Unveiling the mechanistic link between extracellular amyloid fibrils, mechano-signaling and YAP activation in cancer

The tumor microenvironment is a complex ecosystem that plays a critical role in cancer progression and treatment response. Recently, extracellular amyloid fibrils have emerged as novel components of the tumor microenvironment; however, their function remains elusive. In this study, we establish a direct connection between the presence of amyloid fibrils in the secretome and the activation of YAP, a transcriptional co-activator involved in cancer proliferation and drug resistance. Furthermore, we uncover a shared mechano-signaling mechanism triggered by amyloid fibrils in both melanoma and pancreatic ductal adenocarcinoma cells. Our findings highlight the crucial role of the glycocalyx protein Agrin which binds to extracellular amyloid fibrils and acts as a necessary factor in driving amyloid-dependent YAP activation. Additionally, we reveal the involvement of the HIPPO pathway core kinase LATS1 in this signaling cascade. Finally, we demonstrate that extracellular amyloid fibrils enhance cancer cell migration and invasion. In conclusion, our research expands our knowledge of the tumor microenvironment by uncovering the role of extracellular amyloid fibrils in driving mechano-signaling and YAP activation. This knowledge opens up new avenues for developing innovative strategies to modulate YAP activation and mitigate its detrimental effects during cancer progression.

SnapShot: Tolerating replication stress

Completion of DNA replication relies on the ability of replication forks to traverse various types of DNA damage, actively transcribed regions, and structured DNA. The mechanisms enabling these processes are here referred to as DNA damage tolerance pathways. Here, we depict the stalled DNA replication fork structures with main DNA transactions and key factors contributing to the bypass of such blocks, replication restart, and completion. To view this SnapShot, open or download the PDF.

Sen1 and Rrm3 ensure permissive topological conditions for replication termination

Replication forks terminate at TERs and telomeres. Forks that converge or encounter transcription generate topological stress. Combining genetics, genomics, and transmission electron microscopy, we find that Rrm3^hPif1 and Sen1^hSenataxin helicases assist termination at TERs; Sen1 specifically acts at telomeres. rrm3 and sen1 genetically interact and fail to terminate replication, exhibiting fragility at termination zones (TERs) and telomeres. sen1rrm3 accumulates RNA-DNA hybrids and X-shaped gapped or reversed converging forks at TERs; sen1, but not rrm3, builds up RNA polymerase II (RNPII) at TERs and telomeres. Rrm3 and Sen1 restrain Top1 and Top2 activities, preventing toxic accumulation of positive supercoil at TERs and telomeres. We suggest that Rrm3 and Sen1 coordinate the activities of Top1 and Top2 when forks encounter transcription head on or codirectionally, respectively, thus preventing the slowing down of DNA and RNA polymerases. Hence Rrm3 and Sen1 are indispensable to generate permissive topological conditions for replication termination.

Rad51-mediated replication of damaged templates relies on monoSUMOylated DDK kinase

DNA damage tolerance (DDT), activated by replication stress during genome replication, is mediated by translesion synthesis and homologous recombination (HR). Here we uncover that DDK kinase, essential for replication initiation, is critical for replication-associated recombination-mediated DDT. DDK relies on its multi-monoSUMOylation to facilitate HR-mediated DDT and optimal retention of Rad51 recombinase at replication damage sites. Impairment of DDK kinase activity, reduced monoSUMOylation and mutations in the putative SUMO Interacting Motifs (SIMs) of Rad51 impair replication-associated recombination and cause fork uncoupling with accumulation of large single-stranded DNA regions at fork branching points. Notably, genetic activation of salvage recombination rescues the uncoupled fork phenotype but not the recombination-dependent gap-filling defect of DDK mutants, revealing that the salvage recombination pathway operates preferentially proximal to fork junctions at stalled replication forks. Overall, we uncover that monoSUMOylated DDK acts with Rad51 in an axis that prevents replication fork uncoupling and mediates recombination-dependent gap-filling.

Parental histone deposition on the replicated strands promotes error-free DNA damage tolerance and regulates drug resistance

In this study, Dolce et al. investigated connections between Ctf4-mediated processes involved in drug resistance, and conducted a suppressor screen of ctf4Δ sensitivity to the methylating agent MMS. Their findings demonstrate a chromatin-based drug resistance mechanism in which defects in parental histone transfer after replication fork passage impair error-free recombination bypass and lead to up-regulation of TLS-mediated mutagenesis and drug resistance.

Ctf4 is a conserved replisome component with multiple roles in DNA metabolism. To investigate connections between Ctf4-mediated processes involved in drug resistance, we conducted a suppressor screen of ctf4Δ sensitivity to the methylating agent MMS. We uncovered that mutations in Dpb3 and Dpb4 components of polymerase ε result in the development of drug resistance in ctf4Δ via their histone-binding function. Alleviated sensitivity to MMS of the double mutants was not associated with rescue of ctf4Δ defects in sister chromatid cohesion, replication fork architecture, or template switching, which ensures error-free replication in the presence of genotoxic stress. Strikingly, the improved viability depended on translesion synthesis (TLS) polymerase-mediated mutagenesis, which was drastically increased in ctf4 dpb3 double mutants. Importantly, mutations in Mcm2–Ctf4–Polα and Dpb3–Dpb4 axes of parental (H3–H4)₂ deposition on lagging and leading strands invariably resulted in reduced error-free DNA damage tolerance through gap filling by template switch recombination. Overall, we uncovered a chromatin-based drug resistance mechanism in which defects in parental histone transfer after replication fork passage impair error-free recombination bypass and lead to up-regulation of TLS-mediated mutagenesis and drug resistance.

New-Onset Anemia and Associated Risk of ESKD and Death in Non-Dialysis CKD Patients: A Multi-Cohort Observational Study

Background

Anemia is a common complication of chronic kidney disease (CKD), but its incidence in nephrology settings is poorly investigated. Similarly, the risks of adverse outcomes associated with new-onset anemia are not known.

