A survey of lineage-specific genes in Triticeae reveals de novo gene evolution from genomic raw material

Diploid plant genomes typically contain ~35,000 genes, almost all belonging to highly conserved gene families. Only a small fraction are lineage-specific, which are found in only one or few closely related species. Little is known about how genes arise de novo in plant genomes and how often this occurs; however, they are believed to be important for plants diversification and adaptation. We developed a pipeline to identify lineage-specific genes in Triticeae, using newly available genome assemblies of wheat, barley, and rye. Applying a set of stringent criteria, we identified 5942 candidate Triticeae-specific genes (TSGs), of which 2337 were validated as protein-coding genes in wheat. Differential gene expression analyses revealed that stress-induced wheat TSGs are strongly enriched in putative secreted proteins. Some were previously described to be involved in Triticeae non-host resistance and cold response. Additionally, we show that 1079 TSGs have sequence homology to transposable elements (TEs), ~68% of them deriving from regulatory non-coding regions of Gypsy retrotransposons. Most importantly, we demonstrate that these TSGs are enriched in transmembrane domains and are among the most highly expressed wheat genes overall. To summarize, we conclude that de novo gene formation is relatively rare and that Triticeae probably possess ~779 lineage-specific genes per haploid genome. TSGs, which respond to pathogen and environmental stresses, may be interesting candidates for future targeted resistance breeding in Triticeae. Finally, we propose that non-coding regions of TEs might provide important genetic raw material for the functional innovation of TM domains and the evolution of novel secreted proteins

MAF1 is a chronic repressor of RNA polymerase III transcription in the mouse.

Maf1 <sup>-/-</sup> mice are lean, obesity-resistant and metabolically inefficient. Their increased energy expenditure is thought to be driven by a futile RNA cycle that reprograms metabolism to meet an increased demand for nucleotides stemming from the deregulation of RNA polymerase (pol) III transcription. Metabolic changes consistent with this model have been reported in both fasted and refed mice, however the impact of the fasting-refeeding-cycle on pol III function has not been examined. Here we show that changes in pol III occupancy in the liver of fasted versus refed wild-type mice are largely confined to low and intermediate occupancy genes; high occupancy genes are unchanged. However, in Maf1 <sup>-/-</sup> mice, pol III occupancy of the vast majority of active loci in liver and the levels of specific precursor tRNAs in this tissue and other organs are higher than wild-type in both fasted and refed conditions. Thus, MAF1 functions as a chronic repressor of active pol III loci and can modulate transcription under different conditions. Our findings support the futile RNA cycle hypothesis, elaborate the mechanism of pol III repression by MAF1 and demonstrate a modest effect of MAF1 on global translation via reduced mRNA levels and translation efficiencies for several ribosomal proteins

Saffron and its major ingredients’ effect on colon cancer cells with mismatch repair deficiency and microsatellite instability

Background: Colorectal cancer (CRC) is one of the most common cancers worldwide. One of its subtypes is associated with defective mismatch repair (dMMR) genes. Saffron has many potentially protective roles against colon malignancy. However, these roles in the context of dMMR tumors have not been explored. In this study, we aimed to investigate the effects of saffron and its constituents in CRC cell lines with dMMR. Methods: Saffron crude extracts and specific compounds (safranal and crocin) were used in the human colorectal cancer cell lines HCT116, HCT116+3 (inserted MLH1), HCT116+5 (inserted MSH3), and HCT116+3+5 (inserted MLH1 and MSH3). CDC25b, p-H2AX, TPDP1, and GAPDH were analyzed by Western blot. Proliferation and cytotoxicity were analyzed by MTT. The scratch wound assay was also performed. Results: Saffron crude extracts restricted (up to 70%) the proliferation in colon cells with deficient MMR (HCT116) compared to proficient MMR. The wound healing assay indicates that deficient MMR cells are doing better (up to 90%) than proficient MMR cells when treated with saffron. CDC25b and TDP1 downregulated (up to 20-fold) in proficient MMR cells compared to deficient MMR cells, while p.H2AX was significantly upregulated in both cell types, particularly at >10 mg/mL saffron in a concentration-dependent manner. The reduction in cellular proliferation was accompanied with upregulation of caspase 3 and 7. The major active saffron compounds, safranal and crocin reproduced most of the saffron crude extracts' effects. Conclusions: Saffron's anti-proliferative effect is significant in cells with deficient MMR. This novel effect may have therapeutic implications and benefits for MSI CRC patients who are generally not recommended for the 5-fluorouracil-based treatment

Epidemiological evaluation of meniscal ramp lesions in 3214 anterior cruciate ligament–injured knees from the SANTI study group database: a risk factor analysis and study of secondary meniscectomy rates following 769 ramp repairs

