Multiplex epigenome editing of MECP2 to rescue Rett syndrome neurons.

Rett syndrome (RTT) is an X-linked neurodevelopmental disorder caused by loss-of-function heterozygous mutations of methyl CpG-binding protein 2 (MECP2) on the X chromosome in young females. Reactivation of the silent wild-type MECP2 allele from the inactive X chromosome (Xi) represents a promising therapeutic opportunity for female patients with RTT. Here, we applied a multiplex epigenome editing approach to reactivate MECP2 from Xi in RTT human embryonic stem cells (hESCs) and derived neurons. Demethylation of the MECP2 promoter by dCas9-Tet1 with target single-guide RNA reactivated MECP2 from Xi in RTT hESCs without detectable off-target effects at the transcriptional level. Neurons derived from methylation-edited RTT hESCs maintained MECP2 reactivation and reversed the smaller soma size and electrophysiological abnormalities, two hallmarks of RTT. In RTT neurons, insulation of the methylation-edited MECP2 locus by dCpf1-CTCF (a catalytically dead Cpf1 fused with CCCTC-binding factor) with target CRISPR RNA enhanced MECP2 reactivation and rescued RTT-related neuronal defects, providing a proof-of-concept study for epigenome editing to treat RTT and potentially other dominant X-linked diseases.

Differential cofactor dependencies define distinct types of human enhancers.

All multicellular organisms rely on differential gene transcription regulated by genomic enhancers, which function through cofactors that are recruited by transcription factors1,2. Emerging evidence suggests that not all cofactors are required at all enhancers3-5, yet whether these observations reflect more general principles or distinct types of enhancers remained unknown. Here we categorized human enhancers by their cofactor dependencies and show that these categories provide a framework to understand the sequence and chromatin diversity of enhancers and their roles in different gene-regulatory programmes. We quantified enhancer activities along the entire human genome using STARR-seq6 in HCT116 cells, following the rapid degradation of eight cofactors. This analysis identified different types of enhancers with distinct cofactor requirements, sequences and chromatin properties. Some enhancers were insensitive to the depletion of the core Mediator subunit MED14 or the bromodomain protein BRD4 and regulated distinct transcriptional programmes. In particular, canonical Mediator7 seemed dispensable for P53-responsive enhancers, and MED14-depleted cells induced endogenous P53 target genes. Similarly, BRD4 was not required for the transcription of genes that bear CCAAT boxes and a TATA box (including histone genes and LTR12 retrotransposons) or for the induction of heat-shock genes. This categorization of enhancers through cofactor dependencies reveals distinct enhancer types that can bypass broadly utilized cofactors, which illustrates how alternative ways to activate transcription separate gene expression programmes and provide a conceptual framework to understand enhancer function and regulatory specificity.

A distinct core regulatory module enforces oncogene expression in KMT2A-rearranged leukemia.

Acute myeloid leukemia with KMT2A (MLL) rearrangements is characterized by specific patterns of gene expression and enhancer architecture, implying unique core transcriptional regulatory circuitry. Here, we identified the transcription factors MEF2D and IRF8 as selective transcriptional dependencies of KMT2A-rearranged AML, where MEF2D displays partially redundant functions with its paralog, MEF2C. Rapid transcription factor degradation followed by measurements of genome-wide transcription rates and superresolution microscopy revealed that MEF2D and IRF8 form a distinct core regulatory module with a narrow direct transcriptional program that includes activation of the key oncogenes MYC, HOXA9, and BCL2. Our study illustrates a mechanism of context-specific transcriptional addiction whereby a specific AML subclass depends on a highly specialized core regulatory module to directly enforce expression of common leukemia oncogenes.

Partitioning of cancer therapeutics in nuclear condensates.

