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PubMed1998

The use of deconvolution and total least squares in recovering a radiation detector line spread function.

We present a method for obtaining the line spread function (LSF) of any radiation detector from measured data. The problem of finding a LSF is essentially a discrete deconvolution from known values of the input (Monte Carlo generated data) and the output (measured data) which can be put into matrix form. We applied the total least squares (TLS) method which is particularly useful when there are errors in both the input and output data. Results from computer simulation as well as from actual data are shown. In a practical application, however, our technique is currently limited by the ability of the Monte Carlo data to simulate correctly the inherent data from the head of the linear accelerator (linac). To overcome this difficulty we have solved by deconvolution and TLS for a more realistic inherent beam profile of our linac using the information from both profile data as measured with film and the film densitometer response function. The LSF of the densitometer was estimated with a simple method of direct measurement of a slit image and a full width at half maximum (FWHM) of 0.997 mm was recorded. Additionally, using the knowledge of this realistic inherent profile of the linac, a blurring function representing the finite source size effect missing in our current Monte Carlo profile simulation was determined. Finally, with the realistic inherent beam profile we have applied the deconvolution and TLS method to find a LSF for the Markus chamber and found a resulting FWHM of 5.39 mm. The TLS approach for deconvolving can find a useful application for both finding the LSF and correcting for the detector size effect once its LSF is known. This type of correction is required when a high spatial resolution is needed (e.g., in small field off-axis measurements). Convolved and measured profiles are also presented to illustrate the effect of the blurring due to different LSFs.

Biophysical Phenomena↗

PubMed2005

Ubiquitin-binding domains in Y-family polymerases regulate translesion synthesis.

Translesion synthesis (TLS) is the major pathway by which mammalian cells replicate across DNA lesions. Upon DNA damage, ubiquitination of proliferating cell nuclear antigen (PCNA) induces bypass of the lesion by directing the replication machinery into the TLS pathway. Yet, how this modification is recognized and interpreted in the cell remains unclear. Here we describe the identification of two ubiquitin (Ub)-binding domains (UBM and UBZ), which are evolutionarily conserved in all Y-family TLS polymerases (pols). These domains are required for binding of poleta and poliota to ubiquitin, their accumulation in replication factories, and their interaction with monoubiquitinated PCNA. Moreover, the UBZ domain of poleta is essential to efficiently restore a normal response to ultraviolet irradiation in xeroderma pigmentosum variant (XP-V) fibroblasts. Our results indicate that Ub-binding domains of Y-family polymerases play crucial regulatory roles in TLS.

Amino Acid Motifs↗

PubMed2026

Dendritic cells control tertiary lymphoid structure development and maintenance in cancer.

Tertiary lymphoid structures (TLSs) are associated with immunotherapy response, yet the mechanisms controlling their formation and maintenance remain unclear. Using spatial transcriptomics and multiplex imaging across human tumors, we found that CCR7+ mature dendritic cells (DCs) accumulate in TLSs. In a mouse non-small cell lung cancer model that forms mature TLSs, we show that early TLS development requires interferon-γ (IFN-γ)-driven type 1 conventional dendritic cell (cDC1) maturation, migration to tumor-draining lymph nodes (tdLNs), and T cell recruitment. As tumors progress, TLSs persist independently of tdLN T cell egress, coinciding with cDC1 accumulation within intratumoral CCL19 stromal hubs. There, cDC1-major histocompatibility complex class 1 (MHC-I) and -MHC-II concomitant antigen presentation, along with CD40 signaling, sustain TLS, T follicular helper (TFH) cell pool, germinal centers, and tumor-specific immunoglobulin G (IgG). These findings highlight local mature cDC1s as key TLS orchestrators and potential targets to enhance antitumor TLS function.

Animals↗

PubMed2002

Role of an essential triloop hairpin and flanking structures in the 3' untranslated region of Alfalfa mosaic virus RNA in in vitro transcription.