Background: Ramp lesions are characterized by disruption of the peripheral meniscocapsular attachments of the posterior horn of the medial meniscus. Ramp repair performed at the time of ACL reconstruction has been shown to improve knee biomechanics. Hypothesis/Purpose: Primary objectives of this study were to evaluate the incidence and risk factors for ramp lesions in a large series of patients undergoing ACL reconstruction, Secondary objectives were to determine the re-operation rate for failure of ramp repair, defined by subsequent re-operations for partial medial meniscectomy Study Design: Case series Methods: All patients underwent trans-notch posteromedial compartment evaluation of the knee during ACL reconstruction. Ramp repair was performed if a lesion was detected. Potentially important risk factors were analyzed for their association with ramp lesions. A secondary analysis of all patients who underwent ramp repair and had a minimum follow-up of two years was undertaken in order to determine the secondary partial meniscectomy rate for failed ramp repair. Results: The overall incidence of ramp lesions in the study population was 23.9% (769 ramp lesions in 3214 patients). Multivariate analysis demonstrated that the presence of ramp lesions was significantly associated with the following risk factors: male gender, patients aged under 30 years, revision ACLR, chronic injuries, pre-operative side-to-side laxity >6 mm and the presence of concomitant lateral meniscus tears. The secondary meniscectomy rate was 10.8% at a mean follow up of 45.6 months (24.2-66.2). Patients who underwent ACLR + ALLR had a greater than 2-fold reduction in the risk of reoperation for failure of ramp repair as compared with patients who underwent isolated ACLR (hazard ratio, 0.457; 95%CI, 0.226-0.864; P = .021). Conclusion: There is a high incidence of ramp lesions in patients undergoing ACLR. The identification of important risk factors for ramp lesions in this study in an individual patient should help raise an appropriate index of suspicion and prompt posteromedial compartment evaluation. The overall secondary partial meniscectomy rate after ramp repair is 10.8%. Anterolateral ligament reconstruction appears to confer a protective effect on the ramp repair performed at the time of ACLR and results in a significant reduction in secondary meniscectomy rates

ATAC-clock: An aging clock based on chromatin accessibility.

The establishment of aging clocks highlighted the strong link between changes in DNA methylation and aging. Yet, it is not known if other epigenetic features could be used to predict age accurately. Furthermore, previous studies have observed a lack of effect of age-related changes in DNA methylation on gene expression, putting the interpretability of DNA methylation-based aging clocks into question. In this study, we explore the use of chromatin accessibility to construct aging clocks. We collected blood from 159 human donors and generated chromatin accessibility, transcriptomic, and cell composition data. We investigated how chromatin accessibility changes during aging and constructed a novel aging clock with a median absolute error of 5.27 years. The changes in chromatin accessibility used by the clock were strongly related to transcriptomic alterations, aiding clock interpretation. We additionally show that our chromatin accessibility clock performs significantly better than a transcriptomic clock trained on matched samples. In conclusion, we demonstrate that the clock relies on cell-intrinsic chromatin accessibility alterations rather than changes in cell composition. Further, we present a new approach to construct epigenetic aging clocks based on chromatin accessibility, which bear a direct link to age-related transcriptional alterations, but which allow for more accurate age predictions than transcriptomic clocks

Influence of MLH1 on colon cancer sensitivity to poly(ADP-ribose) polymerase inhibitor combined with irinotecan

Poly(ADP-ribose) polymerase inhibitors (PARPi) are currently evaluated in clinical trials in combination with topoisomerase I (Top1) inhibitors against a variety of cancers, including colon carcinoma. Since the mismatch repair component MLH1 is defective in 10-15% of colorectal cancers we have investigated whether MLH1 affects response to the Top1 inhibitor irinotecan, alone or in combination with PARPi. To this end, the colon cancer cell lines HCT116, carrying MLH1 mutations on chromosome 3 and HCT116 in which the wildtype MLH1 gene was replaced via chromosomal transfer (HCT116+3) or by transfection of the corresponding MLH1 cDNA (HCT116 1-2) were used. HCT116 cells or HCT116+3 cells stably silenced for PARP-1 expression were also analysed. The results of in vitro and in vivo experiments indicated that MLH1, together with low levels of Top1, contributed to colon cancer resistance to irinotecan. In the MLH1-proficient cells SN-38, the active metabolite of irinotecan, induced lower levels of DNA damage than in MLH1-deficient cells, as shown by the weaker induction of γ-H2AX and p53 phosphorylation. The presence of MLH1 contributed to induce of prompt Chk1 phosphorylation, restoring G2/M cell cycle checkpoint and repair of DNA damage. On the contrary, in the absence of MLH1, HCT116 cells showed minor Chk1 phosphorylation and underwent apoptosis. Remarkably, inhibition of PARP function by PARPi or by PARP-1 gene silencing always increased the antitumor activity of irinotecan, even in the presence of low PARP-1 expression

Natural history and mid-term prognosis of severe tricuspid regurgitation: A cohort study.