Methods

We performed a pooled analysis of three observational cohort studies including 1031 non-anemic CKD patients with eGFR <60 mL/min/1.73 m² regularly followed in renal clinics. We estimated the incidence of mild anemia (hemoglobin 11–12 g/dL in women and 11–13 g/dL in men) and severe anemia (hemoglobin <11 g/dL or use of erythropoiesis-stimulating agents) during a 3-year follow-up period. Thereafter we estimated the risk of end-stage kidney disease (ESKD) and all-cause death associated with new-onset mild and severe anemia.

Results

The mean age was 63 ± 14 years, 60% were men and 20% had diabetes. The mean estimated glomerular filtration rate (eGFR) was 37 ± 13 mL/min/1.73 m² and the median proteinuria was 0.4 g/day [interquartile range (IQR) 0.1–1.1]. The incidence of mild and severe anemia was 13.7/100 patients-year and 6.2/100 patients-year, respectively. Basal predictors of either mild or severe anemia were diabetes, lower hemoglobin, higher serum phosphate, eGFR <30 mL/min/1.73 m² and proteinuria >0.50 g/day. Male sex, moderate CKD (eGFR 30–44 mL/min/1.73 m²) and moderate proteinuria (0.15–0.50 g/day) predicted only mild anemia. The incidence of anemia increased progressively with CKD stages (from 8.77 to 76.59/100 patients-year) and the proteinuria category (from 13.99 to 25.02/100 patients-year). During a median follow-up of 3.1 years, 232 patients reached ESKD and 135 died. Compared with non-anemic patients, mild anemia was associated with a higher adjusted risk of ESKD {hazard ratio [HR] 1.42 [95% confidence interval (CI) 1.02–1.98]} and all-cause death [HR 1.55 (95% CI 1.04–2.32)]. Severe anemia was associated with an even higher risk of ESKD [HR 1.73 (95% CI 1.20–2.51)] and death [HR 1.83 (95% CI 1.05–3.19)].

Conclusions

New-onset anemia is frequent, particularly in patients with more severe renal damage and in those with diabetes mellitus. The occurrence of anemia, even of a mild degree, is associated with mortality risk and faster progression towards ESKD.

A rapid method to visualize human mitochondrial DNA replication through rotary shadowing and transmission electron microscopy

We report a rapid experimental procedure based on high-density in vivo psoralen inter-strand DNA cross-linking coupled to spreading of naked purified DNA, positive staining, low-angle rotary shadowing, and transmission electron microscopy (TEM) that allows quick visualization of the dynamic of heavy strand (HS) and light strand (LS) human mitochondrial DNA replication. Replication maps built on linearized mitochondrial genomes and optimized rotary shadowing conditions enable clear visualization of the progression of the mitochondrial DNA synthesis and visualization of replication intermediates carrying long single-strand DNA stretches. One variant of this technique, called denaturing spreading, allowed the inspection of the fine chromatin structure of the mitochondrial genome and was applied to visualize the in vivo three-strand DNA structure of the human mitochondrial D-loop intermediate with unprecedented clarity.

Smc5/6 functions with Sgs1-Top3-Rmi1 to complete chromosome replication at natural pause sites

Smc5/6 is essential for genome structural integrity by yet unknown mechanisms. Here we find that Smc5/6 co-localizes with the DNA crossed-strand processing complex Sgs1-Top3-Rmi1 (STR) at genomic regions known as natural pausing sites (NPSs) where it facilitates Top3 retention. Individual depletions of STR subunits and Smc5/6 cause similar accumulation of joint molecules (JMs) composed of reversed forks, double Holliday Junctions and hemicatenanes, indicative of Smc5/6 regulating Sgs1 and Top3 DNA processing activities. We isolate an intra-allelic suppressor of smc6-56 proficient in Top3 retention but affected in pathways that act complementarily with Sgs1 and Top3 to resolve JMs arising at replication termination. Upon replication stress, the smc6-56 suppressor requires STR and Mus81-Mms4 functions for recovery, but not Srs2 and Mph1 helicases that prevent maturation of recombination intermediates. Thus, Smc5/6 functions jointly with Top3 and STR to mediate replication completion and influences the function of other DNA crossed-strand processing enzymes at NPSs.

Telomere damage induces internal loops that generate telomeric circles

Extrachromosomal telomeric circles are commonly invoked as important players in telomere maintenance, but their origin has remained elusive. Using electron microscopy analysis on purified telomeres we show that, apart from known structures, telomeric repeats accumulate internal loops (i-loops) that occur in the proximity of nicks and single-stranded DNA gaps. I-loops are induced by single-stranded damage at normal telomeres and represent the majority of telomeric structures detected in ALT (Alternative Lengthening of Telomeres) tumor cells. Our data indicate that i-loops form as a consequence of the exposure of single-stranded DNA at telomeric repeats. Finally, we show that these damage-induced i-loops can be excised to generate extrachromosomal telomeric circles resulting in loss of telomeric repeats. Our results identify damage-induced i-loops as a new intermediate in telomere metabolism and reveal a simple mechanism that links telomere damage to the accumulation of extrachromosomal telomeric circles and to telomere erosion.

The Self-Locating Catheter: Clinical Experience and Follow-Up

Background

The self-locating catheter invented by Nicola Di Paolo has been used increasingly in Italy and elsewhere since 1994, with about a thousand patients currently implanted every year. Twelve grams of tungsten inserted into the tip of the conventional Tenckhoff catheter during extrusion does not significantly change its form, but suffices to keep the tip firmly in the Douglas cavity.

Objective

The aim of the present study was to confirm our preliminary results in a large population of peritoneal dialysis patients.

Setting

16 Italian nephrology departments.

Results

In addition to confirming the validity of the new catheter, the present results show that patients with the new catheter have fewer episodes of peritonitis, tunnel infection, cuff extrusion, catheter malfunction, obstruction, and leakage.

Conclusion

The present multicenter control study confirms preliminary results and demonstrates that complications of peritoneal dialysis, such as cuff extrusion, infection, peritonitis, early leakage, and obstruction, are statistically less frequent in patients with self-locating catheters than in patients with classic Tenckhoff catheters.