The minus-strand promoter of Alfalfa mosaic virus (AMV), a tripartite plant virus belonging to the family Bromoviridae, is located within the 3'-terminal 145 nucleotides (nt), which can adopt a tRNA-like structure (TLS). This contrasts with the subgenomic promoter for RNA4 synthesis, which requires approximately 40 nt and forms a single triloop hairpin. Detailed analysis of the minus-strand promoter now shows that a similar triloop hairpin, hairpin E (hpE), is crucial for minus-strand synthesis. The loop sequence of hpE appeared to not be essential for RNA synthesis, whereas the identity and base-pairing capability of bases below the triloop were indeed essential. Reducing the size of the bulge loop of hpE triggered transcription from an internal site similar to the process of subgenomic transcription. Similar effects were observed when deleting (part of) the TLS, suggesting that tertiary contacts between hpE and the TLS prevent internal initiation. The data indicate that the minus-strand promoter hpE and the subgenomic promoter hairpin are equivalent in binding the viral polymerase. We propose that the major role of the TLS is to enforce the initiation of transcription by polymerase at the very 3' end of the genome.

3' Untranslated Regions↗

PubMed2006

Complex formation with Rev1 enhances the proficiency of Saccharomyces cerevisiae DNA polymerase zeta for mismatch extension and for extension opposite from DNA lesions.

Rev1, a Y family DNA polymerase (Pol) functions together with Polzeta, a B family Pol comprised of the Rev3 catalytic subunit and Rev7 accessory subunit, in promoting translesion DNA synthesis (TLS). Extensive genetic studies with Saccharomyces cerevisiae have indicated a requirement of both Polzeta and Rev1 for damage-induced mutagenesis, implicating their involvement in mutagenic TLS. Polzeta is specifically adapted to promote the extension step of lesion bypass, as it proficiently extends primer termini opposite DNA lesions, and it is also a proficient extender of mismatched primer termini on undamaged DNAs. Since TLS through UV-induced lesions and various other DNA lesions does not depend upon the DNA-synthetic activity of Rev1, Rev1 must contribute to Polzeta-dependent TLS in a nonenzymatic way. Here, we provide evidence for the physical association of Rev1 with Polzeta and show that this binding is mediated through the C terminus of Rev1 and the polymerase domain of Rev3. Importantly, a rev1 mutant that lacks the C-terminal 72 residues which inactivate interaction with Rev3 exhibits the same high degree of UV sensitivity and defectiveness in UV-induced mutagenesis as that conferred by the rev1Delta mutation. We propose that Rev1 binding to Polzeta is indispensable for the targeting of Polzeta to the replication fork stalled at a DNA lesion. In addition to this structural role, Rev1 binding enhances the proficiency of Polzeta for the extension of mismatched primer termini on undamaged DNAs and for the extension of primer termini opposite DNA lesions.

Base Pair Mismatch↗

PubMed1998

Analysis of damage tolerance pathways in Saccharomyces cerevisiae: a requirement for Rev3 DNA polymerase in translesion synthesis.

The replication of double-stranded plasmids containing a single N-2-acetylaminofluorene (AAF) adduct located in a short, heteroduplex sequence was analyzed in Saccharomyces cerevisiae. The strains used were proficient or deficient for the activity of DNA polymerase zeta (REV3 and rev3delta, respectively) in a mismatch and nucleotide excision repair-defective background (msh2delta rad10delta). The plasmid design enabled the determination of the frequency with which translesion synthesis (TLS) and mechanisms avoiding the adduct by using the undamaged, complementary strand (damage avoidance mechanisms) are invoked to complete replication. To this end, a hybridization technique was implemented to probe plasmid DNA isolated from individual yeast transformants by using short, 32P-end-labeled oligonucleotides specific to each strand of the heteroduplex. In both the REV3 and rev3delta strains, the two strands of an unmodified heteroduplex plasmid were replicated in approximately 80% of the transformants, with the remaining 20% having possibly undergone prereplicative MSH2-independent mismatch repair. However, in the presence of the AAF adduct, TLS occurred in only 8% of the REV3 transformants, among which 97% was mostly error free and only 3% resulted in a mutation. All TLS observed in the REV3 strain was abolished in the rev3delta mutant, providing for the first time in vivo biochemical evidence of a requirement for the Rev3 protein in TLS.

