Bulky Lesions Research Articles

Population sequencing data reveal a compendium of mutational processes in the human germ line.

Mechanistic processes underlying human germline mutations remain largely unknown.Variation in mutation rate and spectra along the genome is informative about the biological mechanisms. We statistically decompose this variation into separate processes using a blind source separation technique. The analysis of a large-scale whole genome sequencing dataset (TOPMed) reveals nine processes that explain the variation in mutation properties between loci. Seven of these processes lend themselves to a biological interpretation. One process is driven by bulky DNA lesions that resolve asymmetrically with respect to transcription and replication. Two processes independently track direction of replication fork and replication timing. We identify a mutagenic effect of active demethylation primarily acting in regulatory regions. We also demonstrate that a recently discovered mutagenic process specific to oocytes can be localized solely from population sequencing data. This process is spread across all chromosomes and is highly asymmetric with respect to the direction of transcription, suggesting a major role of DNA damage.

Randomized Phase II Study of R-CHOP-14 Versus R-CHOP-14 Followed By Chaser As Induction Therapy for High-Dose Chemotherapy (HDT), LEED, and Autologous Stem-Cell Transplantation (ASCT) in Poor-Risk Diffuse Large B-Cell Lymphoma (DLBCL): Japan Clinical Oncology Group (JCOG) Study (JCOG0908)

Randomized Phase II Study of R-CHOP-14 Versus R-CHOP-14 Followed By Chaser As Induction Therapy for High-Dose Chemotherapy (HDT), LEED, and Autologous Stem-Cell Transplantation (ASCT) in Poor-Risk Diffuse Large B-Cell Lymphoma (DLBCL): Japan Clinical Oncology Group (JCOG) Study (JCOG0908)

Paraoxonases 1 and 2 (PON1 and 2) Polymorphisms in Diffuse Large B-Cell Lymphoma (DLBCL): Correlation with Clinical Outcomes

Background: The paraoxonase gene family (PON1, PON2 and PON3) is located on chromosome 7. Their proteins prevent oxidative stress and show anti-inflammatory properties, being related to a wide variety of human illnesses. Oxidative stress is related to malignant transformation in some tumors, and PON Single Nucleotide Polymorphisms have been associated with increased risk of some types of cancers.Purpose: To investigate the genotypic and allelic frequency of polymorphisms of PON1 (192QR and 55LM) and PON2 (148AG and 311SC) genes in patients with DLBCL in a Brazilian population, and to analyze the correlations of these polymorphisms with clinical outcomes.Methods: Subjects were HIV negative patients diagnosed with DLBCL CD20+ between February 2009 and April 2011. Patients (78) were from the Instituto do Cancer do Estado de Sao Paulo. They were followed for survival and disease progression (cut-off date: April 2017). All histopathology slides and blocks were reviewed by a trained pathologist. The DNA was extracted from peripheral blood leukocytes by salting-out extraction method. PON1 and PON2 polymorphisms were detected by PCR/RFLP. Overall Survival (OS) and Progression Free Survival (PFS) were estimated using Kaplan-Meier analysis, and the log-rank test was used to assess differences between the curves. Univariate Cox regression analysis was used to assess the association between clinical characteristics and the survival endpoints. Univariate logistic regression was used to examine the association between covariates and complete response.Results: Complete information was available for 67 patients. Median age at diagnosis: 40 years (20-65). 64.1% patients had Performance Status PS 0-1 at diagnosis; 53.7% were female; 64.1% had low-intermediate risk International Prognostic Index (IPI); 43.2% had Bulky Lesion. All patients received rituximab-based chemotherapy. Frequency of the polymorphisms: PON1 192 (QR/RR: 47%, QQ: 53%), PON1 55 (LM: 35.8%, MM: 10.4%, LL: 52.2%), PON2 148 (AG: 46.2%, GG: 5.9%, AA: 46.2%), PON2 311 (SC: 35.8%, CC: 7.4%, SS: 52.2%). Twenty-three patients (34.3%) died after 5 years of follow-up, with OS 5 years: 65.1% (95% CI 51.9-75.5). PFS in 5 years: 51.8%. At Univariate Cox Regression, PS 2-4 compared to PS 0-1 at diagnosis was associated with increased risk of death (HR: 3.96, 95% CI: 1.71-9.13, p=0.001). Regarding the polymorphisms, PON1 55 LM was associated with increased risk of disease progression (HR: 2.01, 95% CI: 0.98-4.11, p=0.05) when compared to LL. No correlation was observed between the studied polymorphisms and clinical outcomes.Conclusions: PON1 55LM was associated with an increased risk of disease progression. Nevertheless, the clinical significance of this finding deserves further investigation. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Rituximab-Bendamustine in First Line Treatment of Patients with Follicular Lymphoma. Results of Prospective Multicenter Study