The nucleus contains diverse phase-separated condensates that compartmentalize and concentrate biomolecules with distinct physicochemical properties. Here, we investigated whether condensates concentrate small-molecule cancer therapeutics such that their pharmacodynamic properties are altered. We found that antineoplastic drugs become concentrated in specific protein condensates in vitro and that this occurs through physicochemical properties independent of the drug target. This behavior was also observed in tumor cells, where drug partitioning influenced drug activity. Altering the properties of the condensate was found to affect the concentration and activity of drugs. These results suggest that selective partitioning and concentration of small molecules within condensates contributes to drug pharmacodynamics and that further understanding of this phenomenon may facilitate advances in disease therapy.

Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains.

Gene expression is controlled by transcription factors (TFs) that consist of DNA-binding domains (DBDs) and activation domains (ADs). The DBDs have been well characterized, but little is known about the mechanisms by which ADs effect gene activation. Here, we report that diverse ADs form phase-separated condensates with the Mediator coactivator. For the OCT4 and GCN4 TFs, we show that the ability to form phase-separated droplets with Mediator in vitro and the ability to activate genes in vivo are dependent on the same amino acid residues. For the estrogen receptor (ER), a ligand-dependent activator, we show that estrogen enhances phase separation with Mediator, again linking phase separation with gene activation. These results suggest that diverse TFs can interact with Mediator through the phase-separating capacity of their ADs and that formation of condensates with Mediator is involved in gene activation.

Minimally Invasive Decompression and Physiotherapy for Lumbar Spinal Stenosis in Geriatric Patients.

Background Lumbar spinal stenosis (LSS) is the most common indication for spine surgery among the geriatric population. Although decompressive surgery is effective, older patients do not benefit as much as younger patients, and they are frequently excluded from studies assessing postoperative physiotherapy. We sought to evaluate the long-term outcomes after surgery when a novel postoperative physiotherapy regimen was included. Methods We performed a retrospective review of patients with LSS greater than 70 years old who underwent lumbar decompressive surgery by the senior author over the past five years. We evaluated patients who participated in a novel postoperative physiotherapy regimen involving four phases of rehabilitation aimed at progressively independent ambulation. The visual analog scale (VAS), lower extremity motor strength, and functional independence measure (FIM) were collected preoperatively and after physiotherapy to measure outcomes. Results Ten consecutive patients with an average age of 83 years (range: 71 - 96) met the inclusion criteria. Nine patients underwent minimally invasive laminotomies at L4-L5 and one underwent a laminotomy at L3-L4. The average follow-up time was 41.9 months. The preoperative mean VAS was 7.35, and at the end of the study, it was 1.7 (p = 0.005). Three of the four patients with preoperative motor deficits improved. The median transfer and locomotion subscores of the FIM were six preoperatively and increased to seven postoperatively. Neither of these improvements was significant. Conclusions Patients older than 70 years undergoing decompressive surgery and a novel postoperative physiotherapy regimen experienced significant reductions in pain. Independence also increased; however, this did not reach statistical significance.

Corrigendum: Small genomic insertions form enhancers that misregulate oncogenes.

This corrects the article DOI: 10.1038/ncomms14385.

Primary lung metastasis of glioblastoma multiforme with epidural spinal metastasis: Case report.

Extracranial metastasis of glioblastoma multiforme (GBM) is rare, but has recently been reported with increasing frequency. GBM metastases typically present after a biopsy or resection of the primary tumor. An otherwise healthy 54year-old woman presented with recurring pleural effusions originally believed to be from a primary lung malignancy. The patient subsequently experienced a generalized tonic clonic seizure and a right temporal brain mass was discovered. The patient later developed weakness and radiculopathy, and an extramedullary extradural mass spreading from C7 to T6 was discovered. She underwent resection of both central nervous system lesions as well as a lung biopsy, and all pathologic specimens were consistent with GBM. The case presented is unique in that the patient's initial symptoms were related to her metastasis. Furthermore, a purely epidural spread of GBM that respects the leptomeninges and intramedullary parenchyma is highly unusual.

Small genomic insertions form enhancers that misregulate oncogenes.