2-Acetylaminofluorene↗

PubMed2005

Recombinant urate oxidase (rasburicase) in the prophylaxis and treatment of tumor lysis syndrome.

Spontaneous or treatment-induced tumor lysis syndrome (TLS) can cause significant morbidity and potential mortality. Vigorous hydration, alkalinization and inhibition of uric acid synthesis are the most frequently used methods for prevention of TLS. However, this approach requires hospitalization and tedious nursing care, and fails to prevent renal insufficiency in up to 25% of high-risk patients. With increased intensity and efficacy of cancer therapies, and the current trend to deliver treatment in the outpatient setting, novel approaches at management of TLS are needed. Unlike allopurinol, urate oxidase promptly reduces the existing uric acid pool, prevents accumulation of xanthine and hypoxanthine, and does not require alkalinization, facilitating phosphorus excretion. A recombinant form of urate oxidase, rasburicase, is now available. In this chapter we will present an overview of rasburicase development and discuss the impact of rasburicase in the prevention and management of TLS.

Allopurinol↗

PubMed2006

Inflammatory cell phenotyping of the pulmonary interstitium in idiopathic interstitial pneumonia.

BACKGROUND: Several studies have implicated the role of inflammation in the pathogenesis of lung damage in idiopathic interstitial pneumonias (IIPs). Investigations of inflammatory cells in IIP have show that eosinophils, neutrophils and T cells may be associated with a poorer prognosis. OBJECTIVES: The aim of our study was to map, by quantitative analysis, the number of inflammatory cells in the lung tissue of patients with non-specific interstitial pneumonia/non-specific interstitial pneumonia (NSIP/NSIP), acute interstitial pneumonia/diffuse alveolar damage (AIP/DAD) and idiopathic pulmonary fibrosis/usual interstitial pneumonia (IPF/UIP) and to correlate them with lung function tests and survival. METHODS: After immunohistochemical staining, we quantified the content of inflammatory cells [macrophages, neutrophils (elastase+), plasma cells, and CD3, CD4 and CD8 T lymphocytes (TLs)] in 20 NSIP, 20 DAD and 20 UIP surgical lung biopsies. RESULTS: The total density of inflammatory cells was significantly increased in DAD and NSIP when compared to UIP (p = 0.04). TLs were increased in DAD and NSIP when compared to UlP lungs (p < 0.05). The density of inflammatory cells in UIP showed significant differences in normal, intervening and dense fibrosis areas (p < 0.05). The most numerous cells infiltrating the mural fibrosis and honeycombing areas were plasma cells, neutrophils (elastase+), CD20+, CD3+, CD4+ and CD8+ (p < 0.05). In UIP, CD3+ TLs were directly correlated with forced expiratory volume in 1 s/forced vital capacity ratio x 100 (p = 0.05). CD68+ cells presented a significant positive correlation with the forced expiratory volume in 1 s (p = 0.04); neutrophil (elastase+) cells significantly correlated with residual volume (p = 0.02), residual volume/total lung capacity (p = 0.04) and carbon monoxide transfer factor (p = 0.03). The most important predictor of survival in UIP was CD3+ TLs (p = 0.05). CONCLUSION: The total density of inflammatory cells and lymphocytes presents a different distribution within the pulmonary parenchyma in AIP/DAD, NSIP/NSIP and IPF/UIP evolutionary adapted responses to injury. There is a localized distribution of inflammation in the normal, intervening and dense fibrosis areas of UIP for CD3+, associated with a lethal deterioration of the pulmonary function and poor survival. Our findings provide further evidence of the importance of inflammation in the pathophysiology of IIPs.

Adult↗

PubMed1994

Incidence and treatment of tumor lysis syndrome in patients with acute leukemia.

Tumor lysis syndrome (TLS) is a complication associated with electrolyte abnormalities that is observed in patients with acute leukemia who are receiving intense doses of chemotherapy. Forty-one patients with acute leukemia were treated with high-dose combination chemotherapy and were evaluated for TLS. A grading system developed for the evaluation of these patients was applied. Grade I tumor lysis was observed in 22 patients, grade II TLS in 2 patients and grade III in 1 patient. All patients were treated with intravenous fluids, mannitol, allopurinol and in some patients, aluminum-based antacids. Treatment for TLS prior to intensive chemotherapy reduced morbidity and mortality associated with high-dose chemotherapy for acute leukemias.