BACKGROUND. Follicular lymphoma (FL) is lymphoid tumor that occurs in 22% of all non-Hodgkin's lymphomas (NHL) in Russia with median age 65 years. FL has a high chemosensitivity and often recurs: five-year progression-free survival (PFS) with R-CHOP - 40%. Due to high risk of recurrence and median age of FL pts 65 years, we need to reduce toxicity. Rituximab-bendamustine (R-B) versus R-CHOP in common group (without dividing on cytological grade) increases PFS and has lower toxicity, so it is possible to apply it to patients with concomitant pathology.AIM. To study R-B efficiency in different cytological grade of FL.PATIENTS AND METHODS. We performed a prospective, multicenter, open-label trial in Russia since 1 of June 2013 till 1 of June 2017. The study included 65 patients with FL. Median age of patients was 59 years (from 30 to 78 years). Treatment was completed in 60 patients, so this group of patients was analyzed. Ratio between men and women was 1: 2. 29/60 of patients (48%) were older than 60 y.o. Patients received rituximab 375 mg / m2 on day 1 and bendamustine 90 mg / m2 on days 1 and 2 of a 4-week cycle (6 cycles).47/60 (78%) of pts were diagnosed with FL grade 1, 6/60 (10%) -2 grade, 7/60 (12%) - grade 3A. 55/60(91%) pts had nodular tumor growth type, 6/60(10%) - nodular-diffuse, 4/60 (7%) - diffuse. High risk according to FLIPI had 21/53 (39%) of patients with 1-2 cytologic grade of FL and 7/7 (100%) of pts with FL grade 3A.Extranodal lesions were revealed in 23/60 (38%) of cases: in 4/60 of cases - orbit, in 2/60 - parotid gland, in 3/60 - lungs, in 3/60 - intestines, in 1 / 60 - stomach, 2/60 - pancreas, 2/60 - uterus, 2/60 - skin, 1/60 - subcutaneous tissue, 3/60 - vertebrae, in 1/60 - latticed maze and nasal passages. In 20/23 of cases extranodal lesion was revealed in generalized stage of FL (including lymph nodes and bone marrow).Extranodal lesions were found in 35% of pts with FL grade 1-2, and 57% of pts with FL - grade 3A. Bulky also was observed more frequently in pts with FL grade 3 3/7 (43%) than in pts with FL grade 1-2 19/53 (36%).Results. Complete remission (CR) of disease was achieved in 34/60 (55%) pts, partial remission (PR) - 13/60 (21%) pts. Tumor progression observed in 11/60 (18%) cases, pts were withdrawn from the protocol. In 2/60 (6%) pts had stable disease after 4 courses of R-B. Consequently we performed high-dose chemotherapy with autologous stem cell transplantation for patients with stable disease.Frequency of CR and PR was higher in pts with FL grade 1-2 than in FL grade 3: 87% versus 28%. Progressive disease observed more frequently in FL grade 3A - 71% vs pts with FL grade 1-2 (13%). Median follow up was 42 (4-56) months. Bone marrow was sanitized in all cases of its lesion - 33/60 (55%).Conclusions. 3A cytological grade of FL is associated with high FLIPI score, presence of bulky and extranodal lesions. These parameters are predictive unfavorable factors of poor response to R-B induction therapy. The R-B allows performing stem cells mobilization and autoSCT that is actual in FL pts with bone marrow involvement. DisclosuresNo relevant conflicts of interest to declare.

