Analyzing RNA posttranscriptional modifications to decipher the epitranscriptomic code

The discovery of RNA silencing has revealed that non-protein-coding sequences (ncRNAs) can cover essential roles in regulatory networks and their malfunction may result in severe consequences on human health. These findings have prompted a general reassessment of the significance of RNA as a key player in cellular processes. This reassessment, however, will not be complete without a greater understanding of the distribution and function of the over 170 variants of the canonical ribonucleotides, which contribute to the breathtaking structural diversity of natural RNA. This review surveys the analytical approaches employed for the identification, characterization, and detection of RNA posttranscriptional modifications (rPTMs). The merits of analyzing individual units after exhaustive hydrolysis of the initial biopolymer are outlined together with those of identifying their position in the sequence of parent strands. Approaches based on next generation sequencing and mass spectrometry technologies are covered in depth to provide a comprehensive view of their respective merits. Deciphering the epitranscriptomic code will require not only mapping the location of rPTMs in the various classes of RNAs, but also assessing the variations of expression levels under different experimental conditions. The fact that no individual platform is currently capable of meeting all such demands implies that it will be essential to capitalize on complementary approaches to obtain the desired information. For this reason, the review strived to cover the broadest possible range of techniques to provide readers with the fundamental elements necessary to make informed choices and design the most effective possible strategy to accomplish the task at hand.

Perioperative atrial fibrillation and risk of stroke after cardiac surgery: a systematic review and meta-analysis

Background

Perioperative atrial fibrillation (POAF) after cardiac surgery has been associated with an increased risk of stroke. However, many previous studies have not systematically excluded patients with pre-existing AF. As such, the association between new-onset POAF and stroke risk has not been well established.

Purpose

To perform a systematic review and meta-analysis on the short and long-term risks of stroke in patients experiencing new-onset POAF after cardiac surgery.

Methods

We searched MEDLINE, EMBASE, and the Cochrane Library databases for studies comparing the risk of stroke in patients with versus without new-onset POAF after cardiac surgery. Studies were included in our review if they enrolled ≥100 patients and defined POAF as new-onset AF in patients with no history of preoperative AF. Data were independently extracted in duplicate. The quality of studies was assessed using the Newcastle Ottawa Scale. Random-effects meta-analysis was used to calculate summary risk ratios. Short-term stroke risk was calculated using events occurring either in-hospital or ≤30 days after surgery, and long-term risk was calculated using events occurring >30 days after surgery.

Results

After reviewing 11,791 citations, 46 studies met the inclusion criteria. These studies included 364,822 patients, of which 76,388 (20.9%) developed new-onset POAF. The incidence of stroke was higher among patients with POAF versus no POAF (n=44 studies; incidence 2.76% vs. 1.53%; relative risk (RR) 1.91, 95% CI 1.65–2.23; I2 = 78%). A sensitivity analysis of high-quality studies alone yielded similar results (n=9 studies; RR 1.74, 95% CI 1.31–2.30; I2 = 88%). Patients with POAF had a higher incidence of stroke both in the short-term (n=35 studies; 2.71% vs. 1.36%; RR 2.13, 95% CI 1.81–2.51; I2 = 69%) and long-term (n=20 studies; 1.6 vs. 1.0 per 100 patient-years; RR 1.39, 95% CI 1.24–1.57; I2 = 27%). The risk of stroke was increased in POAF patients across all types of cardiac surgery performed, including isolated CABG (n=19 studies; RR 1.93, 95% CI 1.60–2.32; I2 = 62%), isolated transcatheter aortic valve implantation (n=7 studies; RR 1.86, 95% CI 1.32–2.63; I2 = 0%), and studies including multiple procedure types (n=16 studies; RR 1.90, 95% CI 1.44–2.51; I2 = 89%).

Conclusion

New-onset POAF after cardiac surgery is associated with an increased risk of stroke, both in the short and long term. The absolute risk difference is small, and randomized trials are needed to assess the efficacy and safety of treatment interventions in this patient population.

Funding Acknowledgement

Type of funding source: None

An analysis of open reduction of irreducible supracondylar fractures of the humerus in children

OBJECTIVES

To review experience with irreducible supracondylar fractures requiring open reduction in children, and to propose guidelines for an open approach to supracondylar fractures.

DESIGN

A chart review.

SETTING

The Children's Hospital of Eastern Ontario (CHEO), a pediatric centre with a large referral base.

PATIENTS

Forty-one children (18 boys 23 girls, average age 7 years), who had open reduction of irreducible supracondylar fractures at the CHEO over a 10-year period (1985 to 1995). Of these 41 children, 7 were lost to direct follow-up.