Dna2 processes behind the fork long ssDNA flaps generated by Pif1 and replication-dependent strand displacement

Dna2 is a DNA helicase-endonuclease mediating DSB resection and Okazaki fragment processing. Dna2 ablation is lethal and rescued by inactivation of Pif1, a helicase assisting Okazaki fragment maturation, Pol32, a DNA polymerase δ subunit, and Rad9, a DNA damage response (DDR) factor. Dna2 counteracts fork reversal and promotes fork restart. Here we show that Dna2 depletion generates lethal DNA structures activating the DDR. While PIF1 deletion rescues the lethality of Dna2 depletion, RAD9 ablation relieves the first cell cycle arrest causing genotoxicity after few cell divisions. Slow fork speed attenuates DDR in Dna2 deprived cells. Electron microscopy shows that Dna2-ablated cells accumulate long ssDNA flaps behind the forks through Pif1 and fork speed. We suggest that Dna2 offsets the strand displacement activity mediated by the lagging strand polymerase and Pif1, processing long ssDNA flaps to prevent DDR activation. We propose that this Dna2 function has been hijacked by Break Induced Replication in DSB processing.

DNA2 encodes a 5′ flap DNA endonuclease involved in replication and DNA double strand break processing. Here the authors by using a conditional degron system together with electron microscopy characterize the role played by Dna2 and Pif1 helicase during unperturbed DNA replication in S. cerevisiae.

SIRFing the replication fork: Assessing protein interactions with nascent DNA

Branzei and Giannattasio preview work from Roy et al. about a new assay for protein interactions with nascent DNA at replication forks called SIRF.

Roy et al. (2018. J. Cell. Biol.https://doi.org/10.1083/jcb.201709121) describe an ingenious single-cell assay system, in situ analysis of protein interactions at DNA replication forks (SIRF), for the quantitative analysis of protein interactions with nascent DNA at active and stalled replication forks. The sensitive and accurate SIRF methodology is suitable for multiparameter measurements in cell populations.

[Pharmacological and nutritional problems in pregnant patient on chronic dialysis]

Many of information on the safety of drugs during pregnancy were obtained many years ago, before the pregnant women were excluded from the study protocols for possible fetal risks. Because randomized trials in pregnancy are complex and considered unethical. For the same reasons, there are no randomized controlled trials in pregnant women on dialysis. Moreover Compared to the normal subject, the pharmacokinetics and pharmacodynamics in these patients are influenced or by pregnancy or from dialysis techniques or from chronic uremia. Protein energy wasting PEW- is largely present in dialysis subjects. Nausea and vomiting are present in over 85% of pregnancy and may aggravate PEW. Therefore, it is necessary to adopt specific measures to prevent the PEW as well as periodic inspections of weight gain during pregnancy.

Genome-wide localization of Rrm3 and Pif1 DNA helicases at stalled active and inactive DNA replication forks of Saccharomyces cerevisiae

The genome of the budding yeast Saccharomyces cerevisiae is sequenced and the location and dynamic of activation of DNA replication origins are known. G1 synchronized yeast cells can be released into S-phase in the presence of hydroxyurea (HU) (1), which slows down DNA replication and retains replication forks in proximity of DNA replication origins. In this condition, the Chromatin Immuno-Precipitation on chip (ChIP on chip) (2-4) of replisome components allows the precise localization of all active DNA replication forks. This analysis can be coupled with the ssDNA-BromodeoxyUridine (ssDNA-BrdU) Immuno-Precipitation on chip (ssDNA-BrdU IP on chip) technique (5-7), which detects the location of newly synthesized DNA. Comparison of binding and BrdU incorporation profiles allows to locate a factor of interest at DNA replication forks genome wide. We present datasets deposited in the gene expression omnibus (GEO) database under accession number GSE68214, which show how the DNA helicases Rrm3 and Pif1 (8) associate to active and inactive DNA replication forks.

Rad53-Mediated Regulation of Rrm3 and Pif1 DNA Helicases Contributes to Prevention of Aberrant Fork Transitions under Replication Stress

Replication stress activates the Mec1^ATR and Rad53 kinases. Rad53 phosphorylates nuclear pores to counteract gene gating, thus preventing aberrant transitions at forks approaching transcribed genes. Here, we show that Rrm3 and Pif1, DNA helicases assisting fork progression across pausing sites, are detrimental in rad53 mutants experiencing replication stress. Rrm3 and Pif1 ablations rescue cell lethality, chromosome fragmentation, replisome-fork dissociation, fork reversal, and processing in rad53 cells. Through phosphorylation, Rad53 regulates Rrm3 and Pif1; phospho-mimicking rrm3 mutants ameliorate rad53 phenotypes following replication stress without affecting replication across pausing elements under normal conditions. Hence, the Mec1-Rad53 axis protects fork stability by regulating nuclear pores and DNA helicases. We propose that following replication stress, forks stall in an asymmetric conformation by inhibiting Rrm3 and Pif1, thus impeding lagging strand extension and preventing fork reversal; conversely, under unperturbed conditions, the peculiar conformation of forks encountering pausing sites would depend on active Rrm3 and Pif1.

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Rrm3 and Pif1 promote fork reversal and ssDNA gaps at stalled forks in rad53 cells

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Rrm3 and Pif1 associate with stalled DNA replication forks

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Rad53 phosphorylates Rrm3 and Pif1 at stalled forks

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Rrm3 and Pif1 promote chromosome fragility in hydroxyurea-treated rad53 cells

[Hemoperitoneum after drop-out from peritoneal dialysis]

A 55-years-old woman with end-stage renal disease presented on hemodialysis bloody ascitis after transfer from peritoneal dialysis. During the 8 years of peritoneal dialysis, she had exit-site infection and a culture-negative peritonitis. She was dropped-out of hemodialysis for ultrafiltration failure associated with "high" peritoneal transport. Clinic and radiologic findings was suggestive for the encapsulating peritoneal sclerosis, which was confirmed upon biopsy of the peritoneum. The patient was treated successfully with immunosuppressive. Our case is relevant, both because many clinical features that have been described must draw attention to the encapsulating peritoneal sclerosis, rare but life-threatening complication of peritoneal dialysis and because of its favorable outcome, unfortunately infrequent.