Nucleotide Excision Repair: From Molecular Defects to Neurological Abnormalities.

Nucleotide excision repair (NER) is the most versatile DNA repair pathway, which can remove diverse bulky DNA lesions destabilizing a DNA duplex. NER defects cause several autosomal recessive genetic disorders. Xeroderma pigmentosum (XP) is one of the NER-associated syndromes characterized by low efficiency of the removal of bulky DNA adducts generated by ultraviolet radiation. XP patients have extremely high ultraviolet-light sensitivity of sun-exposed tissues, often resulting in multiple skin and eye cancers. Some XP patients develop characteristic neurodegeneration that is believed to derive from their inability to repair neuronal DNA damaged by endogenous metabolites. A specific class of oxidatively induced DNA lesions, 8,5′-cyclopurine-2′-deoxynucleosides, is considered endogenous DNA lesions mainly responsible for neurological problems in XP. Growing evidence suggests that XP is accompanied by defective mitophagy, as in primary mitochondrial disorders. Moreover, NER pathway is absent in mitochondria, implying that the mitochondrial dysfunction is secondary to nuclear NER defects. In this review, we discuss the current understanding of the NER molecular mechanism and focuses on the NER linkage with the neurological degeneration in patients with XP. We also present recent research advances regarding NER involvement in oxidative DNA lesion repair. Finally, we highlight how mitochondrial dysfunction may be associated with XP.

LEO1 is a partner for Cockayne syndrome protein B (CSB) in response to transcription-blocking DNA damage.

Cockayne syndrome (CS) is an autosomal recessive genetic disorder characterized by photosensitivity, developmental defects, neurological abnormalities, and premature aging. Mutations in CSA (ERCC8), CSB (ERCC6), XPB, XPD, XPG, XPF (ERCC4)and ERCC1 can give rise to clinical phenotypes resembling classic CS. Using a yeast two-hybrid (Y2H) screening approach, we identified LEO1 (Phe381-Ser568 region) as an interacting protein partner of full-length and C-terminal (Pro1010-Cys1493) CSB in two independent screens. LEO1 is a member of the RNA polymerase associated factor 1 complex (PAF1C) with roles in transcription elongation and chromatin modification. Supportive of the Y2H results, purified, recombinant LEO1 and CSB directly interact in vitro, and the two proteins exist in a common complex within human cells. In addition, fluorescently tagged LEO1 and CSB are both recruited to localized DNA damage sites in human cells. Cell fractionation experiments revealed a transcription-dependent, coordinated association of LEO1 and CSB to chromatin following either UVC irradiation or cisplatin treatment of HEK293T cells, whereas the response to menadione was distinct, suggesting that this collaboration occurs mainly in the context of bulky transcription-blocking lesions. Consistent with a coordinated interaction in DNA repair, LEO1 knockdown or knockout resulted in reduced CSB recruitment to chromatin, increased sensitivity to UVC light and cisplatin damage, and reduced RNA synthesis recovery and slower excision of cyclobutane pyrimidine dimers following UVC irradiation; the absence of CSB resulted in diminished LEO1 recruitment. Our data indicate a reciprocal communication between CSB and LEO1 in the context of transcription-associated DNA repair and RNA transcription recovery.

Translesion Synthesis Past 5-Formylcytosine-Mediated DNA-Peptide Cross-Links by hPolη Is Dependent on the Local DNA Sequence.