INTERVENTIONS

After closed reduction of displaced supracondylar fractures of the humerus failed, all patients underwent open reduction and percutaneous fixation in the operating room. Before operation, 6 had no radial pulse, 5 lost their pulse with flexion after reduction and 4 had unstable fracture patterns.

MAIN OUTCOME MEASURES

Assessment of elbow range of motion and carrying angle, distal neurovascular status and radiographic measurement of the Baumann angle and the humerocapitellar angle.

RESULTS

In 25 children, the humerus was found to have "buttonholed" through the brachialis muscle; 1 had entrapment of the common flexor muscle at its origin and 1 had entrapment of the triceps. In 15 children there was entrapment or tethering of the median nerve and radial nerve or brachial artery, or both, but this was not predictive of preoperative neurovascular deficit, which was recorded in 21 patients (fully recovered). At follow-up, the Baumann angle and the humerocapitellar angle differed by an average of 2 degrees and 5.3 degrees respectively compared with the unaffected arm. Range of motion was satisfactory in 94% of patients, and there was no significant cubitus varus.

CONCLUSION

Open reduction of supracondylar fractures is a safe and effective procedure, for which orthopedists should should lower their threshold, given certain appropriate indicators.

Randomized comparison of G-CSF + GM-CSF vs G-CSF alone for mobilization of peripheral blood stem cells: effects on hematopoietic recovery after high-dose chemotherapy

Fifty patients with either lymphoid or selected solid tumor malignancies were apheresed an identical number of times for PBSC collection after being randomized to receive either G-CSF 10 microg/kg/day alone (arm I), or G-CSF at the same dose with GM-CSF 5 microg/kg/day (arm II). Growth factor(s) was/were given as the stem cell mobilizing agent for 5 days before the start of PBSC collection, and were continued throughout the 4 days of apheresis. Aspiration and cryopreservation of autologous bone marrow occurred on day 3 or 4 of growth factor(s). Thirty-one of 50 patients received one cycle only at time of evaluation, and 19 patients received two cycles of HDCT, each supported with PBSC with or without autologous bone marrow. No patients received growth factors post-autologous stem cell transplant, unless the absolute neutrophils count (ANC) failed to recover to > or = 100/microl by day +18 post-transplant. The median number of days to recovery of ANC to 100/microl, 500/microl and 1000/microl, and of platelet counts to 20000/microl, 50000/microl and 100000/microl after either cycle 1 or cycle 2 of HDCT and the number of febrile days and platelet and PRBC transfusion requirements was not significantly different between the two arms of the study. The duration of hospitalization was similar between study arms for cycle 1 of HDCT, but was 3.5 days less with arm II compared to arm I (P = 0.0248) for cycle 2 of HDCT. The bone marrow buffy coat and PBSC product mononuclear cell count (x 10(8)/kg) and CD34+ cell count (x 10(6)/kg) collected by each method of stem cell mobilization was not significantly different. There is questionable clinical benefit with PBSC products mobilized with the combination of G-CSF and GM-CSF vs G-CSF alone. Perhaps different dosages, schedules, or other growth factor combinations with G-CSF might enhance these differences.

Fractures of the capitellum in adolescents

Fractures of the capitellum are rare in children. The treatment of these injuries has been controversial. At a major pediatric trauma center, seven capitellar fractures were seen in children between 1988 and 1994. The average age of the children was 14.7 years (range, 11-17). Six of these fractures were type I injuries, with large anterosuperior fragments that required operative reduction and internal fixation in five cases. Internal fixation methods used were K wires in three patients, Herbert screws in one patient, and cannulated screws in one patient. The remaining type I fracture was treated with a closed reduction. The seventh fracture was a type II fracture, treated nonoperatively. Five children did well with their respective treatments, but one required reoperation to remove an exostosis block to flexion. Accurate open reduction and internal fixation for the displaced capitellar fracture in children is an effective treatment to restore normal elbow function.