OBJECTIVES The objective of this study was to characterize a population of patients with severe tricuspid regurgitation (TR) evaluated at a tertiary care center, assess mid-term clinical outcomes, and identify prognostic factors. BACKGROUND The impact of TR on morbidity and mortality is increasingly recognized. Clinical characteristics and long-term outcomes of patients suffering from TR remain unclear. METHODS This is a retrospective observational single-center study from a tertiary care hospital including patients with echocardiographic diagnosis of severe TR between January 2017 and December 2018. We used the Kaplan-Meier method to estimate survival for up to 4 years. After excluding patients with tricuspid valve (TV) intervention and surgery during follow-up, a multivariate analysis was performed to assess predictors of 2-year mortality using the Cox regression model. RESULTS A total of 278 patients (mean age 74.9 ± 13.7 years, 47.8% female) with severe TR were included in the study. The majority (83.1%; n = 231) had secondary TR. Comorbidities such as atrial fibrillation (AFib) (68.0%; n = 189), severe renal failure (44.2%; n = 123), pulmonary hypertension (PHT) (80.9%; n = 225), and right ventricular (RV) dysfunction (59.7%; n = 166) were highly prevalent. More than half of patients with a cardiac implantable electronic device (CIED) (54.3%; n = 44) showed echocardiographic signs of lead-leaflet interaction causing or contributing to TR. The estimated 2- and 4-year all-cause mortality was 50 and 69%, respectively. Using multivariate analysis, age, severe renal failure, heart failure with reduced ejection fraction (HFrEF), and vena contracta width ≥14 mm were identified as predictors of 2-year mortality. Nine percent (n = 25) of the study cohort underwent transcatheter or surgical treatment for TR during follow-up. CONCLUSION Our study shows the high burden of morbidity and the dismal survival of patients with severe TR. It also highlights the extent of the therapeutic need, since the vast majority of patients were left untreated. Additionally, CIED RV lead-associated TR was prevalent suggesting a need for more attention in clinical routine and research

Technical and Clinical Outcomes After Transcatheter Edge-to-Edge Repair of Mitral Regurgitation in Male and Female Patients: Is Equality Achieved?

Currently, no clear impact of sex on short- and long-term survival following transcatheter edge-to-edge mitral valve repair (TEER) is evident, although no data are available on postprocedural life expectancy. Our aim was to assess sex-specific differences in outcomes of patients with mitral regurgitation (MR) treated by TEER. Short-term and 5-year outcomes in men and women undergoing TEER between 2011 and 2018 who were included in the large, multicenter, real-world MitraSwiss registry were analyzed. Outcomes were compared stratified by sex and according to MR cause (primary versus secondary). The impact of TEER on postprocedural life expectancy was estimated by relative survival analysis. Among 1142 patients aged 60 to 89 years, 39.8% were women. They were older, with fewer cardiovascular risk factors and lower functional capacity compared with men. Thirty-day mortality was higher in men than in women (3.3% versus 1.1%; odds ratio, 3.16 [95% CI, 1.16-10.7]; P=0.020). Five-year survival was comparable in both sexes (adjusted hazard ratio for 5-year mortality in men, 1.14 [95% CI, 0.90-1.44], P=0.275). Both men and women with either primary or secondary MR showed similar clinical efficacy over time. TEER provided high relative survival estimates among all groups, and fully restored predicted life expectancy in women with primary MR (5-year relative survival estimate, 97.4% [95% CI, 85.5-107.0]). TEER is not associated with increased short-term mortality in women, whereas 5-year outcomes are comparable between sexes. Moreover, TEER completely restored normal life expectancy in women with primary MR. A residual excess mortality persists in secondary MR, independently of sex

Ancient variation of the AvrPm17 gene in powdery mildew limits the effectiveness of the introgressed rye Pm17 resistance gene in wheat

Introgressions of chromosomal segments from related species into wheat are important sources of resistance against fungal diseases. The durability and effectiveness of introgressed resistance genes upon agricultural deployment is highly variable-a phenomenon that remains poorly understood, as the corresponding fungal avirulence genes are largely unknown. Until its breakdown, the Pm17 resistance gene introgressed from rye to wheat provided broad resistance against powdery mildew (Blumeria graminis). Here, we used quantitative trait locus (QTL) mapping to identify the corresponding wheat mildew avirulence effector AvrPm17. It is encoded by two paralogous genes that exhibit signatures of reoccurring gene conversion events and are members of a mildew sublineage specific effector cluster. Extensive haplovariant mining in wheat mildew and related sublineages identified several ancient virulent AvrPm17 variants that were present as standing genetic variation in wheat powdery mildew prior to the Pm17 introgression, thereby paving the way for the rapid breakdown of the Pm17 resistance. QTL mapping in mildew identified a second genetic component likely corresponding to an additional resistance gene present on the 1AL.1RS translocation carrying Pm17. This gene remained previously undetected due to suppressed recombination within the introgressed rye chromosomal segment. We conclude that the initial effectiveness of 1AL.1RS was based on simultaneous introgression of two genetically linked resistance genes. Our results demonstrate the relevance of pathogen-based genetic approaches to disentangling complex resistance loci in wheat. We propose that identification and monitoring of avirulence gene diversity in pathogen populations become an integral part of introgression breeding to ensure effective and durable resistance in wheat