The non-coding regions of tumour cell genomes harbour a considerable fraction of total DNA sequence variation, but the functional contribution of these variants to tumorigenesis is ill-defined. Among these non-coding variants, somatic insertions are among the least well characterized due to challenges with interpreting short-read DNA sequences. Here, using a combination of Chip-seq to enrich enhancer DNA and a computational approach with multiple DNA alignment procedures, we identify enhancer-associated small insertion variants. Among the 102 tumour cell genomes we analyse, small insertions are frequently observed in enhancer DNA sequences near known oncogenes. Further study of one insertion, somatically acquired in primary leukaemia tumour genomes, reveals that it nucleates formation of an active enhancer that drives expression of the LMO2 oncogene. The approach described here to identify enhancer-associated small insertion variants provides a foundation for further study of these abnormalities across human cancers.

Chromatin Kinases Act on Transcription Factors and Histone Tails in Regulation of Inducible Transcription.

The inflammatory response requires coordinated activation of both transcription factors and chromatin to induce transcription for defense against pathogens and environmental insults. We sought to elucidate the connections between inflammatory signaling pathways and chromatin through genomic footprinting of kinase activity and unbiased identification of prominent histone phosphorylation events. We identified H3 serine 28 phosphorylation (H3S28ph) as the principal stimulation-dependent histone modification and observed its enrichment at induced genes in mouse macrophages stimulated with bacterial lipopolysaccharide. Using pharmacological and genetic approaches, we identified mitogen- and stress-activated protein kinases (MSKs) as primary mediators of H3S28ph in macrophages. Cell-free transcription assays demonstrated that H3S28ph directly promotes p300/CBP-dependent transcription. Further, MSKs can activate both signal-responsive transcription factors and the chromatin template with additive effects on transcription. Specific inhibition of MSKs in macrophages selectively reduced transcription of stimulation-induced genes. Our results suggest that MSKs incorporate upstream signaling inputs and control multiple downstream regulators of inducible transcription.

Activation of proto-oncogenes by disruption of chromosome neighborhoods.

Oncogenes are activated through well-known chromosomal alterations such as gene fusion, translocation, and focal amplification. In light of recent evidence that the control of key genes depends on chromosome structures called insulated neighborhoods, we investigated whether proto-oncogenes occur within these structures and whether oncogene activation can occur via disruption of insulated neighborhood boundaries in cancer cells. We mapped insulated neighborhoods in T cell acute lymphoblastic leukemia (T-ALL) and found that tumor cell genomes contain recurrent microdeletions that eliminate the boundary sites of insulated neighborhoods containing prominent T-ALL proto-oncogenes. Perturbation of such boundaries in nonmalignant cells was sufficient to activate proto-oncogenes. Mutations affecting chromosome neighborhood boundaries were found in many types of cancer. Thus, oncogene activation can occur via genetic alterations that disrupt insulated neighborhoods in malignant cells.

Implementation and Results of a Percutaneous Renal Allograft Biopsy Protocol to Reduce Complication Rate.

Percutaneous renal transplant biopsy (PRTB) is the gold standard for evaluating allograft rejection after renal transplant. Hemorrhage is the predominant complication. We describe the implementation of a standardized protocol for PRTB at a single institution, with the aim of reducing bleeding complications. Utilizing the plan-do-study-act model for quality improvement, we created and deployed a protocol centered on controlling patient's hypertension, platelet function, and anticoagulation status. The 4-year study encompassed a total of 880 PRTBs, before and after implementation of the protocol. Total complication rate, which was 5.8% in the 2 years leading up to implementation of the protocol, was reduced to 2.9% after the protocol was introduced (P = .04). A standardized approach to PRTB can potentially lower complication rates; we present a framework for implementating a quality improvement protocol at other institutions.

Use of multivariate linear regression and support vector regression to predict functional outcome after surgery for cervical spondylotic myelopathy.