Antifungal effects of yeast-derived rhu-GM-CSF in patients receiving high-dose chemotherapy given with or without autologous stem cell transplantation: a retrospective analysis

Systemic fungal infections (SFI) in patients receiving high-dose chemotherapy (HDC) are a frequent cause of morbidity and mortality. Preclinical studies have reported augmented antifungal activity of monocytes, macrophage cells, and neutrophils exposed to certain colony-stimulating factors (CSF), including GM-CSF. We conducted a retrospective descriptive epidemiologic study to examine the characteristics of 145 consecutive patients receiving HDC administered with or without autologous stem cell transplantation (ASCT) and who subsequently received either GM-CSF and G-CSF, G-CSF alone, GM-CSF +/- IL-3 or no CSF. The analysis of this patient population sought to define the incidence of SFI and its relationship to therapy with monocyte/macrophage-stimulating (MMS group) cytokines (GM-CSF and G-CSF; GM-CSF +/- IL-3) or to cytokines which do not result in monocyte/macrophage stimulation (NMMS group, G-CSF alone or no CSF). Risk factors for the development of SFI were balanced between the MMS (n = 70) and NMMS (n = 75) groups. Two patients (2.9%) in the MMS and nine patients (12%) in the NMMS groups developed SFI. The risk ratio for developing SFI in the NMMS group compared to the MMS group was 4.20 (P = 0.023). This relationship was confounded, however, by the diagnosis of hematologic tumor or solid tumor (RR = 3.15, P = 0.082). SFI was the primary cause or major contributing factor in five of the 10 total deaths in our study population. Four SFI-related deaths occurred in the NMMS group and one SFI-related death occurred in the MMS group. Our data suggest a protective role for GM-CSF, IL-3 or other MMS cytokines in preventing SFI in patients receiving HDC. This should be further investigated as a potential complementary approach to conventional strategies in antifungal prophylaxis for patients receiving HDC.

Randomized study of growth factors post-peripheral-blood stem-cell transplant: neutrophil recovery is improved with modest clinical benefit

PURPOSE

To evaluate the clinical value of growth factors (GFs) with peripheral-blood stem cells (PBSC) collected following mobilization with GFs, we randomized patients to receive or not to receive GFs following transplant.

PATIENTS AND METHODS

Thirty-seven patients were apheresed after receiving the combination of granulocyte colony-stimulating factor (G-CSF) with granulocyte-macrophage colony-stimulating factor (GM-CSF) at doses of 10 micrograms/kg/d and 5 micrograms/kg/d, respectively, for 6 days before apheresis and during a median of 4 days of collections. One day after the infusion of autologous marrow and PBSC, patients were randomly assigned to receive no GFs or a combination of G-CSF (7.5 micrograms/kg/d) and GM-CSF (2.5 micrograms/kg/d), both as a 2-hour intravenous (i.v.) infusion twice per day until the neutrophil count was greater than 1,500/microL.

RESULTS

The median days to recovery to an absolute neutrophil count (ANC) of 100/microL (9 v 11.5, P = .0005), 500/microL (10 v 16, P = .0004), or 1,000/microL (12 v 21, P = .0008) was shortened with the use of GFs, post-PBSC infusion. In addition, the duration of hospitalization was shorter (19 v 21 days, P = .0112) in the arm receiving GFs post-PBSC infusion. There was no significant difference between the two study arms in the duration of fever, documented septic episodes, or RBC or platelet transfusion requirements.

CONCLUSION

Despite faster neutrophil recovery and shortened duration of hospitalization with GFs administered after PBSC transplantation, the measured clinical variables of febrile days, septic episodes, and transfusion requirements were similar between the study arms. The use of GFs post-PBSC transfusion is associated with a modest clinical benefit.

Effects of interferon-alpha monotherapy on hepatic drug metabolism in cancer patients

1. The influence of interferon-alpha (IFN alpha) on the clearances of theophylline (TH), antipyrine (AP) and hexobarbitone (HB) was studied in seven cancer patients given IFN alpha as their only treatment. In addition, IFN alpha effects on drug clearance were correlated with changes in serum inflammatory cytokines and acute phase proteins. 2. A 'baseline' study was performed by administering an oral drug 'cocktail' of TH (150 mg), AP (250 mg) and HB (250 mg) with saline injected simultaneously and again 24 h later. One week later, an 'acute' study was performed at the initiation of IFN alpha therapy, 3 x 10(6) units injected with the drug cocktail and again 24 h later. After 2 weeks of IFN alpha treatment three times per week, a 'chronic' study was performed with IFN alpha injected the day prior to, simultaneously with, as well as 24 h after the drug cocktail. 3. Plasma samples were collected over 48 h and the clearances of TH, AP and HB were estimated. Serum samples were collected at various times for the measurement of tumor necrosis factor (TNF), interleukin-1 (IL-1), interleukin-6 (IL-6), C-reactive protein (C-RP) and alpha 1-acid glycoprotein (AGP). 4. IFN alpha caused a 33% decrease in the oral clearance of TH during the chronic study compared with baseline (P < or = 0.05). Although IFN alpha inhibited TH clearance by 16% during the acute study and AP clearance by 20-21% during both acute and chronic studies, these changes did not reach statistical significance. IFN alpha caused minimal changes in HB clearance. There were no chronic effects of IFN alpha on serum cytokines or acute phase proteins. 5. The findings confirm that the most commonly used dose of IFN alpha inhibits the hepatic clearance in humans of some but not all drugs and that this inhibition persists during IFN alpha therapy. Because inhibition was not associated with increases in serum cytokines or acute phase proteins, the mechanism by which IFN alpha inhibits cytochrome P450 activities in vivo does not appear to involve inflammatory mediators such as TNF. IL-1 or IL-6.