Adolescent↗

PubMed2001

Local recurrences following transoral laser surgery for early glottic carcinoma: frequency, management, and outcome.

Although transoral laser surgery (TLS) for the treatment of early stage glottic carcinoma is now widely used, the patterns of local recurrences, related re-treatment methods, and results have not been documented comprehensively. Two hundred fifty-two patients with glottic carcinoma stage I or II were treated for cure with TLS alone and followed up for 24 to 139 months (mean, 62 months). Their charts were retrospectively reviewed to identify local recurrence patterns. Thirty-five patients (13.9%) presented with local recurrences or second laryngeal primaries 4 to 84 months (mean, 23 months) after initial treatment. Of the 161 patients classified T1N0M0, 21 (13.0%) suffered local recurrences, and in the 91 classified T2N0M0, 14 (15.4%) tumors recurred. If tumors recurring more than 60 months after initial treatment are considered second primary tumors rather than recurrences, then only 18 (11.2%) of 161 patients classified T1N0M0 would have had a recurrence. However, the difference in local control between patients with stage I versus stage II disease would still not be significant (p = .41). Of the 35 patients with local recurrences, 16 (45%) were managed with total laryngectomy, 10 (28.6%) with further TLS, 4 (11.4%) with partial laryngectomy, and 2 (5.7%) with radiotherapy, and 3 (8.6%) had no curative treatment. Accordingly, 16 patients (45.7%) with local treatment failure could be treated with further organ-sparing treatment methods. The actuarial overall survival, disease-specific survival, and organ preservation rates 5 years after the diagnosis of recurrent disease were 43.6%, 74.6%, and 33.7%. Transoral laser surgery leads to local control rates that are comparable to those found after radiotherapy for lesions classified T1 and leads to slightly better control rates for lesions classified T2, but the results are inferior to those achieved with conventional partial laryngectomy. However, if local recurrence occurs, then more re-treatment options are available after TLS as compared to initial radiotherapy or open surgery.

Carcinoma, Squamous Cell↗

PubMed2006

Cap- and initiator tRNA-dependent initiation of TYMV polyprotein synthesis by ribosomes: evaluation of the Trojan horse model for TYMV RNA translation.

Turnip yellow mosaic virus (TYMV) RNA directs the translation of two overlapping open reading frames. Competing models have been previously published to explain ribosome access to the downstream polyprotein cistron. The Trojan horse model, based on cell-free experiments, proposes noncanonical cap-independent initiation in which the 3'-terminal tRNA-like structure (TLS) functionally replaces initiator tRNA, and the valine bound to the TLS becomes cis-incorporated into viral protein. The initiation coupling model, based on in vivo expression and ribosome toe-printing studies, proposes a variation of canonical leaky scanning. Here, we have re-examined the wheat germ extract experiments that led to the Trojan horse model, incorporating a variety of controls. We report that (1) translation in vitro from the polyprotein AUG of TYMV RNA is unchanged after removal of the 3' TLS but is stimulated by the presence of a 5'-cap; (2) the presence of free cap analog or edeine (which interferes with initiation at the ribosomal P site and its tRNA(i) (Met) involvement) inhibits translation from the polyprotein AUG; (3) the toe-prints of immediately post-initiation ribosomes on TYMV RNA are similar with and without an intact TLS; and (4) significant deacylation of valyl-TYMV RNA in wheat germ extract can complicate the detection of cis-incorporation. These results favor the initiation coupling model.

Amino Acid Sequence↗

PubMed2007

Clarifying the role of rasburicase in tumor lysis syndrome.