DNA-protein cross-links (DPCs) are unusually bulky DNA lesions that form when cellular proteins become trapped on DNA following exposure to ultraviolet light, free radicals, aldehydes, and transition metals. DPCs can also form endogenously when naturally occurring epigenetic marks [5-formyl cytosine (5fC)] in DNA react with lysine and arginine residues of histones to form Schiff base conjugates. Our previous studies revealed that DPCs inhibit DNA replication and transcription but can undergo proteolytic cleavage to produce smaller DNA-peptide conjugates. We have shown that 5fC-conjugated DNA-peptide cross-links (DpCs) placed within the CXA sequence (X = DpC) can be bypassed by human translesion synthesis (TLS) polymerases η and κ in an error-prone manner. However, the local nucleotide sequence context can have a strong effect on replication bypass of bulky lesions by influencing the geometry of the ternary complex among the DNA template, polymerase, and the incoming dNTP. In this work, we investigated polymerase bypass of 5fC-DNA-11-mer peptide cross-links placed in seven different sequence contexts (CXC, CXG, CXT, CXA, AXA, GXA, and TXA) in the presence of human TLS polymerase η. Primer extension products were analyzed by gel electrophoresis, and steady-state kinetics of the misincorporation of dAMP opposite the DpC lesion in different base sequence contexts was investigated. Our results revealed a strong impact of nearest neighbor base identity on polymerase η activity in the absence and presence of a DpC lesion. Molecular dynamics simulations were used to structurally explain the experimental findings. Our results suggest a possible role of local DNA sequence in promoting TLS-related mutational hot spots in the presence and absence of DpC lesions.

Sequence‐Based Structural Stability Modulate Biological Processing of AFB 1 ‐Fapy‐dG Adduct by NEIL1 DNA glycosylase

Dietary exposure to aflatoxin B1 (AFB1) is a significant risk factor for developing hepatocellular carcinomas (HCCs). Following ingestion and bioactivation by microsomal P450s, AFB1 reacts with the N7-position of guanine, leading to formation of highly genotoxic AFB1-Fapy-dG adducts. AFB1 5′-interface intercalation stabilizes DNA duplex significantly through strong base-stacking interactions with neighbor base-pairs. Also being sterically bulky DNA lesion, it was unexpectedly found to be excised by DNA glycosylase NEIL1, base-excision repair enzyme, from DNA in both synthetic oligodeoxynucleotides and liver DNA of exposed mice. We hypothesized that the DNA sequence context in which the AFB1-Fapy-dG adduct is formed might modulate duplex stability and consequently alter the efficiencies of NEIL1-initiated repair, ultimately contributing towards AFB1associated mutational spectrum. To test this, site-specific AFB1-Fapy-dG adducts were synthesized in three sequence contexts where 5′ neighbor base was varied. We observed differential DNA thermal stability specific to 5′-neighbor base-pair using UV absorbance and NMR-based melting studies. Furthermore, sequence-dependent stability differences also guided NEIL1-mediated base removal tendency where single turnover kinetic analyses showed an inverse correlation between the modified duplex stability and the NEIL1-catalyzed excision rates.

Primary cutaneous T-cell lymphomas in childhood and adolescence.

Primary cutaneous lymphomas are extranodal non-Hodgkin lymphomas of T- or B- cell origin, that predominantly affect older patients but have been reported in all age groups and as early as in the first years of life. Diagnosis of cutaneous lymphomas is challenging and requires high clinical suspicion and close collaboration between dermatologists, pediatric oncologists and pathologists. Skin involvement of non-Hodgkin lymphomas in children or adolescents can either be primary cutaneous or secondary due to an underlying nodal lymphoma. The most common primary cutaneous lymphomas encountered in children are of T-cell origin, with mycosis fungoides being the most prevalent cutaneous T-cell lymphoma, followed by CD30+ lymphoproliferative disorders. While cutaneous lymphomas share clinicopathologic characteristics between juvenile and adult forms, there are important differences in terms of clinical presentation, diagnosis and treatment. The hypopigmented variant of mycosis fungoides seems to be overrepresented in the pediatric age group. Prognosis and treatment of mycosis fungoides are stage dependent. The majority of children present with early-stage disease and respond well to topical corticosteroids and phototherapy.

The Interaction Efficiency of XPD-p44 With Bulky DNA Damages Depends on the Structure of the Damage.