Isolated dislocation of the radial head

Fifty-four patients (12 bilateral) with isolated dislocations of the radial head were encountered over a 20-year period. The congenital varieties (26 patients) included isolated unilateral, familial, synostosis-related, and syndrome-related. The acquired types (28 patients) involved trauma, neuromuscular impairment, or adaptive dislodgments. Acute, traumatic dislocation (17 patients) was the most common presentation. Others were diagnosed incidentally, or associated with discomfort, dysfunction, or deformity. Closed reduction of an acute traumatic dislocation was generally successful (16 of 17 patients). Realignment attempts (three cases) on late diagnosed traumatic cases and isolated congenital types were invariably unsuccessful, eventually requiring radial head excision. Four patients underwent excision of the head of the radius as primary treatment.

Allogeneic bone marrow transplantation: procedures and complications

Bone marrow transplantation (BMT) is discussed in terms of immunology, procedures, and complications and their treatment. Any patient with a disorder of the hematopoietic or immune system or a disease in which a transferable hematopoietic cell can supply a missing enzyme is a candidate for BMT. A priority in allogeneic BMT is the identification of a compatible donor through matching of human lymphocyte antigens (HLAs). The greater the disparity in HLAs, the greater the chance of rejection. The ideal donor is a monozygotic twin or an HLA-matched sibling, but only 30% of patients have such a donor. Before receiving the bone marrow infusion, patients must be conditioned to create space in the marrow for donor cells, suppress the immune system, and eradicate any tumor in patients with malignancies. Conditioning is achieved by the combination of total body irradiation and cyclophosphamide treatment; busulfan, etoposide, and cytarabine have also been used. For patients given unmanipulated marrow, the number of nucleated cells infused is about 3 X 10(8) per kilogram. Signs of engraftment are usually seen 14-21 days later. Toxic effects related to conditioning appear during this period and include infection, gastroenteritis, mucositis, and congestive heart failure. The most serious complication is graft-versus-host disease (GVHD), which can affect multiple organ systems. Prednisone, methylprednisolone, methotrexate, antithymocyte globulin, and cyclosporine have been used in an effort to prevent or treat GVHD. Bone marrow transplantation offers the chance of long-term survival to many patients with terminal disease, but associated morbidity and mortality rates remain high. Research is needed to address the problems of infection, leukemic relapse, and GVHD and the difficulty in obtaining and matching donors.

The scintigraphic and radiographic appearance of the ischiopubic synchondroses in normal children and in osteomyelitis

Five cases of hematogenous osteomyelitis of the ischiopubic synchondrosis (IPS) were encountered among 180 patients with osteomyelitis treated over a 5-year period. Symptoms were poorly localized in all these IPS osteomyelitis patients. The IPS can normally show expansion and irregular mineralization radiographically and focal hyperconcentration of radiophosphates on scintigrams. Findings are frequently asymmetrical negating comparison with the contralateral side. In the cases of osteomyelitis, radiographs were abnormal at the time of presentation in only one of these five cases. In two of the four patients who had radionuclide bone scans, activity at the IPS exceeded that seen in a normal control population, but all showed loss of definition of the IPS and regional increased uptake permitting an early diagnosis.

Osteomyelitis of the ischiopubic synchondrosis

Infection of the ischiopubic synchondrosis (IPS) is a diagnostic dilemma. This article reviews four such cases. All patients complained of ipsilateral groin pain, were febrile, and had elevated erythrocyte sedimentation rates. Initial radiographs were interpreted as normal but later showed increasingly lucent zones at the IPS. Radionuclide bone scans demonstrated diffusely increased uptake in the vicinity of the IPS. This contrasts with the discrete pattern seen with a normal IPS. Blood cultures were positive. Satisfactory outcomes were obtained with conservative treatment. Clinical presentation, laboratory results, radiographs, and bone scans must be correlated to distinguish this syndrome from a "normal radiologic variant".