Multi-transcriptome analysis following an acute skeletal muscle growth stimulus yields tools for discerning global and MYC regulatory networks.

Myc is a powerful transcription factor implicated in epigenetic reprogramming, cellular plasticity, and rapid growth as well as tumorigenesis. Cancer in skeletal muscle is extremely rare despite marked and sustained Myc induction during loading-induced hypertrophy. Here, we investigated global, actively transcribed, stable, and myonucleus-specific transcriptomes following an acute hypertrophic stimulus in mouse plantaris. With these datasets, we define global and Myc-specific dynamics at the onset of mechanical overload-induced muscle fiber growth. Data collation across analyses reveals an under-appreciated role for the muscle fiber in extracellular matrix remodeling during adaptation, along with the contribution of mRNA stability to epigenetic-related transcript levels in muscle. We also identify Runx1 and Ankrd1 (Marp1) as abundant myonucleus-enriched loading-induced genes. We observed that a strong induction of cell cycle regulators including Myc occurs with mechanical overload in myonuclei. Additionally, in vivo Myc-controlled gene expression in the plantaris was defined using a genetic muscle fiber-specific doxycycline-inducible Myc-overexpression model. We determined Myc is implicated in numerous aspects of gene expression during early-phase muscle fiber growth. Specifically, brief induction of Myc protein in muscle represses Reverbα, Reverbß, and Myh2 while increasing Rpl3, recapitulating gene expression in myonuclei during acute overload. Experimental, comparative, and in silico analyses place Myc at the center of a stable and actively transcribed, loading-responsive, muscle fiber-localized regulatory hub. Collectively, our experiments are a roadmap for understanding global and Myc-mediated transcriptional networks that regulate rapid remodeling in postmitotic cells. We provide open webtools for exploring the five RNA-seq datasets as a resource to the field.

BAIAP2L1 accelerates breast cancer progression and chemoresistance by activating AKT signaling through binding with ribosomal protein L3.

BAI1-associated protein 2-like 1 (BAIAP2L1), also known as insulin receptor tyrosine kinase substrate, modulates the insulin network; however, its function in breast cancer has not been explored. Immunohistochemical analysis of 140 breast cancer specimens (77 triple-negative and 63 nontriple-negative cases) indicated that BAIAP2L1 expression was higher in breast cancer tissues (56/140, 40%) than in normal breast tissues (28.3%, 15/53; p < 0.001). BAIAP2L1 expression in breast cancer was correlated with triple-negative breast cancer (p = 0.0013), advanced TNM stage (p = 0.001), lymph node metastasis (p = 0.001), and poor patient prognosis (p = 0.001). BAIAP2L1 overexpression could accelerate breast cancer proliferation, invasion, and stemness in vivo and in vitro, possibly through the activation of AKT, Snail, and cyclin D1. Treatment with the AKT inhibitor LY294002 reduced the effects of BAIAP2L1 overexpression on breast cancer cells. BAIAP2L1 may bind to the AA202-288 of ribosomal protein L3 (RPL3) within its SRC homology 3 (SH3) domain, the loss of which may abolish the transduction of the AKT signaling pathway by promoting the degradation of PIK3CA. Moreover, BAIAP2L1 overexpression may induce chemotherapy resistance, with BAIAP2L1 expression being higher in patients with advanced Miller grades than those with lower grades. Our results indicated that BAIAP2L1 promotes breast cancer progression through the AKT signaling pathway by interacting with RPL3 through its SH3 domain.

Ribosomal Proteins Control or Bypass p53 during Nucleolar Stress.

The nucleolus is the site of ribosome biogenesis, a complex process that requires the coordinate activity of all three RNA polymerases and hundreds of non-ribosomal factors that participate in the maturation of ribosomal RNA (rRNA) and assembly of small and large subunits. Nevertheless, emerging studies have highlighted the fundamental role of the nucleolus in sensing a variety of cellular stress stimuli that target ribosome biogenesis. This condition is known as nucleolar stress and triggers several response pathways to maintain cell homeostasis, either p53-dependent or p53-independent. The mouse double minute (MDM2)-p53 stress signaling pathways are activated by multiple signals and are among the most important regulators of cellular homeostasis. In this review, we will focus on the role of ribosomal proteins in p53-dependent and p53-independent response to nucleolar stress considering novel identified regulators of these pathways. We describe, in particular, the role of ribosomal protein uL3 (rpL3) in p53-independent nucleolar stress signaling pathways.

Novel compound heterozygous variants in the RPL3L gene causing dilated cardiomyopathy type-2D: a case report and literature review.