This study introduces the use of multivariate linear regression (MLR) and support vector regression (SVR) models to predict postoperative outcomes in a cohort of patients who underwent surgery for cervical spondylotic myelopathy (CSM). Currently, predicting outcomes after surgery for CSM remains a challenge. We recruited patients who had a diagnosis of CSM and required decompressive surgery with or without fusion. Fine motor function was tested preoperatively and postoperatively with a handgrip-based tracking device that has been previously validated, yielding mean absolute accuracy (MAA) results for two tracking tasks (sinusoidal and step). All patients completed Oswestry disability index (ODI) and modified Japanese Orthopaedic Association questionnaires preoperatively and postoperatively. Preoperative data was utilized in MLR and SVR models to predict postoperative ODI. Predictions were compared to the actual ODI scores with the coefficient of determination (R(2)) and mean absolute difference (MAD). From this, 20 patients met the inclusion criteria and completed follow-up at least 3 months after surgery. With the MLR model, a combination of the preoperative ODI score, preoperative MAA (step function), and symptom duration yielded the best prediction of postoperative ODI (R(2)=0.452; MAD=0.0887; p=1.17 × 10(-3)). With the SVR model, a combination of preoperative ODI score, preoperative MAA (sinusoidal function), and symptom duration yielded the best prediction of postoperative ODI (R(2)=0.932; MAD=0.0283; p=5.73 × 10(-12)). The SVR model was more accurate than the MLR model. The SVR can be used preoperatively in risk/benefit analysis and the decision to operate.

Utilization of a novel digital measurement tool for quantitative assessment of upper extremity motor dexterity: a controlled pilot study.

BACKGROUND: The current methods of assessing motor function rely primarily on the clinician's judgment of the patient's physical examination and the patient's self-administered surveys. Recently, computerized handgrip tools have been designed as an objective method to quantify upper-extremity motor function. This pilot study explores the use of the MediSens handgrip as a potential clinical tool for objectively assessing the motor function of the hand. METHODS: Eleven patients with cervical spondylotic myelopathy (CSM) were followed for three months. Eighteen age-matched healthy participants were followed for two months. The neuromotor function and the patient-perceived motor function of these patients were assessed with the MediSens device and the Oswestry Disability Index respectively. The MediSens device utilized a target tracking test to investigate the neuromotor capacity of the participants. The mean absolute error (MAE) between the target curve and the curve tracing achieved by the participants was used as the assessment metric. The patients' adjusted MediSens MAE scores were then compared to the controls. The CSM patients were further classified as either "functional" or "nonfunctional" in order to validate the system's responsiveness. Finally, the correlation between the MediSens MAE score and the ODI score was investigated. RESULTS: The control participants had lower MediSens MAE scores of 8.09%±1.60%, while the cervical spinal disorder patients had greater MediSens MAE scores of 11.24%±6.29%. Following surgery, the functional CSM patients had an average MediSens MAE score of 7.13%±1.60%, while the nonfunctional CSM patients had an average score of 12.41%±6.32%. The MediSens MAE and the ODI scores showed a statistically significant correlation (r=-0.341, p<1.14×10⁻5). A Bland-Altman plot was then used to validate the agreement between the two scores. Furthermore, the percentage improvement of the the two scores after receiving the surgical intervention showed a significant correlation (r=-0.723, p<0.04). CONCLUSIONS: The MediSens handgrip device is capable of identifying patients with impaired motor function of the hand. The MediSens handgrip scores correlate with the ODI scores and may serve as an objective alternative for assessing motor function of the hand.

Comparison of operating field sterility in open versus minimally invasive microdiscectomies of the lumbar spine.

BACKGROUND: Postoperative wound infection is a preventable risk that can lead to significant adverse outcomes and increased cost of care. Minimally invasive surgeries (MIS) have been found to have lower rates of postoperative infection compared with the traditional approach. To assess if the reported difference is related to intraoperative contamination or to other factors, we assessed the surgical field for sterility. METHODS: We compared 10 MIS versus 10 traditional microdiscectomies. Swabs of the operating field were obtained before and after the procedure from multiple sites in the operating room. Positive and negative controls were taken of the skin immediately before and after preparation of the incision site. All swabs were plated out on Columbia blood agar plates and grown for 48 hours. Colony counting was performed to determine growth. RESULTS: There was no statistically significant difference in the colony counts of swab sites in traditional microdiscectomies compared with MIS microdiscectomies. There was no significant contamination of the operating field using either approach. CONCLUSIONS: In this prospective study, we found that there was no significant difference in bacterial counts in swabs of operative sites in either traditional or MIS microdiscectomies, suggesting that the decreased rate of postoperative infection in the reported literature for MIS cases may be related to other factors, such as patient selection and/or postoperative care.