The successful elimination of bulky DNA damages via the nucleotide excision repair (NER) system is largely determined by the damage recognition step. This step consists of primary recognition and verification of the damage. The TFIIH helicase XPD plays a key role in the verification step during NER. To date, the mechanism of damage verification is not sufficiently understood and requires further detailed research. This study is a systematic investigation of the interaction of ctXPD (Chaetomium thermophilum) as well as ctXPD-ctp44 with model DNAs, which contain structurally different bulky lesions with previously estimated NER repair efficiencies. We have used ATPase and DNA binding studies to assess the interaction of ctXPD with damaged DNA. The result of the analysis of ctXPD-ctp44 binding to DNA containing fluorescent and photoactivatable lesions demonstrates the relationship between the affinity of XPD for DNAs containing bulky damages and the ability of the NER system to eliminate the damage. Photo-cross-linking of ctXPD with DNA probes containing repairable and unrepairable photoactivatable damages reveals differences in the DNA interaction efficiency in the presence and absence of ctp44. In general, the results obtained indicate the ability of ctXPD-ctp44 to interact with a damage and suggest a significant role for ctp44 subunit in the verification process.

Excision of Oxidatively Generated Guanine Lesions by Competitive DNA Repair Pathways.

The base and nucleotide excision repair pathways (BER and NER, respectively) are two major mechanisms that remove DNA lesions formed by the reactions of genotoxic intermediates with cellular DNA. It is generally believed that small non-bulky oxidatively generated DNA base modifications are removed by BER pathways, whereas DNA helix-distorting bulky lesions derived from the attack of chemical carcinogens or UV irradiation are repaired by the NER machinery. However, existing and growing experimental evidence indicates that oxidatively generated DNA lesions can be repaired by competitive BER and NER pathways in human cell extracts and intact human cells. Here, we focus on the interplay and competition of BER and NER pathways in excising oxidatively generated guanine lesions site-specifically positioned in plasmid DNA templates constructed by a gapped-vector technology. These experiments demonstrate a significant enhancement of the NER yields in covalently closed circular DNA plasmids (relative to the same, but linearized form of the same plasmid) harboring certain oxidatively generated guanine lesions. The interplay between the BER and NER pathways that remove oxidatively generated guanine lesions are reviewed and discussed in terms of competitive binding of the BER proteins and the DNA damage-sensing NER factor XPC-RAD23B to these lesions.

Initial clinical evaluation of indigenous 90Y-DOTATATE in sequential duo-PRRT approach (177Lu-DOTATATE and 90Y-DOTATATE) in neuroendocrine tumors with large bulky disease: Observation on tolerability, 90Y-DOTATATE post- PRRT imaging characteristics (bremsstrahlung and PETCT) and early adverse effects.

177Lu-DOTATATE peptide receptor radionuclide therapy (PRRT) alone has lesser potential in the clinical setting of neuroendocrine tumor (NET) with large bulky disease and nonhomogeneous somatostatin receptors (SSTR) distribution, owing to lower energy (Eβmax 0.497 MeV) and a shorter particle penetration range (maximum 2–4 mm) of 177Lu. In large bulky NETs, 90Yttrium (90Y) has the theoretical advantages because of a longer beta particle penetration range (a maximum soft tissue penetration of 11 mm). Therefore, a combination of 177Lu and 90Y is a theoretically sound concept that can result in better response in metastatic NET with large-bulky lesion and non-homogeneous SSTR distribution. The aim of the study was to determine the feasibility of combining 90Y-DOTATATE with 177Lu-DOTATATE PRRT as sequential duo-PRRT in metastatic NET with (≥5 cm) including the post 90Y-DOTATATE-PRRT imaging and also to determine early toxicity of the duo-PRRT approach. A total of 9 patients received combination of 177Lu-DOTATATE with 90Y-DOTATATE (indigenously prepared and approved) through sequential duo-PRRT approach. These 9 NET patients were included and analyzed in this study. All 9 patients had undergone post-PRRT 90Y-DOTATATE imaging, including a whole-body planar bremsstrahlung imaging followed by regional single-photon emission computed tomography (SPECT)-computed tomography (CT) imaging and also a regional positron emission tomography–computed tomography imaging. Grading of 90Y-DOTATATE and 177Lu-DOTATATE uptake was done on post-PRRT imaging by both modalities. The size of the lesions ranged from 5.5 cm to 16 cm with average size of 10 cm before sequential duo-PRRT was decided. Sequential duo-PRRT was administered because of stable, unresponsive disease following 177Lu-DOTATATE in 5 patients (55.6%), progressive disease after 177Lu-DOTATATE in 2 patients (22.2%), and with neoadjuvant intent in 2 patients (22.2%). The total cumulative dose of 177Lu-DOTATATE before duo-pRRT ranged from 11.84 GBq to 37 GBq per patient and average administered dose of 27.21 GBq per patient in this study. Out of 9 patients, 8 patients received single cycle of 90Y-DOTATATE (ranging from 2.66 GBq to 3.4 GBq per patient with average administered dose of 3.12 GBq per patient). One patient received two cycles of 90Y-DOTATATE (total dose of 6.2 GBq). Out of 9 patients, 8 patients showed excellent tracer concentration in lesions on post-PRRT 90Y-DOTATATE imaging and the remaining 1 patient showed fairly adequate 90Y-DOTATATE tracer uptake in lesion on visual analysis. There was matched 90Y-DOTATATE uptake with 68Ga-DOTATATE and also with 177LuDOTATATE in all 9 patients. The sequential duo-PRRT was well tolerated by all patients. Two patients (22.2%) developed mild nausea, one patient (11.1%) developed transient mild-grade hemoglobin toxicity, and one patient (11.1%) developed mild-grade gastrointestinal symptoms (loose motion and abdominal pain). No nephrotoxicity, hepatotoxicity, and other hematological toxicity was observed. The combination of the indigenous 90Y-DOTATATE with 177Lu-DOTATATE PRRT in NET as sequential duo-PRRT was well tolerated, feasible and safe in stable, unresponsive/progressive disease following single isotope 177Lu-DOTATATE therapy and also in neoadjuvant PRRT setting with large bulky lesion (≥≥5cm). Post-PRRT 90Y-DOTATATE imaging showed excellent 90Y-DOTATATE uptake in nearly all NET patients. Mild-grade early adverse effects were easily manageable and controllable in this sequential duo-PRRT approach.

