Linear models for diallel crosses: a review with R functions

SENP1 inhibits ferroptosis and promotes head and neck squamous cell carcinoma by regulating ACSL4 protein stability via SUMO1

Head and neck squamous cell carcinoma (HNSCC) is currently one of the most common malignancies with a poor prognosis worldwide. Meanwhile, small ubiquitin‑like modifier (SUMO) specific peptidase 1 (SENP1) was associated with ferroptosis. However, the specific functions and underlying mechanisms of action of SENP1 in ferroptosis and tumor progression of HNSCC remain to be established. The findings of the present study implicated a novel ferroptosis pathway in the initiation and progression of HNSCC, providing new functional targets to guide future therapy. In the present study, The Cancer Genome Atlas database was employed to establish a gene model related to ferroptosis and verified SENP1 as a key gene via transcriptome sequencing. Expression of SENP1 in HNSCC tissue and CAL‑27 cells was detected based on reverse transcription‑quantitative PCR and western blot analysis. Proliferation and migration abilities of cells were determined using Cell Counting Kit‑8, wound healing and Transwell experiments. Expression levels of iron, glutathione (GSH) and lipid peroxidation end‑product malondialdehyde (MDA) under conditions of silencing of SENP1 with shRNA lentivirus were assayed. Additionally, the relationship between SENP1 and long‑chain acyl‑coenzyme A synthase 4 (ACSL4) was validated with the aid of immunoblotting and co‑immunoprecipitation (co‑IP). Finally, the influence of shSENP1 on the expression of key ferroptosis proteins, glutathione peroxidase 4 (GPX4) and solute carrier family 7 member 11, was evaluated via western blotting. It was revealed that SENP1 was significantly overexpressed in HNSCC and associated with low patient survival. Silencing of SENP1 led to significant suppression of cell proliferation, migration and invasion, increase in the contents of iron ions and MDA and decline in GSH levels in HNSCC cells, thereby enhancing ferroptosis and inhibiting disease progression. Conversely, overexpression of SENP1 suppressed ferroptosis and promoted progression of HNSCC. Co‑IP and western blot analyses revealed a SUMOylation link between SENP1 and ACSL4. SENP1 reduced the stability of ACSL4 protein through deSUMOylation, leading to inhibition of ferroptosis. SENP1 silencing further inhibited the expression of the key iron death protein, GPX4, to regulate ferroptosis. Taken together, SENP1 deficiency promoted ferroptosis and inhibited tumor progression through reduction of SUMOylation of ACSL4 in HNSCC. The collective results of the present study supported the utility of SENP1 as an effective predictive biomarker for targeted treatment of HNSCC.

Differential Transcriptomic Landscapes of SARS-CoV-2 Variants in Multiple Organs from Infected Rhesus Macaques

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the persistent coronavirus disease 2019 (COVID-19) pandemic, which has resulted in millions of deaths worldwide and brought an enormous public health and global economic burden. The recurring global wave of infections has been exacerbated by growing variants of SARS-CoV-2. In this study, the virological characteristics of the original SARS-CoV-2 strain and its variants of concern (VOCs; including Alpha, Beta, and Delta) in vitro, as well as differential transcriptomic landscapes in multiple organs (lung, right ventricle, blood, cerebral cortex, and cerebellum) from the infected rhesus macaques, were elucidated. The original strain of SARS-CoV-2 caused a stronger innate immune response in host cells, and its VOCs markedly increased the levels of subgenomic RNAs, such as N, Orf9b, Orf6, and Orf7ab, which are known as the innate immune antagonists and the inhibitors of antiviral factors. Intriguingly, the original SARS-CoV-2 strain and Alpha variant induced larger alteration of RNA abundance in tissues of rhesus monkeys than Beta and Delta variants did. Moreover, a hyperinflammatory state and active immune response were shown in the right ventricles of rhesus monkeys by the up-regulation of inflammation- and immune-related RNAs. Furthermore, peripheral blood may mediate signaling transmission among tissues to coordinate the molecular changes in the infected individuals. Collectively, these data provide insights into the pathogenesis of COVID-19 at the early stage of infection by the original SARS-CoV-2 strain and its VOCs.

Evaluation of reciprocal F1 crosses of Fayoumi with two exotic chicken breeds 1: additive and non-additive effects on egg production traits

The present study estimates additive and non-additive effects on egg production traits in genotypes generated through pure mating and reciprocal crossing of Fayoumi (FM) with Koekoek (KK) and White Leghorn (WL). Age at first egg (AFE) and body weight at first egg (BWAFE) were determined when the first bird in the pen laid its first egg, and egg weight at first egg (EWAFE) was the average weight of eggs laid consecutively during the first 10 days. Egg number (EN) and egg weight (EW) were recorded daily from AFE to 40 weeks of age. Egg mass (EM) was the product of EN and EW. EN of hens initially housed and hens alive during the experiment were used to calculate hen-housed egg production (HHEP) and hen-day egg production (HDEP), respectively. All the traits showed statistically significant differences among the genotypes. The results revealed the importance of additive and non-additive effects, where purebred effect (PE), general combining ability (GCA), maternal effect (ME), specific combining ability (SCA), and residual reciprocal effect (RRE) significantly affected most of the traits. The KK and WL had a higher PE, and GCA was highest in KK, with FM and WL showing a higher ME. The FM x WL had higher SCA and RRE. The KK x FM and FM x WL outperformed their main and reciprocal crosses, respectively, and purebred contemporaries. Therefore, a synthetic breeding program involving KK as a sire and FM, WL, FM x WL, and KK x FM as a dam would be feasible.