Oral fludarabine and rituximab as initial therapy for chronic lymphocytic leukemia or small lymphocytic lymphoma: population-based experience matches clinical trials.

Clinical trials report that fludarabine and rituximab (FR) as initial therapy for chronic lymphocytic leukemia (CLL) improves progression-free and overall survival (OS) when compared historically to fludarabine alone. To determine whether similar results are achievable with oral FR in a community-based setting, we conducted a population-based analysis of patients treated for CLL or small lymphocytic lymphoma (SLL) in British Columbia, where FR is standard initial therapy. Ninety-eight patients received FR for CLL/SLL from 2004 to 2009. Two- and 4-year OS was 90% and 73%, respectively (median not reached); 2- and 4-year treatment-free survival (TFS) was 69% and 54% (median 4.0 years). Age ≥ 60 years or ≥ 70 years had no effect on OS or TFS. Toxicity led to treatment discontinuation in 13%. FR with oral fludarabine was safely, conveniently and successfully given to community-based patients, irrespective of age, for first-line therapy for CLL/SLL, achieving OS and TFS similar to those in clinical trials.

Dysmetabolic hyperferritinemia is associated with normal transferrin saturation, mild hepatic iron overload, and elevated hepcidin.

Hyperferritinemia is common in individuals with the metabolic syndrome (dysmetabolic hyperferritinemia), but its pathophysiology and the degree to which it reflects tissue iron overload remains unclear. We conducted a cross-sectional study evaluating ten cases with dysmetabolic hyperferritinemia for liver iron overload and compared their serum iron indices and urine hepcidin levels to healthy controls. Seven out of ten cases had mild hepatic iron overload by magnetic resonance imaging (MRI) (median, 75 micromol/g dry weight). Cases had higher serum ferritin than controls (median, 672 microg/L vs. 105 microg/L, p < 0.001), but the median transferrin saturation was not significantly different (38% vs. 36%, p = 0.5). Urinary hepcidin was elevated in dysmetabolic hyperferritinemia (median; 1,584 g/mg of creatinine vs. 799 ng/mg of creatinine, p = 0.05). Dysmetabolic hyperferritinemia is characterized by hyperferritinemia with normal transferrin saturation, elevated hepcidin levels, and mild liver iron overload in a subset of patients.

Acute leukemia in patients sixty years of age and older: a twenty year single institution review.

OBJECTIVES: Acute leukemia, particularly acute myeloid leukemia, occurs more frequently in the elderly, a growing segment of the North American population. To evaluate our progress in the diagnosis, treatment and outcome of this condition, we reviewed our experience of all patients > or =60 years of age diagnosed with acute leukemia over a 20-year period at Saint Paul's Hospital, a university-based hospital in Vancouver, Canada. METHODS: A retrospective chart review was performed of 103 patients > or =60 years of age diagnosed with acute leukemia (acute myeloid leukemia-81; acute lymphoid leukemia-15; acute leukemia not otherwise specified-7). RESULTS: Median age was 72 (range 60-88) years. Bone marrow aspirate yielded cytogenetic information on 57 patients and 18 (31.6%) had an unfavourable karyotype. Fifty-three (51%) patients received induction chemotherapy (treated) and 50 (49%) were palliated (untreated). Treated patients were younger [median 67 years (range 60-79)] than untreated patients [76 years (61-88)], (P < 0.0001). Of the treated patients, 33 (62%) achieved a complete remission. The median overall survival for the group was 104 (1-2689) days, and for treated versus untreated patients-219 (1-2689) and 39 (2-1229) days, respectively (P = 0.0021). Univariate variables predictive of prolonged survival included induction chemotherapy (P = 0.0027), de novo leukemia (P = 0.0420), and younger age, with a relative increase in death in older subgroups (60-69, 70-79, 80+), (P = 0.0311). Induction chemotherapy was the only predictor of prolonged survival in multivariate analysis (P = 0.0027). CONCLUSIONS: The prognosis of acute leukemia in older patients remains poor, and even though induction chemotherapy seem to prolong survival in patients able to receive treatment, most ultimately die of leukemia.