A CSB-PAF1C axis restores processive transcription elongation after DNA damage repair

Bulky DNA lesions in transcribed strands block RNA polymerase II (RNAPII) elongation and induce a genome-wide transcriptional arrest. The transcription-coupled repair (TCR) pathway efficiently removes transcription-blocking DNA lesions, but how transcription is restored in the genome following DNA repair remains unresolved. Here, we find that the TCR-specific CSB protein loads the PAF1 complex (PAF1C) onto RNAPII in promoter-proximal regions in response to DNA damage. Although dispensable for TCR-mediated repair, PAF1C is essential for transcription recovery after UV irradiation. We find that PAF1C promotes RNAPII pause release in promoter-proximal regions and subsequently acts as a processivity factor that stimulates transcription elongation throughout genes. Our findings expose the molecular basis for a non-canonical PAF1C-dependent pathway that restores transcription throughout the human genome after genotoxic stress.

Molecular Aspects of the Isolated Limb Infusion Procedure.

For decades, isolated limb infusion (ILI) and hyperthermic isolated limb perfusion (HILP) have been used to treat melanoma in-transit metastases and unresectable sarcoma confined to the limb utilizing the effect of loco-regional high-dose chemotherapy to the isolated limb. Both procedures are able to provide high response rates in patients with numerous or bulky lesions in whom other loco-regional treatments are becoming ineffective. In comparison to systemic therapies, on the other hand, ILI and HILP have the advantage of not being associated with systemic side-effects. Although in principle ILI and HILP are similar procedures, ILI is technically simpler to perform and differs from HILP in that it takes advantage of the hypoxic and acidotic environment that develops in the isolated limb, potentiating anti-tumour activity of the cytotoxic agents melphalan +/− actinomycin-D. Due to its simplicity, ILI can be used in both preclinical and clinical studies to test new cytotoxic regimens and combinations with the aim to overcome tumour resistance. In the future, administration of cytotoxic agents by ILI, in combination with systemic treatments such as BRAF/MEK/KIT inhibitors, immunotherapy (CTLA-4 blockade), and/or programmed death (PD-1) pathway inhibitors, has the potential to improve responses further by inducing increased tumour cell death while limiting the ability of the tumour to suppress the immune response.

A Method for Assessing the Efficiency of the Nucleotide Excision Repair System Ex Vivo.