BACKGROUND: Dilated cardiomyopathy type-2D (CMD2D) is a rare heart disease causing a severe cardiomyopathy with neonatal onset and rapid progression to cardiac decompensation and death in untreated patients. CMD2D is an autosomal recessive disease resulting from variants in the RPL3L gene, which encodes the 60 S ribosomal protein exclusively expressed in skeletal and cardiac muscle and plays an essential role in myoblast growth and fusion. Previous reports have only associated CMD2D with a small duplication and seven nucleotide substitution in the RPL3L gene. CASE PRESENTATION: In this study, we report the case of a 31 days old Chinese infant patient with severe dilated cardiomyopathy (DCM) and rapid decompensation along with other cardiac malformations. In addition to previously reported clinical features, the patient showed the previously unreported complication of occasional premature atrial contractions and a first-degree atrioventricular block. Whole-exome sequencing (WES) revealed compound heterozygous variants (c.80G > A (p.Gly27Asp) and c.1074dupA (p.Ala359fs*6)) in RPL3L (NM_005061.3). The latter novel variant may result in the absence of protein production with a significant decrease in mRNA level, suggesting it is a loss-of-function mutation. CONCLUSIONS: This is the first case report of RPL3L-associated neonatal dilated cardiomyopathy in China. The molecular confirmation of the patient expands the genetic spectrum of CMD2D, and the clinical manifestation of CMD2D in the patient provides additional clinical information regarding this disease.

Compound Heterozygous Missense Variants in RPL3L Genes Associated with Severe Forms of Dilated Cardiomyopathy: A Case Report and Literature Review.

Whole exome sequencing has identified an infant girl with fulminant dilated cardiomyopathy (DCM), leading to severe acute heart failure associated with ribosomal protein large 3-like (RPL3L) gene pathologic variants. Other genetic tests for mitochondrial disorders by sequence analysis and deletion testing of the mitochondrial genome were negative. Secondary causes for DCM due to metabolic and infectious etiologies were ruled out. She required a Berlin-Excor left ventricular assist device due to worsening of her heart failure as a bridge to orthotopic heart transplantation. At three months follow-up after heart transplantation, she has been doing well. We reviewed the literature on published RPL3L-related DCM cases and their outcomes. Bi-allelic variants in RPL3L have been reported in only seven patients from four unrelated families in the literature. RPL3L is a newer and likely pathogenic gene associated with a severe form of early-onset dilated cardiomyopathy with poor prognosis necessitating heart transplantation.

Mining of chicken muscle growth genes and the function of important candidate gene RPL3L in muscle development.

The birth weight of chickens does not significantly affect the weight at slaughter, while the different growth rate after birth was one of the important reasons for the difference in slaughter weight. Also, the increase in chickens' postnatal skeletal muscle weight is the main cause of the slaughter weight gain, but which genes are involved in this biological process is still unclear. In this study, by integrating four transcriptome datasets containing chicken muscles at different developmental times or different chicken tissues in public databases, a total of nine candidate genes that may be related to postnatal muscle development in chickens were obtained, including RPL3L, FBP2, ASB4, ASB15, CKMT2, PGAM1, YIPF7, PFKM, and LDHA. One of these candidate genes is RPL3L, whose 42 bp insertion/deletion (indel) mutation significantly correlated with multiple carcass traits in the F2 resource population from Xinghua chickens crossing with White Recessive Rock (WRR) chickens, including live weight, carcass weight, half eviscerated weight, eviscerated weight, breast meat weight, wing weight, leg muscle shear force, and breast muscle shear force. Also, there was a very significant difference between different genotypes of the RPL3L 42 bp indel mutation in these trains. Further experiments showed that RPL3L was highly expressed in chicken skeletal muscle, and its overexpression could promote the proliferation and inhibit the differentiation of chicken myoblasts by regulating ASB4 and ASB15 expression. Our findings demonstrated that the RPL3L 42 bp indel may be one of the molecular markers of chicken weight-related traits.

Identification of two variants in AGRN and RPL3L genes in a patient with catecholaminergic polymorphic ventricular tachycardia suggesting new candidate disease genes and digenic inheritance.

Catecholaminergic polymorphic ventricular tachycardia (CPVT) is an arrhythmogenic syndrome characterized by life-threatening arrhythmias, a normal resting electrocardiogram and the absence of overt structural heart abnormalities. Mutations in RyR2 gene account for the large part of CPVT cases. Less frequently, mutations in CASQ2 gene have been linked to the recessive form of the disease. Overall, approximately 35% of CPVT patients remain without a genetic etiology implying that other genes might be found causative of the disease. Here, we present a 6-year-old boy born to first-degree related parents, with a typical phenotype of CPVT and a family history of sudden cardiac death of his brother at 7 years. A trio-based whole exome sequencing was performed, and we identified a homozygous variant in AGRN gene and a heterozygous variant in RPL3L gene. We hypothesized that the presence of the homozygous variant in AGRN accounts for the CPVT phenotype in this family and the heterozygous variant in RPL3L gene may act as a modifier gene. Further studies are needed to determine the role of these genes in CPVT.

Further Evidence of Autosomal Recessive Inheritance of RPL3L Pathogenic Variants with Rapidly Progressive Neonatal Dilated Cardiomyopathy.