Hyperferritinemia in the Chinese and Asian community: a retrospective review of the University of British Columbia experience.

BACKGROUND AND METHODS: Elevated serum ferritin is a common clinical finding. The etiology of hyperferritinemia in the Asia-Pacific population is less clear due to a low prevalence of known HFE mutations such as C282Y and H63D, as well as an increased prevalence of viral hepatitis and hereditary anemia. A retrospective case review of 80 patients of Asian ethnicity referred to three subspecialists in tertiary care teaching hospitals between January 1997 and March 2005 for assessment of hyperferritinemia was performed. RESULTS: Only four patients (5%) had iron overload on liver biopsy or quantitative phlebotomy. Forty-nine patients (61%) had secondary causes for their hyperferritinemia, of which 26 had liver disease; 16 of those patients also had viral hepatitis. Thirteen patients fulfilled criteria for the insulin resistance syndrome. Other causes included hematological disorders (n=10), malignancy (n=2) and inflammatory arthritis (n=2). Twenty-seven cases (34%) of unexplained hyperferritinemia were found. Of a total of 22 patients who underwent liver biopsy, significant iron deposition was found in one patient. Fifteen patients underwent C282Y and H63D genotyping, with two cases of H63D heterozygosity. Fourteen patients had first-degree relatives with hyperferritinemia. Three families were identified with more than two members affected, which is suggestive of a possible hereditary hyperferritinemia syndrome. CONCLUSION: Secondary causes of elevated ferritin in the Asian population, particularly liver disease, are common, but primary iron overload syndromes appear to be rare. In a significant proportion of patients, the etiology remains unexplained. The genetic basis for hyperferritinemia in Asians is poorly defined and requires further study.

Clinical progression and outcome of patients with monoclonal B-cell lymphocytosis.

Monoclonal B-cell lymphocytosis (MBL) is a clonal lymphoproliferation with the immunophenotype of chronic lymphocytic leukemia (CLL) but a B-lymphocyte count of less than 5 x 10(9)/l and no lymphadenopathy, organomegaly, cytopenias or symptoms. We performed a retrospective analysis of patients with MBL (n = 46), Rai stage 0 CLL (n = 112) and Rai stage > or =1 CLL (n = 54). Median follow-up and range was 30 (0.1-120) months for MBL, 60 (0.1-309) months for stage 0 CLL and 54 (0.1-309) months for stage > or =1 CLL. None of the MBL patients required treatment compared with 24 of 112 (21%) stage 0 CLL and 28 of 54 (52%) stage > or =1 CLL patients (p < 0.0003). No MBL underwent aggressive transformation compared with 1 of 112 (0.8%) stage 0 CLL and 6 of 54 (11%) stage > or =1 CLL patients (p < 0.0003). Progression-free survival (PFS) appeared improved in MBL compared to stage 0 CLL, although this did not reach statistical significant (p = 0.07) due to the relatively short follow-up in the MBL group; two year PFS was 97.2% for MBL, 93.1% for stage 0 CLL, and 68% for stage > or =1 CLL patients (p < 0.0001 for stage > or =1 CLL compared with MBL and stage 0 CLL). This is the first study of outcome in MBL which demonstrates that patients have an improved disease course compared to stage 0 CLL patients. Over a median 2.5 years of follow-up, no MBL patients required treatment or died of CLL-related causes.