Tumor lysis syndrome (TLS) is a complication of malignancies with high tumor cell proliferation, tumor burden, and chemosensitivity. It manifests with the release of intracellular components and results in hyperkalemia, hyperphosphatemia, hypocalcemia, and hyperuricemia. These biochemical abnormalities may lead to serious complications such as renal failure, cardiac dysrhythmias, and death. Rasburicase, a recombinant urate oxidase enzyme, is a new agent indicated in the treatment or prophylaxis of hyperuricemia in pediatric patients with cancer who are at high risk for TLS. We reviewed the evidence for treatment with this agent compared with standard therapy with allopurinol. Rasburicase may be considered for use in patients with hyperuricemia at presentation and in patients at high risk for TLS that would otherwise result in a delay in chemotherapy. However, randomized controlled trials are required to establish the comparative efficacy of rasburicase in the adult population. Preliminary evidence suggests that single-dose or reduced-dose rasburicase may be effective in the prophylaxis and the treatment of hyperuricemia and TLS. However, to our knowledge, there is no evidence comparing clinically relevant outcomes such as acute renal failure or dialysis.

Allopurinol↗

PubMed2006

Translesion synthesis DNA polymerases and control of genome stability.

Eukaryotic and prokaryotic genomes are replicated with amazingly high fidelity to assure faithful transmission of genetic information from one generation to the next. The accuracy of replication relies heavily on the ability of replicative DNA polymerases to efficiently select correct nucleotides for the polymerization reaction and excise mistakenly incorporated nucleotides using their intrinsic exonucleases. Cell also possess a variety of specialized DNA polymerases that help to overcome replication blocks when occasional unrepaired DNA lesions stall the replication machinery. The translesion synthesis (TLS) polymerases have an extremely low fidelity during copying undamaged DNA substrates, such that uncontrolled participation of these polymerases in DNA replication could present a threat to the genome stability. In this article, we discuss the properties of prokaryotic and eukaryotic TLS polymerases and their roles in modulating the rate of spontaneous and genotoxicant-induced mutations. We also review recent insights into the molecular mechanisms regulating the participation of error-prone TLS polymerases in the genome replication. Finally, we discuss the relationship between the functions of TLS polymerases and human disease.

DNA Damage↗

PubMed1998

Management of tumor lysis syndrome with standard continuous arteriovenous hemodialysis: case report and a review of the literature.

Tumor lysis syndrome (TLS) is a critical illness with few treatment options. This report describes the clinical course of a patient with non-Hodgkin's lymphoma, who developed TLS and required renal replacement therapy. Institution of the standard therapeutic approach, intermittent hemodialysis, was not possible because of persistent hypotension. Instead, the patient was treated with a short course of continuous arteriovenous hemofiltration (CAVH) and conventional continuous arteriovenous hemodialysis (CAVHD) with dialysate flow rate of 1 L/h), which resulted in effective control of serum uric acid, potassium, urea nitrogen, phosphorus, and extracellular fluid volume. This case is in distinction to a previous report of TLS treatment with CAVHD using 4 L/h dialysate flow rate. We conclude that continuous renal replacement therapies with standard dialysate flow rates and replacement volumes should be considered for the treatment of TLS, particulary if the syndrome is accompanied by hypotension.

Acute Kidney Injury↗

PubMedDate not supplied

Clinical versus laboratory tumor lysis syndrome in children with acute leukemia.

Renal and metabolic complications of tumor lysis syndrome (TLS) were recognized frequently in the 1960s and 1970s. Strategies were designed to prevent TLS. We conducted a retrospective chart review study to identify the current TLS risk in children with acute leukemia. Children were considered to have "laboratory tumor lysis syndrome" (LTLS) if two of the following metabolic changes occurred within 4 days of the start of chemotherapy: a 25% increase in serum phosphate, potassium, uric acid, or blood urea nitrogen levels, or a 25% decline in serum calcium concentration. Clinical TLS (CTLS) was defined as LTLS plus a serum potassium level higher than 6.0 mmol/L or acute renal failure. Twenty-one of 30 children developed LTLS; one developed CTLS. Absolute blast count, pretreatment white blood cell count, pretreatment lactic dehydrogenase, and sex or tumor DNA index did not correlate with the development of LTLS. LTLS is still frequent in children undergoing chemotherapy for acute leukemia; CTLS, however, is much less common.

Adolescent↗

PubMed2003

DNA polymerase zeta: new insight into eukaryotic mutagenesis and mammalian embryonic development.