Heritability of temperature-mediated flower size plasticity in Arabidopsis thaliana

Phenotypic plasticity is a heritable trait that provides sessile organisms a strategy to rapidly mitigate negative effects of environmental change. Yet, we have little understanding of the mode of inheritance and genetic architecture of plasticity in different focal traits relevant to agricultural applications. This study builds on our recent discovery of genes controlling temperature-mediated flower size plasticity in Arabidopsis thaliana and focuses on dissecting the mode of inheritance and combining ability of plasticity in the context of plant breeding. We created a full diallel cross using 12 A. thaliana accessions displaying different temperature-mediated flower size plasticities, scored as the fold change between two temperatures. Griffing's analysis of variance in flower size plasticity indicated that non-additive genetic action shapes this trait and pointed at challenges and opportunities when breeding for reduced plasticity. Our findings provide an outlook of flower size plasticity that is important for developing resilient crops for future climates.

Genotype × environment interaction obscures genetic sources of variation in seed size in Dithyrea californica but provides the opportunity for selection on phenotypic plasticity

PREMISE

In many species, seed size influences individual fitness, but its heritability is low, impeding its evolution. In heterogeneous environments, even if heritability of seed size is low, genetic variation in phenotypic plasticity for seed size may provide the opportunity for selection, but this possibility has rarely been investigated in wild species. The evolutionary trajectory of seed size depends on whether additive, maternal, or non-additive genetic variance dominates; moreover, the expression of any of these sources of variance may be environment-dependent, reflecting genetic variation in plasticity. In this study, we examined these sources of variation in seed size and their response to drought in Dithyrea californica.

METHODS

We used a diallel design to estimate variance components for seed size in three greenhouse-raised populations sampled from California and northern Mexico. We replicated diallels in two watering treatments to examine genetic parameters and genotype × environment interactions affecting seed size. We estimated general (GCA) and specific (SCA) combining ability, reciprocal effects (RGCA and RSCA), and their interactions with water availability, and we sought evidence that sexual conflict influences seed size.

RESULTS

Norms of reaction revealed genetic variation in plasticity for seed size in each population. Seed size in D. californica is determined by the combination of watering treatment, GCA and RGCA; parental identity and water availability do not consistently affect seed size, and we detected no evidence for sexual conflict.

CONCLUSIONS

Multiple sources of genetic variation in phenotypic plasticity for seed size have the potential to influence its evolutionary trajectory in heterogenous environments.

Glucocorticoids enhance chemotherapy-driven stress granule assembly and impair granule dynamics leading to cell death

Stress granules (SGs) can assemble in cancer cells upon chemotoxic stress. Glucocorticoids function during stress responses and are administered with chemotherapies. The roles of glucocorticoids in SG assembly and disassembly pathways are unknown. We examined whether combining glucocorticoids such as cortisone with chemotherapies from the vinca alkaloid family, which dismantle the microtubule network, affects SG assembly and disassembly pathways and influences cell viability in cancer cells and human-derived organoids. Cortisone augmented SG formation when combined with vinorelbine (VRB). Live-cell imaging showed that cortisone increased SG assembly rates but reduced SG clearance rates after stress, by increasing protein residence times within the SGs. Mechanistically, VRB and cortisone signaled through the integrated stress response mediated by eIF2α (also known as EIF2S1), yet induced different kinases, with cortisone activating the GCN2 kinase (also known as EIF2AK4). Cortisone increased VRB-induced cell death and reduced the population of cells trapped in mitotic catastrophe. These effects were mediated by the core SG proteins G3BP1 and G3BP2. In conclusion, glucocorticoids induce SG assembly and cell death when administered with chemotherapies, suggesting that combining glucocorticoids with chemotherapies can enhance cancer cell chemosensitivity.

Summary: Combining cortisone with the chemotherapy vinorelbine enhances the assembly of stress granules that are less likely to be cleared from the cells, augmenting vinorelbine-induced cell death.

The Association of MEG3 lncRNA with Nuclear Speckles in Living Cells

Nuclear speckles are nuclear bodies containing RNA-binding proteins as well as RNAs including long non-coding RNAs (lncRNAs). Maternally expressed gene 3 (MEG3) is a nuclear retained lncRNA found to associate with nuclear speckles. To understand the association dynamics of MEG3 lncRNA with nuclear speckles in living cells, we generated a fluorescently tagged MEG3 transcript that could be detected in real time. Under regular conditions, transient association of MEG3 with nuclear speckles was observed, including a nucleoplasmic fraction. Transcription or splicing inactivation conditions, known to affect nuclear speckle structure, showed prominent and increased association of MEG3 lncRNA with the nuclear speckles, specifically forming a ring-like structure around the nuclear speckles. This contrasted with metastasis-associated lung adenocarcinoma (MALAT1) lncRNA that is normally highly associated with nuclear speckles, which was released and dispersed in the nucleoplasm. Under normal conditions, MEG3 dynamically associated with the periphery of the nuclear speckles, but under transcription or splicing inhibition, MEG3 could also enter the center of the nuclear speckle. Altogether, using live-cell imaging approaches, we find that MEG3 lncRNA is a transient resident of nuclear speckles and that its association with this nuclear body is modulated by the levels of transcription and splicing activities in the cell.