Disease Burden, Risk Factors, and Temporal Trends in Breast Cancer in Low‐ and Middle‐Income Countries: A Global Study

Introduction: Breast cancer poses significant health risks to women and strains healthcare systems extensively. In low‐ and middle‐income countries (LMICs), limited resources and inadequate healthcare infrastructures further exacerbate the challenges of breast cancer prevention, treatment, and awareness. Methods: We examined the prevalence, risk factors, and trends of breast cancer in LMICs. Data on disability‐adjusted life years (DALYs) and breast cancer risk factors were extracted from the Global Burden of Disease (GBD) databases for 203 countries or territories from 1990 to 2019. LMIC DALY rates were examined using joinpoint regression analysis. Results: Among the income groups, the lower middle‐income category had the highest DALYs value, with 1787 years per 100,000 people. LMICs collectively accounted for 74% of the global burden of DALYs lost due to breast cancer in 2019. However, it remained relatively consistent in lower middle income countries (LMCs). In LMCs, the risk associated with metabolic syndromes was higher compared to that with behavioral factors alone. For the past three decades, breast cancer incidences increased significantly in LMCs (average annual percent change [AAPC]: 1.212, confidence intervals [CI]: 1.51–1.87, p < 0.001), upper middle income countries (AAPC: 1.701, CI: 1.12–1.48, p < 0.001), and low‐income countries (AAPC: 1.002, CI: 1.57–1.68, p < 0.001). Conclusion: This research shows how breast cancer in LMICs is aggravated by low resources and healthcare infrastructure. To effectively combat breast cancer in these areas, future strategies must prioritize improvements in healthcare infrastructure, awareness campaigns, and early detection mechanisms

Whole-Genome Analysis of ZF-HD Genes among Three <i>Dendrobium</i> Species and Expression Patterns in <i>Dendrobium chrysotoxum</i>

ZF-HD transcription factors, which are unique to land plants, are involved in the regulation of abiotic stress response and related signaling pathways, and play a crucial role in plant growth and development. Dendrobium is one of the largest genera of orchids, with a high ornamental and ecological value. However, the specific functions of the ZF-HDs in Dendrobium remain unknown. In this study, we identified a total of 53 ZF-HDs from D. chrysotoxum (17), D. catenatum (23), and D. huoshanense (13), and analyzed their physicochemical properties, phylogenetic relationships, chromosomal locations, protein structures, conserved motifs, and expression patterns. The phylogenetic relationships revealed that 53 ZF-HDs were classified into six subfamilies (ZHDI–V and MIF), and all ZF-HD proteins contained motif 1 and motif 4 conserved domains, while a minority of these proteins had exons. The analysis of cis-elements in the promoters of ZF-HDs from three Dendrobium species showed that growth- and development-related elements were the most prevalent, followed by hormone response and abiotic stress response elements. Through collinearity analysis, 14 DchZF-HDs were found to be collinear with DhuZF-HDs, and 12 DchZF-HDs were found to be collinear with DcaZF-HDs. Furthermore, RT-qPCR analysis revealed that DchZF-HDs play a regulatory role in the development of lateral organs during the flowering process. The results indicated that DchZHD2 plays a role in the unpigmented bud stage, while DchMIF8 and DchZHD16 play significant roles during the pigmented bud and initial bloom stages. Hence, this study provides a crucial basis for further exploring ZF-HDs functions in regulating the floral organs of orchids

Genome-Wide Identification and Expression Analysis of the GRAS Gene Family and Their Responses to Heat Stress in <i>Cymbidium goeringii</i>

The GRAS gene family, responsible for encoding transcription factors, serves pivotal functions in plant development, growth, and responses to stress. The exploration of the GRAS gene family within the Orchidaceae has been comparatively limited, despite its identification and functional description in various plant species. This study aimed to conduct a thorough examination of the GRAS gene family in Cymbidum goeringii, focusing on its physicochemical attributes, phylogenetic associations, gene structure, cis-acting elements, and expression profiles under heat stress. The results show that a total of 54 CgGRASs were pinpointed from the genome repository and categorized into ten subfamilies via phylogenetic associations. Assessment of gene sequence and structure disclosed the prevalent existence of the VHIID domain in most CgGRASs, with around 57.41% (31/54) CgGRASs lacking introns. The Ka/Ks ratios of all CgGRASs were below one, indicating purifying selection across all CgGRASs. Examination of cis-acting elements unveiled the presence of numerous elements linked to light response, plant hormone signaling, and stress responsiveness. Furthermore, CgGRAS5 contained the highest quantity of cis-acting elements linked to stress response. Experimental results from RT-qPCR demonstrated notable variations in the expression levels of eight CgGRASs after heat stress conditions, particularly within the LAS, HAM, and SCL4/7 subfamilies. In conclusion, this study revealed the expression pattern of CgGRASs under heat stress, providing reference for further exploration into the roles of CgGRAS transcription factors in stress adaptation