Information about the mechanisms that generate mutations in eukaryotes is likely to be useful for understanding human health concerns, such as genotoxicity and cancer. Eukaryotic mutagenesis is largely the outcome of attacks by endogenous and environmental agents. Except for DNA repair, cell cycle checkpoints and DNA damage avoidance, cells have also evolved DNA damage tolerance mechanism, by which lesion-targeted mutation might occur in the genome during replication by specific DNA polymerases to bypass the lesions (translesion DNA synthesis, TLS), or mutation on undamaged DNA templates (untargeted mutation) might be induced. DNA polymerase zeta (pol zeta), which was found firstly in budding yeast Saccharomyces cerevisiae and consists of catalytic subunit scRev3 and stimulating subunit scRev7, has received more attention in recent years. Pol zeta is a member of DNA polymerase eta subfamily, which belongs to DNA polymerase B family, and exists in almost all eukaryotes. Human homolog of the scRev3 gene is located in chromosome region 6q21, and the mouse equivalent maps to chromosome 10, distal to the c-myb gene and close to the Macs gene. Alternative splicing, upstream out-of frame ATG can be found in yeast scRev3, mouse and human homologs. Furthermore, the sequence from 253-323 immediate upstream of the AUG initiator codon has the potential to form a stem-loop hairpin secondary structure in REV3 mRNA, suggesting that human REV3 protein may be expressed at low levels in human cells under normal growth conditions. The functional domain analysis showed that yeast Rev3-980 tyrosine in conserved region II is at the polymerase active site. Human REV3 amino acid residues 1 776-2 195 provide a REV7 binding domain, and REV7 amino acid residues 1-211 provide a bind domain for REV1, REV3 and REV7 itself. More interestingly, REV7 interacts with hMAD2 and therefore might function in the cell cycle control by affecting the activation of APC (anaphase promoting complex). Currently it has been known that pol zeta is involved in most spontaneous mutation, lesion-targeted mutation via TLS, chemical carcinogen induced untargeted mutation and somatic hypermutation of antibody genes in mammalian. In TLS pathway, pol zeta acts as a "mismatch extender" with combination of other DNA polymerases, such as pol iota. Unlike in yeast, it was found that pol zeta also functioned in mouse embryonic development more recently. It was hypothesized that the roles of pol zeta in TLS and cell cycle control might contribute to mouse embryonic lethality.

Animals↗

PubMed2003

Steroid-induced tumor lysis syndrome in a patient with preleukemia.

Tumor lysis syndrome (TLS) is a well recognized complication of chemotherapy and radiotherapy for leukemia, lymphoma as well as rapidly growing malignancies. Less described is the occurrence of TLS following steroid therapy alone. Herein, we report on a 32-year-old male with myelodysplastic syndrome, characterized by refractory anemia with excess blasts in transformation, who developed acute oliguric renal failure 12 hours after methylprednisolone 1.0 g for presumed autoimmune thrombocytopenia. Laboratory investigations revealed typical findings of TLS, including hyperkalemia, marked hyperuricemia, hyperphosphotemia, hypocalcemia and urine uric acid to creatinine ratio 1.8 (> 1.0). Long hemodialysis (8 hours) was initiated for 3 consecutive sessions. Renal function recovered 1 week later. This case high-lights that single-dose steroid administration in a patient with hematological malignancy may cause the potential life-threatening complications of TLS. Prophylactic management prior to the use of steroid therapy for a variety of purposes is absolutely required in high-risk patients.

Acute Kidney Injury↗

PubMed1999

[Acute lymphoblastic leukemia complicated with tumor lysis syndrome--four cases report].

OBJECTIVE: To report four acute lymphoblastic leukemia(ALL) patients who developed tumor lysis syndrome(TLS) after initial chemotherapy. METHODS: The clinical features and blood biochemical changes of four patients with TLS were analysed. RESULTS: TLS was characterized by hyperuricemia, hyperkalemia, hyperphosphatemia and hypocalcemia. Three cases had renal dysfunction and the other died of acute renal failure. After allopurinol therapy and alkalinization of urine, the blood biochemical parameter became normalization in all the three cases. CONCLUSIONS: TLS can be effectively controlled by early recognition and administration of allopurinol therapy and alkalinization of urine.

Adult↗