Molecular properties of a fermented manure preparation used as field spray in biodynamic agriculture

Manure products fermented underground in cow horns and commonly used as field spray (preparation 500) in the biodynamic farming system, were characterized for molecular composition by solid-state nuclear magnetic resonance [(13) C cross-polarization magic-angle-spinning NMR ((13) C-CPMAS-NMR)] spectroscopy and offline tetramethylammonium hydroxide thermochemolysis gas chromatography-mass spectrometry. Both thermochemolysis and NMR spectroscopy revealed a complex molecular structure, with lignin aromatic derivatives, polysaccharides, and alkyl compounds as the predominant components. CPMAS-NMR spectra of biodynamic preparations showed a carbon distribution with an overall low hydrophobic character and significant contribution of lignocellulosic derivatives. The results of thermochemolysis confirmed the characteristic highlighted by NMR spectroscopy, revealing a molecular composition based on alkyl components of plant and microbial origin and the stable incorporation of lignin derivatives. The presence of biolabile components and of undecomposed lignin compounds in the preparation 500 should be accounted to its particularly slow maturation process, as compared to common composting procedures. Our results provide, for the first time, a scientific characterization of an essential product in biodynamic agriculture, and show that biodynamic products appear to be enriched of biolabile components and, therefore, potentially conducive to plant growth stimulation.

Prevalence and progression of cardiovascular calcifications in peritoneal dialysis patients: A prospective study

BACKGROUND

Patients on dialysis may have abnormal serum levels of Ca, P and parathyroid hormone, with related bone diseases. This population has an increased risk of death, with cardiovascular calcification (CC) a contributing factor. Patients on peritoneal dialysis appear to be at increased risk of hyperlipidemia, a contributing factor to atherosclerotic plaque formation. Although several studies have described the presence and progression of CC in hemodialysis populations, there are fewer data in patients on peritoneal dialysis.

STUDY DESIGN

The Renal Osteodystrophy and Calcifications: Key factors in Peritoneal Dialysis (ROCK-PD) study was a 36-month, prospective observational study conducted in Italy. The study examined the presence and progression of CC in two cardiac valves and five arterial sites. The potential associations of serum Ca and P with mortality and cardiovascular morbidity, demographic, clinical and blood chemistry variables was investigated.

RESULTS

CC was present in 77% of patients at baseline (N=369) and in 90% of patients by study end (N=145), progressing in 73% of patients. There were 42 deaths (11%). Analyses showed a marked correlation between baseline P levels and the presence of left ventricular hypertrophy. However, there were no consistent correlations between serum Ca or P with mortality or morbidity.

CONCLUSIONS

CC was common in peritoneal dialysis patients and progressed in a majority of patients.

Exo1 competes with repair synthesis, converts NER intermediates to long ssDNA gaps, and promotes checkpoint activation

Ultraviolet (UV) light induces DNA-damage checkpoints and mutagenesis, which are involved in cancer protection and tumorigenesis, respectively. How cells identify DNA lesions and convert them to checkpoint-activating structures is a major question. We show that during repair of UV lesions in noncycling cells, Exo1-mediated processing of nucleotide excision repair (NER) intermediates competes with repair DNA synthesis. Impediments of the refilling reaction allow Exo1 to generate extended ssDNA gaps, detectable by electron microscopy, which drive Mec1 kinase activation and will be refilled by long-patch repair synthesis, as shown by DNA combing. We provide evidence that this mechanism may be stimulated by closely opposing UV lesions, represents a strategy to redirect problematic repair intermediates to alternative repair pathways, and may also be extended to physically different DNA damages. Our work has significant implications for understanding the coordination between repair of DNA lesions and checkpoint pathways to preserve genome stability.

Checkpoint mechanisms at the intersection between DNA damage and repair

In response to genomic insults cells trigger a signal transduction pathway, known as DNA damage checkpoint, whose role is to help the cell to cope with the damage by coordinating cell cycle progression, DNA replication and DNA repair mechanisms. Accumulating evidence suggests that activation of the first checkpoint kinase in the cascade is not due to the lesion itself, but it requires recognition and initial processing of the lesion by a specific repair mechanism. Repair enzymes likely convert a variety of physically and chemically different lesions to a unique common structure, a ssDNA region, which is the checkpoint triggering signal. Checkpoint kinases can modify the activity of repair mechanisms, allowing for efficient repair, on one side, and modulating the generation of the ssDNA signal, on the other. This strategy may be important to allow the most effective repair and a prompt recovery from the damage condition. Interestingly, at least in some cases, if the damage level is low enough the cell can deal with the lesions and it does not need to activate the checkpoint response. On the other hand if damage level is high or if the lesions are not rapidly repairable, checkpoint mechanisms become important for cell survival and preservation of genome integrity.

[Are dialysis-patients a risk population for cholelithiasis? Study in an apulian population]

AIM

The cholelithiasis (CL) has a 10-20% prevalence in the adult population. The end stage renal disease and dialysis would seem factors of risk since uremic patients show increased bile cholesterol, increased saturation indices and lithogenicity. Nevertheless the studies to confirm this hypothesis have furnished contradictory results. The aim of the study was to appraise prevalence of CL in dialysis-patients.

METHODS

The authors examined 127 patients (92 in hemodialysis and 35 in peritoneal dialysis) comparing them with a non-uremic control group (CNU) and the prevalence in the general population taking as champion the town of Castellana, near to ''S. Maria Degli Angeli'' Hospital, where, previously, an epidemiological study was performed. Sonographic examination was done with Esaote/Biomedica AU3 instrument with 3.5/5 mHz transducer. The evidence of gallstone(s) by ultrasonography or previously cholecystectomy have been considered diagnostics.