The nucleotide excision repair (NER) is one of the main repair systems present in the cells of living organisms. It is responsible for the removal of a wide range of bulky DNA lesions. We succeeded in developing a method for assessing the efficiency of NER in the cell (ex vivo), which is a method based on the recovery of TagRFP fluorescent protein production through repair of the damage that blocks the expression of the appropriate gene. Our constructed plasmids containing bulky nFlu or nAnt lesions near the tagrfp gene promoter were shown to undergo repair in eukaryotic cells (HEK 293T) and that they can be used to analyze the efficiency of NER ex vivo. A comparative analysis of the time dependence of fluorescent cells accumulation after transfection with nFlu- and nAnt-DNA revealed that there are differences in how efficient their repair by the NER system of HEK 293T cells can be. The method can be used to assess the cell repair status and the repair efficiency of different structural damages.

Retrospective evaluation of patients with primary mediastinal large B-Cell lymphoma: Real life experience

Aim: Primary mediastinal large B-cell lymphoma (PMBCL) is a type of lymphoma that forms approximately 3 % of non-Hodgkin lymphomas that often encounter with mass. The aim of this study was to present the epidemiological characteristics, response rates of the treatment and the survival of PMBCL patients in our single center. Materials and Methods: Patient demographics, treatment regimens, survival rates of PMBCL patients were retrospectively analyzed. Results: There are 15 patients in our study. Most of the patients were female (n:9, 60%). The median age at the time of diagnosis was 35.4. Nine patients applied with a bulky lesion in the mediastinum. Most of the patients have been treated with DA-EPOCH-R (dose-adjusted etoposide, doxorubicin, cyclophosphamide, vincristine and prednisone with rituximab) (n:13, 87%) and 2 (n:2, 13%) patients have been treated with R-CHOP (doxorubicin, cyclophosphamide, vincristine and prednisone with rituximab) regimens for 6 cycles. Eight patients (53.3%) received involved-field radiotherapy on the mediastinum. After the first-row chemotherapy, total remission rate was 93.3%. Thirteen (87%) of the patients were still in remission and alive. The median follow-up time in our study was 43 months (13 -81). Mean disease-free survival was 67.43 months and overall survival was 72.87 months. The overall and disease-free survival rate was 86.7 % and 80%. Conclusions: In our study, most patients responded to the treatment and are still being followed in remission.

Light-induced modulation of DNA recognition by the Rad4/XPC damage sensor protein.

Biomolecular structural changes upon binding/unbinding are key to their functions. However, characterization of such dynamical processes is difficult as it requires ways to rapidly and specifically trigger the assembly/disassembly as well as ways to monitor the resulting changes over time. Recently, various chemical strategies have been developed to use light to trigger changes in oligonucleotide structures, and thereby their activities. Here we report that photocleavable DNA can be used to modulate the DNA binding of the Rad4/XPC DNA repair complex using light. Rad4/XPC specifically recognizes diverse helix-destabilizing/distorting lesions including bulky organic adduct lesions and functions as a key initiator for the eukaryotic nucleotide excision repair (NER) pathway. We show that the 6-nitropiperonyloxymethyl (NPOM)-modified DNA is recognized by the Rad4 protein as a specific substrate and that the specific binding can be abolished by light-induced cleavage of the NPOM group from DNA in a dose-dependent manner. Fluorescence lifetime-based analyses of the DNA conformations suggest that free NPOM-DNA retains B-DNA-like conformations despite its bulky NPOM adduct, but Rad4-binding causes it to be heterogeneously distorted. Subsequent extensive conformational searches and molecular dynamics simulations demonstrate that NPOM in DNA can be housed in the major groove of the DNA, with stacking interactions among the nucleotide pairs remaining largely unperturbed and thus retaining overall B-DNA conformation. Our work suggests that photoactivable DNA may be used as a DNA lesion surrogate to study DNA repair mechanisms such as nucleotide excision repair.

Role of Human NADPH Quinone Oxidoreductase (NQO1) in Oxygen-Mediated Cellular Injury and Oxidative DNA Damage in Human Pulmonary Cells.

