the validation set data and receiver operating characteristic (ROC) curves. Furthermore, we employed various methods, including Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, immune infiltration, and correlation analyses with CD274 (PD-L1) to explore the model's predictive efficacy in immunotherapeutic responses. Additionally, we investigated the potential underlying biological pathways that contribute to divergent treatment responses. Results: We successfully developed a model capable of predicting the prognosis of patients with TNBC. The areas under the curve (AUC) values for the 1-, 3-, and 5-year survival predictions were 0.618, 0.652, and 0.826, respectively. Employing this risk model, we stratified the samples into high- and low-risk groups. Through KEGG enrichment analysis, we observed that the high-risk group predominantly exhibited enrichment in metabolism-related pathways such as drug and chlorophyll metabolism, whereas the low-risk group demonstrated significant enrichment in cytokine pathways. Furthermore, immune landscape analysis revealed noteworthy variations between (PD-L1) expression and risk scores, indicating that our model effectively predicted the response of patients to immune-based treatments. Conclusion: Our study demonstrates the potential of CXCL13, GBP2, and GZMB as prognostic indicators of clinical outcomes and immunotherapy responses in patients with TNBC. These findings provide valuable insights and novel avenues for developing immunotherapeutic approaches targeting TNBC.

Roles of Major RNA Adenosine Modifications in Head and Neck Squamous Cell Carcinoma.

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer malignancy worldwide and is known to have poor prognosis. The pathogenesis behind the development of HNSCC is not fully understood. Modifications on RNA are involved in many pathophysiological processes, such as tumor development and inflammation. Adenosine-related RNA modifications have shown to be linked to cancer and may play a role in cancer occurrence and development. To date, there are at least 170 different chemical RNA modifications that modify coding and non-coding RNAs (ncRNAs). These modifications affect RNA stability and transcription efficiency. In this review, we focus on the current understanding of the four major RNA adenosine modifications (N6-Methyladenosine, N1-Methyladenosine, Alternative Polyadenylation Modification and A-to-I RNA editing) and their potential molecular mechanisms related to HNSCC development and progression. We also touch on how these RNA modifications affect treatment of HNSCCs.

Rectangle and [2]catenane from cluster modular construction.

Reaction of [Et4N][Tp*WS3] (1) with [Cu(MeCN)4]PF6, CsCl, isonicotinic acid and CuCN, and treatment of [Et4N][Tp*WS3(CuCl)3] (2)/[Et4N][{Tp*WS3Cu3Cl}2(µ-Cl)2(µ4-Cl)] (3) with AgOTf and bpp (Tp* = hydridotris(3,5-dimethylpyrazol-1-yl)borate; bpp = 1,3-di(4-pyridyl)propane) give rise to [Et4N]2[{Tp*WS3Cu3(CN)0.5}2(µ-Cl)2(µ4-Cl)]2(PF6)2 (4) and [(Tp*WS3Cu3)2(µ3-Cl)2(bpp)3]2(OTf)4 (5), respectively. Compounds 4 and 5 feature cluster-based rectangle and [2]catenane architecture, and both exhibit enhanced third-order nonlinear optical responses relative to those of 1.

Tungsten(VI)-Copper(I)-Sulfur Cluster-Supported Metal-Organic Frameworks Bridged by in Situ Click-Formed Tetrazolate Ligands.

Six analogous two-dimensional (2D) [Tp*WS3Cu3]-based (Tp* = hydridotris(3,5-dimethylpyrazol-1-yl)borate) networks, namely, {[(Tp*WS3Cu3)2L3](µ3-N3)}n (2: L = 5-methyltetrazolate (Mtta); 3a: L = 5-ethyltetrazolate (Etta)) and {[(Tp*WS3Cu3)2L3]BF4}n (3b: L = Etta; 4: L = 5-propyltetrazolate (Ptta); 5: L = 5-butyltetrazolate (Btta); 6: L = 5-pentyltetrazolate (Petta)) were synthesized by reactions of [Et4N][Tp*WS3] (1), [Cu(CH3CN)4]BF4, NaN3, and NH4BF4 in different nitrile solvents (CH3(CH2)nCN, n = 0, 1, 2, 3, and 4) under solvothermal conditions. In the structures of 2-6, each alkyl tetrazolate L as a bridging ligand was generated in situ from the "click" reaction between azide and nitrile. These 2D (6,3) networks support two types of voids wherein the pendant alkyl groups are accommodated. A tetrahedron cage-like cluster [Tp*W(µ3-S)3(µ3-S')Cu3]4 (7) was also formed in some of the above reactions and can be readily separated by solvent extraction. The proportion of 7 increased with the elongation of the alkyl chains and finally became the exclusive product when heptylnitrile was employed. Further use of CuCN as a surrogate for [Cu(CH3CN)4]BF4 with the aim of introducing additional CN bridges into the network led us to isolate a tetrazolate-free compound, {[Et4N]{(Tp*WS3Cu3)[Cu2(CN)4.5]}2·2PhCH2CN}n (8·2PhCH2CN), a unique 2D network that features {(Tp*WS3Cu3)[Cu2(CN)5]}22-, {(Tp*WS3Cu3)3[Cu3(CN)7]2[Cu(CN)3]}4-, and {(Tp*WS3Cu3)[Cu4(CN)9]}26- ring subunits. Compounds 5-8 are soluble in DMF and exhibit a reverse saturable absorption and self-focusing third-order nonlinear optical (NLO) effect at 532 nm with hyperpolarizability γ values in the range of 4.43 × 10-30 to 5.40 × 10-30 esu, which are 400-500 times larger than that of their precursor 1. The results provide an interesting insight into the synergetic synthetic strategy related to the assembly of the [Tp*WS3Cu3]2+ cluster core, the "click" formation of the tetrazolate ligands, and the construction of the [Tp*WS3Cu3]2+ cluster-based 2D networks.

Determining the Functions of HIV-1 Tat and a Second Magnesium Ion in the CDK9/Cyclin T1 Complex: A Molecular Dynamics Simulation Study.

The current paradigm of cyclin-dependent kinase (CDK) regulation based on the well-established CDK2 has been recently expanded. The determination of CDK9 crystal structures suggests the requirement of an additional regulatory protein, such as human immunodeficiency virus type 1 (HIV-1) Tat, to exert its physiological functions. In most kinases, the exact number and roles of the cofactor metal ions remain unappreciated, and the repertoire has thus gained increasing attention recently. Here, molecular dynamics (MD) simulations were implemented on CDK9 to explore the functional roles of HIV-1 Tat and the second Mg2+ ion at site 1 (Mg12+). The simulations unveiled that binding of HIV-1 Tat to CDK9 not only stabilized hydrogen bonds (H-bonds) between ATP and hinge residues Asp104 and Cys106, as well as between ATP and invariant Lys48, but also facilitated the salt bridge network pertaining to the phosphorylated Thr186 at the activation loop. By contrast, these H-bonds cannot be formed in CDK9 owing to the absence of HIV-1 Tat. MD simulations further revealed that the Mg12+ ion, coupled with the Mg22+ ion, anchored to the triphosphate moiety of ATP in its catalytic competent conformation. This observation indicates the requirement of the Mg12+ ion for CDK9 to realize its function. Overall, the introduction of HIV-1 Tat and Mg12+ ion resulted in the active site architectural characteristics of phosphorylated CDK9. These data highlighted the functional roles of HIV-1 Tat and Mg12+ ion in the regulation of CDK9 activity, which contributes an important complementary understanding of CDK molecular underpinnings.