RESULTS

Gallstones were detected in 33 of the 127 dialysis-patients (25.9% prevalence). In the CNU the prevalence was 15% (P=0.046). Furthermore the comparison of prevalence of CL between dialysis-patients and the Castellana population was greater in dialysis-population considering the attended rate (13 vs 9.6) and had a greater attributable risk (35%). A global greater prevalence of CL in older patients (>60 years) showed a possible role of the increasing age as a correlated factor to the CL. Any other considered parameter has shown significant correlations.

CONCLUSIONS

These results underline a greater risk of CL in the dialysis-patient.

The interplay among chromatin dynamics, cell cycle checkpoints and repair mechanisms modulates the cellular response to DNA damage

Cells are continuously under the assault of endogenous and exogenous genotoxic stress that challenges the integrity of DNA. To cope with such a formidable task cells have evolved surveillance mechanisms, known as checkpoints, and a variety of DNA repair systems responding to different types of DNA lesions. These lesions occur in the context of the chromatin structure and, as expected for all DNA transactions, the cellular response to DNA damage is going to be influenced by the chromatin enviroment. In this review, we will discuss recent studies implicating chromatin remodelling factors and histone modifications in the response to DNA double-strand breaks (DSBs) and in checkpoint activation in response to UV lesions.

DNA nucleotide excision repair-dependent signaling to checkpoint activation

Eukaryotic cells respond to a variety of DNA insults by triggering a common signal transduction cascade, known as checkpoint response, which temporarily halts cell-cycle progression. Although the main players involved in the cascade have been identified, there is still uncertainty about the nature of the structures that activate these surveillance mechanisms. To understand the role of nucleotide excision repair (NER) in checkpoint activation, we analyzed the UV-induced phosphorylation of the key checkpoint proteins Chk1 and p53, in primary fibroblasts from patients with xeroderma pigmentosum (XP), Cockayne syndrome (CS), trichothiodystrophy (TTD), or UV light-sensitive syndrome. These disorders are due to defects in transcription-coupled NER (TC-NER) and/or global genome NER (GG-NER), the NER subpathways repairing the transcribed strand of active genes or the rest of the genome, respectively. We show here that in G0/G1 and G2/M phases of the cell cycle, triggering of the DNA damage cascade requires recognition and processing of the lesions by the GG-NER. Loss of TC-NER does not affect checkpoint activation. Mutations in XPD, XPB, and in TTDA, encoding subunits of the TFIIH complex, involved in both transcription and NER, impair checkpoint triggering. The only exception is represented by mutations in XPD, resulting in combined features of XP and CS (XP/CS) that lead to activation of the checkpoint cascade after UV radiation. Inhibition of RNA polymerase II transcription significantly reduces the phosphorylation of key checkpoint factors in XP/CS fibroblasts on exposure to UV damage.

Yeast Rev1 is cell cycle regulated, phosphorylated in response to DNA damage and its binding to chromosomes is dependent upon MEC1

Translesion DNA synthesis (TLS) is one of the mechanisms involved in lesion bypass during DNA replication. Three TLS polymerases (Pol) are present in the yeast Saccharomyces cerevisiae: Pol zeta, Pol eta and the product of the REV1 gene. Rev1 is considered a deoxycytidyl transferase because it almost exclusively inserts a C residue in front of the lesion. Even though REV1 is required for most of the UV-induced and spontaneous mutagenesis events, the role of Rev1 is poorly understood since its polymerase activity is often dispensable. Rev1 interacts with several TLS polymerases in mammalian cells and may act as a platform in the switching mechanism required to substitute a replicative polymerase with a TLS polymerase at the sites of DNA lesions. Here we show that yeast Rev1 is a phosphoprotein, and the level of this modification is cell cycle regulated under normal growing conditions. Rev1 is unphosphorylated in G1, starts to be modified while cells are passing S phase and it becomes hyper-phosphorylated in mitosis. Rev1 is also hyper-phosphorylated in response to a variety of DNA damaging agents, including treatment with a radiomimetic drug mostly causing double-strand breaks (DSB). By using the chromosome spreading technique we found the Rev1 is bound to chromosomes throughout the cell cycle, and its binding does not significantly increase in response to genotoxic stress. Therefore, Rev1 phosphorylation does not appear to modulate its binding to chromosomes, suggesting that such modification may influence other aspects of the TLS process. Rev1 binding under damaged and undamaged conditions, is at least partially dependent on MEC1, a gene playing a pivotal role in the DNA damage checkpoint cascade. This genetic dependency may suggest a role for MEC1 in spontaneous mutagenesis events, which require a functional REV1 gene.

Global approach to cardiovascular risk in chronic kidney disease: reality and opportunities for intervention

The current implementation into nephrology clinical practice of guidelines on treatment of cardiovascular (CV) risk factors in chronic kidney disease (CKD) is unknown. We designed a cross-sectional analysis to evaluate the prevalence and treatment of eight modifiable CV risk factors in 1058 predialysis CKD patients (stage 3: n=486; stage 4: n=430, stage 5: n=142) followed for at least 1 year in 26 Italian renal clinics. The median nephrology follow-up was 37 months (range: 12-391 months). From stages 3 to 5, hypertension was the main complication (89, 87, and 87%), whereas smoking, high calcium-phosphate product and malnutrition were uncommon. The prevalence of proteinuria (25, 38, and 58%), anemia (16, 32, and 51%) and left ventricular hypertrophy (51, 55, and 64%) significantly increased, while hypercholesterolemia was less frequent in stage 5 (49%) than in stages 4 and 3 (59%). The vast majority of patients received multidrug antihypertensive therapy including inhibitors of renin-angiotensin system; conversely, diuretic treatment was consistently inadequate for both frequency and dose despite scarce implementation of low salt diet (19%). Statins were not prescribed in most hypercholesterolemics (78%), and epoietin treatment was largely overlooked in anemics (78%). The adjusted risk for having a higher number of uncontrolled risk factors rose in the presence of diabetes (odds ratio 1.29, 95% confidence interval 1.00-1.66), history of CV disease (odds ratio 1.48, 95% confidence interval 1.15-1.90) and CKD stages 4 and 5 (odds ratio 1.75, 95% confidence interval 1.37-2.22 and odds ratio 2.85, 95% confidence interval 2.01-4.04, respectively). In the tertiary care of CKD, treatment of hypertension is largely inadequate, whereas therapy of anemia and dyslipidemia is frequently omitted. The risk of not achieving therapeutic targets is higher in patients with diabetes, CV disease and more advanced CKD.