Supplemental oxygen administration is frequently used in premature infants and adults with pulmonary insufficiency. NADPH quinone oxidoreductase (NQO1) protects cells from oxidative injury by decreasing reactive oxygen species (ROS). In this investigation, we tested the hypothesis that overexpression of NQO1 in BEAS-2B cells will mitigate cell injury and oxidative DNA damage caused by hyperoxia and that A-1221C single nucleotide polymorphism (SNP) in the NQO1 promoter would display altered susceptibility to hyperoxia-mediated toxicity. Using stable transfected BEAS-2B cells, we demonstrated that hyperoxia decreased cell viability in control cells (Ctr), but this effect was differentially mitigated in cells overexpressing NQO1 under the regulation of the CMV viral promoter, the wild-type NQO1 promoter (NQO1-NQO1), or the NQO1 promoter carrying the SNP. Interestingly, hyperoxia decreased the formation of bulky oxidative DNA adducts or 8-hydroxy-2′-deoxyguanosine (8-OHdG) in Ctr cells. qPCR studies showed that mRNA levels of CYP1A1 and NQO1 were inversely related to DNA adduct formation, suggesting the protective role of these enzymes against oxidative DNA injury. In SiRNA experiments entailing the NQO1-NQO1 promoter, hyperoxia caused decreased cell viability, and this effect was potentiated in cells treated with CYP1A1 siRNA. We also found that hyperoxia caused a marked induction of DNA repair genes DDB2 and XPC in Ctr cells, supporting the idea that hyperoxia in part caused attenuation of bulky oxidative DNA lesions by enhancing nucleotide excision repair (NER) pathways. In summary, our data support a protective role for human NQO1 against oxygen-mediated toxicity and oxidative DNA lesions in human pulmonary cells, and protection against toxicity was partially lost in SNP cells. Moreover, we also demonstrate a novel protective role for CYP1A1 in the attenuation of oxidative cells and DNA injury. Future studies on the mechanisms of attenuation of oxidative injury by NQO1 should help in developing novel approaches for the prevention/treatment of ARDS in humans.

DNA-Histone Cross-Links: Formation and Repair.

The nucleosome is a stretch of DNA wrapped around a histone octamer. Electrostatic interactions and hydrogen bonds between histones and DNA are vital for the stable organization of nucleosome core particles, and for the folding of chromatin into more compact structures, which regulate gene expression via controlled access to DNA. As a drawback of tight association, under genotoxic stress, DNA can accidentally cross-link to histone in a covalent manner, generating a highly toxic DNA-histone cross-link (DHC). DHC is a bulky lesion that can impede DNA transcription, replication, and repair, often with lethal consequences. The chemotherapeutic agent cisplatin, as well as ionizing and ultraviolet irradiations and endogenously occurring reactive aldehydes, generate DHCs by forming either stable or transient covalent bonds between DNA and side-chain amino groups of histone lysine residues. The mechanisms of DHC repair start to unravel, and certain common principles of DNA-protein cross-link (DPC) repair mechanisms that participate in the removal of cross-linked histones from DNA have been described. In general, DPC is removed via a two-step repair mechanism. First, cross-linked proteins are degraded by specific DPC proteases or by the proteasome, relieving steric hindrance. Second, the remaining DNA-peptide cross-links are eliminated in various DNA repair pathways. Delineating the molecular mechanisms of DHC repair would help target specific DNA repair proteins for therapeutic intervention to combat tumor resistance to chemotherapy and radiotherapy.

The Ubiquitin Ligase TRAIP: Double-Edged Sword at the Replisome.

In preparation for cell division, the genome must be copied with high fidelity. However, replisomes often encounter obstacles, including bulky DNA lesions caused by reactive metabolites and chemotherapeutics, as well as stable nucleoprotein complexes. Here, we discuss recent advances in our understanding of TRAIP, a replisome-associated E3 ubiquitin ligase that is mutated in microcephalic primordial dwarfism. In interphase, TRAIP helps replisomes overcome DNA interstrand crosslinks and DNA-protein crosslinks, whereas in mitosis it triggers disassembly of all replisomes that remain on chromatin. We describe a model to explain how TRAIP performs these disparate functions and how they help maintain genome integrity.