Genome-Wide Identification and Expression Analysis of the SPL Gene Family in Three Orchids

SPL transcription factors regulate important processes such as plant growth and development, metabolic regulation, and abiotic stress. They play crucial roles in the development of flower organs. However, little is known about the characteristics and functions of the SPLs in the Orchidaceae. In this study, Cymbidium goeringii Rchb. f., Dendrobium chrysotoxum Lindl., and Gastrodia elata BI. were used as research objects. The SPL gene family of these orchids was analyzed on a genome-wide scale, and their physicochemical properties, phylogenetic relationships, gene structures, and expression patterns were studied. Transcriptome and qRT-PCR methods were combined to investigate the regulatory effect of SPLs on the development of flower organs during the flowering process (bud, initial bloom, and full bloom). This study identifies a total of 43 SPLs from C. goeringii (16), D. chrysotoxum (17), and G. elata (10) and divides them into eight subfamilies according to the phylogenetic tree. Most SPL proteins contained conserved SBP domains and complex gene structures; half of the genes had introns longer than 10 kb. The largest number and variety of cis-acting elements associated with light reactions were enriched, accounting for about 45% of the total (444/985); 13/43 SPLs contain response elements of miRNA156. GO enrichment analysis showed that the functions of most SPLs were mainly enriched in the development of plant flower organs and stems. In addition, expression patterns and qRT-PCR analysis suggested the involvement of SPL genes in the regulation of flower organ development in orchids. There was little change in the expression of the CgoSPL in C. goeringii, but DchSPL9 and GelSPL2 showed significant expression during the flowering process of D. chrysotoxum and G. elata, respectively. In summary, this paper provides a reference for exploring the regulation of the SPL gene family in orchids

Construction and validation of a fatty acid metabolism-related gene signature for predicting prognosis and therapeutic response in patients with prostate cancer

Background Reprogramming of fatty acid metabolism is a newly-identified hallmark of malignancy. However, no studies have systematically investigated the fatty acid metabolism related-gene set in prostate cancer (PCa). Methods A cohort of 381 patients with gene expression and clinical data from The Cancer Genome Atlas was used as the training set, while another cohort of 90 patients with PCa from GEO (GSE70769) was used as the validation set. Differentially expressed fatty acid metabolism-related genes were subjected to least absolute shrinkage and selection operator (LASSO)-Cox regression to establish a fatty acid metabolism-related risk score. Associations between the risk score and clinical characteristics, immune cell infiltration, tumor mutation burden (TMB), tumor immune dysfunction and exclusion (TIDE) score, and response to chemotherapy were analyzed. Finally, the expression level of genes included in the model was validated using real-time PCR. Results A prognostic risk model based on five fatty acid metabolism related genes (ALDH1A1, CPT1B, CA2, CROT, and NUDT19) were constructed. Tumors with higher risk score were associated with larger tumor size, lymph node involvement, higher Gleason score, and poorer biochemical recurrence (BCR)-free survival. Furthermore, the high- and low-risk tumors exhibited distinct immune cell infiltration features and immune-related pathway activation. High-risk tumors were associated with favorable response to immunotherapy as indicated by high TMB and low TIDE score, but poor response to bicalutamide and docetaxel chemotherapy. Conclusion This study established a fatty acid metabolism-related gene signature which was predictive of BCR and response to chemotherapy and immunotherapy, providing a novel therapeutic biomarker for PCa

Genome-Wide Identification of the ARF Gene Family in Three <i>Dendrobium</i> Species and Its Expression Pattern Analysis in <i>D. nobile</i> Flower