Alk1 and Alk2 are two new cell cycle-regulated haspin-like proteins in budding yeast

Haspin is a protein kinase identified in mouse and human cells, and genes coding for haspin-like proteins are present in virtually all eukaryotic genomes sequenced so far. Two haspin homologues, called Alk1 and Alk2, are present in the yeast Saccharomyces cerevisiae. Both Alk1 and Alk2 exhibit a weak auto-kinase activity in vitro, are phosphoproteins in vivo and are hyperphosphorylated in response to DNA damage. The amount and modification of the two proteins is greatly regulated during the cell cycle. In fact, Alk1 and Alk2 levels peak in mitosis and late-S/G2, respectively, and phosphorylation of both proteins is maximal in mitosis. Control of protein stability plays a major role in Alk2 regulation. The half-life of Alk2 is particularly short in G1; mutagenesis and genetic analysis indicate that its degradation is controlled by the APC pathway. Overexpression of ALK2, but not of ALK1, causes a mitotic arrest, which is correlated to the kinase activity of the protein. This finding, together with its cell cycle regulation, suggests a role for Alk2 in the control of mitosis.

The 9-1-1 checkpoint clamp physically interacts with polzeta and is partially required for spontaneous polzeta-dependent mutagenesis in Saccharomyces cerevisiae

The use of translesion synthesis (TLS) polymerases to bypass DNA lesions during replication constitutes an important mechanism to restart blocked/stalled DNA replication forks. Because TLS polymerases generally have low fidelity on undamaged DNA, the cell must regulate the interaction of TLS polymerases with damaged versus undamaged DNA to maintain genome integrity. The Saccharomyces cerevisiae checkpoint proteins Ddc1, Rad17, and Mec3 form a clamp-like structure (the 9-1-1 clamp) that has physical similarity to the homotrimeric sliding clamp proliferating cell nuclear antigen, which interacts with and promotes the processivity of the replicative DNA polymerases. In this work, we demonstrate both an in vivo and in vitro physical interaction between the Mec3 and Ddc1 subunits of the 9-1-1 clamp and the Rev7 subunit of the Polzeta TLS polymerase. In addition, we demonstrate that loss of Mec3, Ddc1, or Rad17 results in a decrease in Polzeta-dependent spontaneous mutagenesis. These results suggest that, in addition to its checkpoint signaling role, the 9-1-1 clamp may physically regulate Polzeta-dependent mutagenesis by controlling the access of Polzeta to damaged DNA.

[Contrast-induced acute renal failure]

The administration of radiocontrast media (RC) can lead to usually a reversible form of acute renal failure (ARF) that begins soon after the contrast is administered. A functional definition of RC-induced ARF varies among different studies: most commonly reported as a proportional rise in serum creatinine (Cr), 25 or 50% above baseline or an absolute rise of 0.5-1.0 mg/dL within 48 hr after exposure to RC. Serum Cr returns to baseline over 8-12 days. Sometimes ARF is irreversible, contributing to an increase in mortality. Iodinated RC are either ionic or non-ionic and, at the concentrations required for arteriography or computed tomography, are of variable osmolality. Considering the main ARF risk factors, a rise in plasma Cr is: negligible with normal renal function, even if the patient is diabetic; 4-11% with mild to moderate renal insufficiency alone (plasma Cr between 1.5 and 4.0 mg/dL); 9-38% with mild to moderate renal insufficiency and diabetes mellitus; > or =50% if baseline plasma Cr is >4-5 mg/dL, particularly in patients with diabetic nephropathy. This risk, however, is increased further by more advanced renal dysfunction, marked volume depletion, severe heart failure, or multiple contrast studies within 72-hr. Pathogenesis is not well understood, but the mechanism by which nephrotoxins induce renal injury is generally by either vascular or direct tubular effects. In the case of RC ARF, there appears to be an influence of both mechanisms, although altered renal hemodynamics predominates. Both are thought to occur from exposure to the hyperosmolar agent. The best treatment for contrast-induced renal failure is prevention. Some preventive measures include the use, if clinically possible, of ultrasonography, magnetic resonance imaging or CT scanning without RC agents, particularly, in high-risk patients; the use of lower contrast doses and the avoidance of frequent repetitive studies; the avoidance of volume depletion or non-steroidal anti-inflammatory drugs; the administration of intravenous saline and the antioxidant acetylcysteine; the use of low or iso-osmolal non-ionic contrast agents, particularly in high risk patients.

DNA decay and limited Rad53 activation after liquid holding of UV-treated nucleotide excision repair deficient S. cerevisiae cells

The DNA damage checkpoint is a surveillance mechanism activated by DNA lesions and devoted to the maintenance of genome stability. It is considered as a signal transduction cascade, involving a sensing step, the activation of a set of protein kinases and the transmission and amplification of the damage signal through several phosphorylation events. In budding yeast many players of this pathway have been identified. Recent work showed that G1 and G2 checkpoint activation in response to UV irradiation requires prior recognition and processing of UV lesions by nucleotide excision repair (NER) factors that likely recruit checkpoint proteins near the damage. However, another report suggested that NER was not required for checkpoint function. Since the functional relationship between repair mechanisms and checkpoint activation is a very important issue in the field, we analyzed, under different experimental conditions, whether lesion processing by NER is required for checkpoint activation. We found that DNA damage checkpoint can be triggered in an NER-independent manner only if cells are subjected to liquid holding after UV treatment. This incubation causes a time-dependent breakage of DNA strands in NER-deficient cells and leads to partial activation of the checkpoint kinase. The analysis of the genetic requirements for this alternative activation pathway suggest that it requires Mec1 and the Rad17 complex and that the observed DNA breaks are likely to be due to spontaneous decay of damaged DNA.