Neonatal dilated cardiomyopathy (DCM) is rare with high etiologic heterogeneity. Recently, biallelic, autosomal recessive, pathogenic variants in RPL3L (ribosomal protein L3-like) have been reported in the literature with severe early-onset DCM. In the present brief report, we identified two pathogenic RPL3L variants, each harbored in unaffected heterozygous parents: mother (RPL3L c.1076_1080delCCGTG (p.Ala359Glyfs*4)) and father (RPL3L c.80G > A (p.Gly27Asp)). Pathogenic variants were segregated as autosomal recessive to two offspring born with compound heterozygous RPL3L variants and affected by neonatal DCM. This is the second report in the literature to the best of our knowledge and our findings support the pathogenicity of biallelic RPL3L pathologic variants associated with rapidly progressive neonatal DCM and heart failure with a poor prognosis.

The Chloroplast Phylogenomics and Systematics of Zoysia (Poaceae).

The genus Zoysia Willd. (Chloridoideae) is widely distributed from the temperate regions of Northeast Asia-including China, Japan, and Korea-to the tropical regions of Southeast Asia. Among these, four species-Zoysia japonica Steud., Zoysia sinica Hance, Zoysia tenuifolia Thiele, and Zoysia macrostachya Franch. & Sav.-are naturally distributed in the Korean Peninsula. In this study, we report the complete plastome sequences of these Korean Zoysia species (NCBI acc. nos. MF953592, MF967579~MF967581). The length of Zoysia plastomes ranges from 135,854 to 135,904 bp, and the plastomes have a typical quadripartite structure, which consists of a pair of inverted repeat regions (20,962~20,966 bp) separated by a large (81,348~81,392 bp) and a small (12,582~12,586 bp) single-copy region. In terms of gene order and structure, Zoysia plastomes are similar to the typical plastomes of Poaceae. The plastomes encode 110 genes, of which 76 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Fourteen genes contain single introns and one gene has two introns. Three evolutionary hotspot spacer regions-atpB~rbcL, rps16~rps3, and rpl32~trnL-UAG-were recognized among six analyzed Zoysia species. The high divergences in the atpB~rbcL spacer and rpl16~rpl3 region are primarily due to the differences in base substitutions and indels. In contrast, the high divergence between rpl32~trnL-UAG spacers is due to a small inversion with a pair of 22 bp stem and an 11 bp loop. Simple sequence repeats (SSRs) were identified in 59 different locations in Z. japonica, 63 in Z. sinica, 62 in Z. macrostachya, and 63 in Z. tenuifolia plastomes. Phylogenetic analysis showed that the Zoysia (Zoysiinae) forms a monophyletic group, which is sister to Sporobolus (Sporobolinae), with 100% bootstrap support. Within the Zoysia clade, the relationship of (Z. sinica, Z japonica), (Z. tenuifolia, Z. matrella), (Z. macrostachya, Z. macrantha) was suggested.

Correlating Chemical Sensitivity with Low Level Activation of Mechanotransduction Pathways in Hematologic Malignancies.

Large-scale screening has revealed that human hematopoietic cancer cell lines are generally more sensitive to various classes of drugs than cell lines established from solid tumors. A detailed examination of data in the Cancer Therapeutics Response Portal (http://portals.broadinstitute.org/ctrp/) suggests that this enhanced sensitivity is due to lower basal levels of activation of TAZ-TEAD mechanotransduction pathways in hematopoietic versus non-hematopoietic cells. Translation inhibitors such as omacetaxine mepesuccinate (homoharringtonine) fall into this category of hematopoietic-selective compounds. Moreover, additional molecular determinants of sensitivity suggest that homoharringtonine might show therapeutic efficacy in certain patients with advanced hematologic malignancies despite activation of these pathways.

Enhancement of 5-FU sensitivity by the proapoptotic rpL3 gene in p53 null colon cancer cells through combined polymer nanoparticles.

Colon cancer is one of the leading causes of cancer-related death worldwide and the therapy with 5-fluorouracil (5-FU) is mainly limited due to resistance. Recently, we have demonstrated that nucleolar stress upon 5-FU treatment leads to the activation of ribosome-free rpL3 (L3) as proapoptotic factor. In this study, we analyzed L3 expression profile in colon cancer tissues and demonstrated that L3 mRNA amount decreased with malignant progression and the intensity of its expression was inversely related to tumor grade and Bcl-2/Bax ratio. With the aim to develop a combined therapy of 5-FU plus plasmid encoding L3 (pL3), we firstly assessed the potentiation of the cytotoxic effect of 5-FU on colon cancer cells by L3. Next, 10 µM 5-FU and 2 µg of pL3 were encapsulated in biocompatible nanoparticles (NPs) chemically conjugated with HA to achieve active tumor-targeting ability in CD44 overexpressing cancer cells. We showed the specific intracellular accumulation of NPs in cells and a sustained release for 5-FU and L3. Analysis of cytotoxicity and apoptotic induction potential of combined NPs clearly showed that the 5-FU plus L3 were more effective in inducing apoptosis than 5-FU or L3 alone. Furthermore, we show that the cancer-specific chemosensitizer effect of combined NPs may be dependent on L3 ability to affect 5-FU efflux by controlling P-gp (P-glycoprotein) expression. These results led us to propose a novel combined therapy with the use of 5-FU plus L3 in order to establish individualized therapy by examining L3 profiles in tumors to yield a better clinical outcomes.