The ARF gene family is a representative transcription factor that plays a crucial role in the regulation of various growth and development processes in plants. Although the ARF gene family has been identified in five Orchidaceae species, limited research has been conducted on the ARF gene within Dendrobium. To explore ARF family genes in different Dendrobium species, we selected chromosome-level genomic data from D. nobile, D. chrysotoxum, and D. huoshanense for genome-wide identification, and to analyze expression patterns in the D. nobile flower. In this study, 13, 18, and 23 ARF genes were identified in the genomes of D. chrysotoxum, D. huoshanense, and D. nobile, respectively. These genes were then subsequently classified into four classes (Classes I, II, III, and IV) based on our phylogenetic analysis. Additional protein sequence analysis found that 30 ARF proteins with three classically conserved structural domains (BDB, MR, and RD) were present in the three Dendrobium species. Our gene structure comparative analysis also found the same evolutionary branch with similar intron-exon structural features. Specifically, Class I and Class III display longer introns that potentially constitute a distinctive characteristic of Dendrobium. Gene expression patterns analysis showed the potential involvement of DnoARF 5, 7, 10, 11, 12, 13, 16, 17, and 23 in initial differentiation and flower bud formation. Likewise, transcriptomic analysis and RT-qPCR expression profiles indicated flower-specific expression patterns for four ARF genes (DnoARF5, DnoARF6, DnoARF16, and DnoARF22), which suggest an important impact on flower development and regulation. Ultimately, this study provides comprehensive data to elucidate the potential functions of ARF genes in three Dendrobium species and suggests new insights for further exploration concerning the function and regulatory mechanisms in Dendrobium during flower development

Genome-Wide Identification of TCP Gene Family in <i>Dendrobium</i> and Their Expression Patterns in <i>Dendrobium chrysotoxum</i>

The TCP gene family are plant-specific transcription factors that play important roles in plant growth and development. Dendrobium chrysotoxum, D. nobile, and D. huoshanense are orchids with a high ornamental value, but few studies have investigated the specific functions of TCPs in Dendrobium flower development. In this study, we used these three Dendrobium species to analyze TCPs, examining their physicochemical properties, phylogenetic relationships, gene structures, and expression profiles. A total of 50 TCPs were identified across three Dendrobium species; they were divided into two clades—Class-I (PCF subfamily) and Class-II (CIN and CYC/TB1 subfamilies)—based on their phylogenetic relationships. Our sequence logo analysis showed that almost all Dendrobium TCPs contain a conserved TCP domain, as well as the existence of fewer exons, and the cis-regulatory elements of the TCPs were mostly related to light response. In addition, our transcriptomic data and qRT-PCR results showed that DchTCP2 and DchTCP13 had a significant impact on lateral organs. Moreover, changes in the expression level of DchTCP4 suggested its important role in the phenotypic variation of floral organs. Therefore, this study provides a significant reference for the further exploration of TCP gene functions in the regulation of different floral organs in Dendrobium orchids

Genome-Wide Identification of the YABBY Gene Family in <i>Dendrobium</i> Orchids and Its Expression Patterns in <i>Dendrobium chrysotoxum</i>

The small plant-specific YABBY gene family plays key roles in diverse developmental processes in plants. Dendrobium chrysotoxum, D. huoshanense, and D. nobile are perennial herbaceous plants belonging to Orchidaceae with a high ornamental value. However, the relationships and specific functions of the YABBY genes in the Dendrobium species remain unknown. In this study, six DchYABBYs, nine DhuYABBYs, and nine DnoYABBYs were identified from the genome databases of the three Dendrobium species, which were unevenly distributed on five, eight, and nine chromosomes, respectively. The 24 YABBY genes were classified into four subfamilies (CRC/DL, INO, YAB2, and FIL/YAB3) based on their phylogenetic analysis. A sequence analysis showed that most of the YABBY proteins contained conserved C2C2 zinc-finger and YABBY domains, while a gene structure analysis revealed that 46% of the total YABBY genes contained seven exons and six introns. All the YABBY genes harbored a large number of Methyl Jasmonate responsive elements, as well as anaerobic induction cis-acting elements in the promoter regions. Through a collinearity analysis, one, two, and two segmental duplicated gene pairs were identified in the D. chrysotoxum, D. huoshanense, and D. nobile genomes, respectively. The Ka/Ks values of these five gene pairs were lower than 0.5, indicating that the Dendrobium YABBY genes underwent negative selection. In addition, an expression analysis revealed that DchYABBY2 plays a role in ovary and early-stage petal development, while DchYABBY5 is essential for lip development and DchYABBY6 is crucial for early sepal formation. DchYABBY1 primarily regulates sepals during blooming. Furthermore, there is the potential involvement of DchYABBY2 and DchYABBY5 in gynostemium development. The results of a comprehensive genome-wide study would provide significant clues for future functional investigations and pattern analyses of YABBY genes in different flower parts during flower development in the Dendrobium species