The DNA damage checkpoint response requires histone H2B ubiquitination by Rad6-Bre1 and H3 methylation by Dot1

The cellular response to DNA lesions entails the recruitment of several checkpoint and repair factors to damaged DNA, and chromatin modifications may play a role in this process. Here we show that in Saccharomyces cerevisiae epigenetic modification of histones is required for checkpoint activity in response to a variety of genotoxic stresses. We demonstrate that ubiquitination of histone H2B on lysine 123 by the Rad6-Bre1 complex, is necessary for activation of Rad53 kinase and cell cycle arrest. We found a similar requirement for Dot1-dependent methylation of histone H3. Loss of H3-Lys(79) methylation does not affect Mec1 activation, whereas it renders cells checkpoint-defective by preventing phosphorylation of Rad9. Such results suggest that histone modifications may have a role in checkpoint function by modulating the interactions of Rad9 with chromatin and active Mec1 kinase.

The self-locating catheter: clinical experience and follow-up

BACKGROUND

The self-locating catheter invented by Nicola Di Paolo has been used increasingly in Italy and elsewhere since 1994, with about a thousand patients currently implanted every year. Twelve grams of tungsten inserted into the tip of the conventional Tenckhoff catheter during extrusion does not significantly change its form, but suffices to keep the tip firmly in the Douglas cavity.

OBJECTIVE

The aim of the present study was to confirm our preliminary results in a large population of peritoneal dialysis patients.

SETTING

16 Italian nephrology departments.

RESULTS

In addition to confirming the validity of the new catheter, the present results show that patients with the new catheter have fewer episodes of peritonitis, tunnel infection, cuff extrusion, catheter malfunction, obstruction, and leakage.

CONCLUSION

The present multicenter control study confirms preliminary results and demonstrates that complications of peritoneal dialysis, such as cuff extrusion, infection, peritonitis, early leakage, and obstruction, are statistically less frequent in patients with self-locating catheters than in patients with classic Tenckhoff catheters.

Physical and functional interactions between nucleotide excision repair and DNA damage checkpoint

The mechanisms used by checkpoints to identify DNA lesions are poorly understood and may involve the function of repair proteins. Looking for mutants specifically defective in activating the checkpoint following UV lesions, but proficient in the response to methyl methane sulfonate and double-strand breaks, we isolated cdu1-1, which is allelic to RAD14, the homolog of human XPA, involved in lesion recognition during nucleotide excision repair (NER). Rad14 was also isolated as a partner of the Ddc1 checkpoint protein in a two-hybrid screening, and physical interaction was proven by co-immunoprecipitation. We show that lesion recognition is not sufficient for checkpoint activation, but processing, carried out by repair factors, is required for recruiting checkpoint proteins to damaged DNA. Mutations affecting the core NER machinery abolish G1 and G2 checkpoint responses to UV, preventing activation of the Mec1 kinase and its binding to chromosomes. Conversely, elimination of transcription-coupled or global genome repair alone does not affect checkpoints, suggesting a possible interpretation for the heterogeneity in cancer susceptibility observed in different NER syndrome patients.

Correlation between checkpoint activation and in vivo assembly of the yeast checkpoint complex Rad17-Mec3-Ddc1

Rad17-Mec3-Ddc1 forms a proliferating cell nuclear antigen-like complex that is required for the DNA damage response in Saccharomyces cerevisiae and acts at an early step of the signal transduction cascade activated by DNA lesions. We used the mec3-dn allele, which causes a dominant negative checkpoint defect in G1 but not in G2, to test the stability of the complex in vivo and to correlate its assembly and disassembly with the mechanisms controlling checkpoint activation. Under physiological conditions, the mutant complex is formed both in G1 and G2, although the mutant phenotype is detectable only in G1, suggesting that is not the presence of the mutant complex per se to cause a checkpoint defect. Our data indicate that the Rad17-Mec3-Ddc1 complex is very stable, and it takes several hours to replace Mec3 with Mec3-dn within a wild type complex. On the other hand, the mutant complex is rapidly assembled when starting from a condition where the complex is not pre-assembled, indicating that the critical factor for the substitution is the disassembly step rather than complex formation. Moreover, the kinetics of mutant complex assembly, starting from conditions in which the wild type form is present, parallels the kinetics of checkpoint inactivation, suggesting that the complex acts in a stoichiometric way, rather than catalytically.

[Credentialing for diagnostic and interventional nephrology]

It is necessary to define the credentialing process that allows the nephrologist to achieve certification and accreditation in the following essential procedures of diagnostic and interventional nephrology: renal echography; renal and bone biopsies; the creation of vascular (arteriovenous fistula [FAV], grafts) or peritoneal access for permanent dialysis; the management and treatment of possible complications; and the implantation of central venous catheters for temporary or definitive hemodialysis.

BACKGROUND

The acquisition of credentials for the interventional nephrologist includes the completion of training programs, the identification of appraisal indices, certification, possible recertification, and accreditation. The specialist validation allows the nephrologist to act as a tutor and supply the credentials for the interventional procedures in nephrology. The use of echography has remarkably simplified the procedure of percutaneous renal biopsy, a technical diagnostic invasive technique, practiced exclusively by the nephrologist the ecography-guided technique has reduced the risks of greater complications to less than 0.5%. However, guidelines are lacking on the training required to accredit a nephrologist in this technique. The initial placement of a shunt, vascular or peritoneal, to carry out dialysis treatment is usually performed by the nephrologist, radiologist, or surgeon. However, the successful long-term management of the dialysis patient generally demands a multidisciplinary approach. The poor management of the dialysis shunt can contribute to reduced patient life expectancy and increased costs of care. Therefore, it is essential that those who perform such interventional procedures must be certified and accredited according to strict protocol guidelines. In Italy (as opposed to the United States) most peritoneal shunt placements are performed by the nephrologist. However, international scientific society guidelines on this procedure, where they exist, are generic, allowing for the adaptation of particular techniques by various nephrologic centers. The criteria for the acquisition of credentials in one particular procedure must be uniform, logical, consistent, and applicable, comprising of a recognition of the basic procedure and a course of appropriate practical training. The criteria for training and credentialing in diagnostic and interventional nephrology should encompass the following points: The establishment of guidelines for the performance of all procedures that ensures suitable and effective treatment, including during emergencies, and considering the hospital context in which the procedures are performed. The recognition that scientific society guidelines for one specialty or procedure may not be appropriate or applicable to credentialing in another specialty or procedure. The ability of guidelines to adapt to improvements in technique and new technologies. The stipulations of insurance coverage and legal counselling must be taken into consideration whenever accreditation criteria are developed.

CONCLUSIONS

An adequately certified and accredited background improves the quality of care, reduces costs and waiting list time, and reduces those complications that could increase the length of hospitalization.

The DNA polymerase alpha-primase complex: multiple functions and interactions

DNA polymerase alpha (pol alpha) holds a special position among the growing family of eukaryotic DNA polymerases. In fact, pol alpha is associated with DNA primase to form a four subunit complex and, as a consequence, is the only enzyme able to start DNA synthesis de novo. Because of this peculiarity the major role of the DNA polymerase alpha-primase complex (pol-prim) is in the initiation of DNA replication at chromosomal origins and in the discontinuous synthesis of Okazaki fragments on the lagging strand of the replication fork. However, pol-prim seems to play additional roles in other complex cellular processes, such as the response to DNA damage, telomere maintenance, and the epigenetic control of higher order chromatin assembly.

Can peritoneal dialysis be used as a long term therapy for end stage renal disease?

Over the last 25 years, since the introduction of CAPD, the use of PD has increased greatly and over this period many advances in technique have been made. As is well known, that home and self-dialysis, such as PD, cost less than in-center HD and can provide excellent survival and a high level of patient rehabilitation. To date however, the demonstration that PD can provide long term dialysis has been limited to a small number of patients. The next few decades will see a marked increase in the worldwide dialysis population, particularly as older and sicker patients are accepted into dialysis. It is likely that worldwide pressures related to cost containment will favour the use of cost effective therapies, such as PD. However, the increased use of PD will continue, only if we continue to improve its efficacy and do not waste the economic benefits gained over HD. We are challenged to improve and develop PD in a way that optimises patient medical and psychosocial outcomes while minimizing costs. This may be achieved by using more biocompatible solutions, hopefully inexpensive, that will maintain the peritoneal membrane intact for long periods, will better preserve the membrane's transport characteristics over time, and thus reduce the main causes of drop out from dialysis.

A dominant-negative MEC3 mutant uncovers new functions for the Rad17 complex and Tel1

The Rad17-Mec3-Ddc1 complex is essential for the cellular response to genotoxic agents and is thought to be important for sensing DNA lesions. Deletion of any of the RAD17, MEC3 or DDC1 genes abolishes the G(1) and G(2) and impairs the intra-S DNA-damage checkpoints. We characterize a dominant-negative mec3-dn mutation that has an unexpected phenotype. It inactivates the G(1) checkpoint while it leaves the G(2) response functional, thus revealing a difference in the requirements of the DNA-damage response in different phases of the cell cycle. In an attempt to identify the molecular defect imparted by the mutation, we dissected step-by-step the signaling cascade, which is triggered by DNA lesions and requires the activity of Mec1 and Rad53 kinases. The analysis of the phosphorylation state of checkpoint factors and critical protein interactions showed that, in mec3-dn cells, the signal transduction cascade is triggered normally, and the central kinase Mec1 can be activated. In G(1) cells expressing the mutation, the signaling cannot proceed any further along the pathway, indicating that the Rad17 complex acts after the activation of Mec1, possibly recruiting targets for the kinase. We also show that the function of the G(2) checkpoint in mutant cells is maintained by an uncharacterized activity of Tel1, the yeast homologue of ATM. This work thus reports a previously undiscovered role for Tel1 in checkpoint control.

IgE-mediated allergy to corn: a 50 kDa protein, belonging to the Reduced Soluble Proteins, is a major allergen

BACKGROUND

Although corn is often cited as an allergenic food, very few studies have been devoted to the identification of corn allergens and corn allergy has been rarely confirmed by double-blind, placebo-controlled food challenge (DBPCFC). Recently, Pastorello et al. (1) identified some salt-soluble IgE-binding proteins of corn flour as potential allergens. One of these, corresponding to corn Lipid Transfer Protein (LTP), appeared to be the major one. The aim of this study was to verify the clinical significance of the skin prick test (SPT) and CAP-FEIA CAP-System IgE fluozoenzyme immunosorbent assay (Pharmacia Diagnostic, Uppsala, Sweden) positivities to corn and to identify the presence of IgE-binding proteins in the corn flour salt-insoluble protein fractions (comprising up to 96% of the total protein) using sera of patients with DBPCFC-documented food allergy to corn. In addition the effect of cooking and proteolytic digestion on the corn allergens was investigated.

METHODS

Sixteen subjects with SPT and CAP-FEIA positivities to corn flour were examined. Only six of them complained of suffering from urticaria and/or other symptoms after ingestion of corn-based foods. The patients were food challenged with cooked corn flour (polenta). IgE-binding proteins were detected by immunoblotting. The digestibility of the IgE-binding proteins was examined during a pepsin attack followed by a pancreatin digestion performed on a cooked corn flour sample.

RESULTS

Oral challenge was positive only for six patients with symptoms after ingestion of corn. A 50 kDa protein, belonging to the corn Reduced Soluble Protein (RSP) fraction was recognized by the serum IgE of all the DBPCFC-positive subjects and resulted to be resistant to both heating and peptic/pancreatic digestion. SPT with the purified RSP fraction gave positive results for all of the DBPCFC-positive patients examined.

CONCLUSIONS

SPT and CAP-FEIA positivities to corn flour had no clinical significance for most of the patients and food allergy to corn has to be proved by DBPCFC. A salt-unextractable protein of 50 kDa, belonging to the RSP fraction, represents a potential allergen in food hypersensitivity to corn because of its stability to cooking and digestion.