Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample.

Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) that died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding 28 chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth's death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.

The Energetics and Physiological Impact of Cohesin Extrusion.

Cohesin extrusion is thought to play a central role in establishing the architecture of mammalian genomes. However, extrusion has not been visualized in vivo, and thus, its functional impact and energetics are unknown. Using ultra-deep Hi-C, we show that loop domains form by a process that requires cohesin ATPases. Once formed, however, loops and compartments are maintained for hours without energy input. Strikingly, without ATP, we observe the emergence of hundreds of CTCF-independent loops that link regulatory DNA. We also identify architectural "stripes," where a loop anchor interacts with entire domains at high frequency. Stripes often tether super-enhancers to cognate promoters, and in B cells, they facilitate Igh transcription and recombination. Stripe anchors represent major hotspots for topoisomerase-mediated lesions, which promote chromosomal translocations and cancer. In plasmacytomas, stripes can deregulate Igh-translocated oncogenes. We propose that higher organisms have coopted cohesin extrusion to enhance transcription and recombination, with implications for tumor development.

Cohesin Loss Eliminates All Loop Domains.

The human genome folds to create thousands of intervals, called "contact domains," that exhibit enhanced contact frequency within themselves. "Loop domains" form because of tethering between two loci-almost always bound by CTCF and cohesin-lying on the same chromosome. "Compartment domains" form when genomic intervals with similar histone marks co-segregate. Here, we explore the effects of degrading cohesin. All loop domains are eliminated, but neither compartment domains nor histone marks are affected. Loss of loop domains does not lead to widespread ectopic gene activation but does affect a significant minority of active genes. In particular, cohesin loss causes superenhancers to co-localize, forming hundreds of links within and across chromosomes and affecting the regulation of nearby genes. We then restore cohesin and monitor the re-formation of each loop. Although re-formation rates vary greatly, many megabase-sized loops recovered in under an hour, consistent with a model where loop extrusion is rapid.

Large DNA Methylation Nadirs Anchor Chromatin Loops Maintaining Hematopoietic Stem Cell Identity.

Higher-order chromatin structure and DNA methylation are implicated in multiple developmental processes, but their relationship to cell state is unknown. Here, we find that large (>7.3 kb) DNA methylation nadirs (termed "grand canyons") can form long loops connecting anchor loci that may be dozens of megabases (Mb) apart, as well as inter-chromosomal links. The interacting loci cover a total of ∼3.5 Mb of the human genome. The strongest interactions are associated with repressive marks made by the Polycomb complex and are diminished upon EZH2 inhibitor treatment. The data are suggestive of the formation of these loops by interactions between repressive elements in the loci, forming a genomic subcompartment, rather than by cohesion/CTCF-mediated extrusion. Interestingly, unlike previously characterized subcompartments, these interactions are present only in particular cell types, such as stem and progenitor cells. Our work reveals that H3K27me3-marked large DNA methylation grand canyons represent a set of very-long-range loops associated with cellular identity.

The fundamental role of chromatin loop extrusion in physiological V(D)J recombination.

The RAG endonuclease initiates Igh V(D)J assembly in B cell progenitors by joining D segments to JH segments, before joining upstream VH segments to DJH intermediates1. In mouse progenitor B cells, the CTCF-binding element (CBE)-anchored chromatin loop domain2 at the 3' end of Igh contains an internal subdomain that spans the 5' CBE anchor (IGCR1)3, the DH segments, and a RAG-bound recombination centre (RC)4. The RC comprises the JH-proximal D segment (DQ52), four JH segments, and the intronic enhancer (iEµ)5. Robust RAG-mediated cleavage is restricted to paired V(D)J segments flanked by complementary recombination signal sequences (12RSS and 23RSS)6. D segments are flanked downstream and upstream by 12RSSs that mediate deletional joining with convergently oriented JH-23RSSs and VH-23RSSs, respectively6. Despite 12/23 compatibility, inversional D-to-JH joining via upstream D-12RSSs is rare7,8. Plasmid-based assays have attributed the lack of inversional D-to-JH joining to sequence-based preference for downstream D-12RSSs9, as opposed to putative linear scanning mechanisms10,11. As RAG linearly scans convergent CBE-anchored chromatin loops4,12-14, potentially formed by cohesin-mediated loop extrusion15-18, we revisited its scanning role. Here we show that the chromosomal orientation of JH-23RSS programs RC-bound RAG to linearly scan upstream chromatin in the 3' Igh subdomain for convergently oriented D-12RSSs and, thereby, to mediate deletional joining of all D segments except RC-based DQ52, which joins by a diffusion-related mechanism. In a DQ52-based RC, formed in the absence of JH segments, RAG bound by the downstream DQ52-RSS scans the downstream constant region exon-containing 3' Igh subdomain, in which scanning can be impeded by targeted binding of nuclease-dead Cas9, by transcription through repetitive Igh switch sequences, and by the 3' Igh CBE-based loop anchor. Each scanning impediment focally increases RAG activity on potential substrate sequences within the impeded region. High-resolution mapping of chromatin interactions in the RC reveals that such focal RAG targeting is associated with corresponding impediments to the loop extrusion process that drives chromatin past RC-bound RAG.

Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development.

The three-dimensional arrangement of the human genome comprises a complex network of structural and regulatory chromatin loops important for coordinating changes in transcription during human development. To better understand the mechanisms underlying context-specific 3D chromatin structure and transcription during cellular differentiation, we generated comprehensive in situ Hi-C maps of DNA loops in human monocytes and differentiated macrophages. We demonstrate that dynamic looping events are regulatory rather than structural in nature and uncover widespread coordination of dynamic enhancer activity at preformed and acquired DNA loops. Enhancer-bound loop formation and enhancer activation of preformed loops together form multi-loop activation hubs at key macrophage genes. Activation hubs connect 3.4 enhancers per promoter and exhibit a strong enrichment for activator protein 1 (AP-1)-binding events, suggesting that multi-loop activation hubs involving cell-type-specific transcription factors represent an important class of regulatory chromatin structures for the spatiotemporal control of transcription.

Glucagon-like peptide-1 receptor agonists in adolescents with overweight or obesity with or without type 2 diabetes multimorbidity-a systematic review and network meta-analysis.

AIM: To synthesize the evidence on the effects of glucagon-like peptide-1 receptor agonists (GLP-1RAs) in adolescents with overweight or obesity. MATERIALS AND METHODS: For this systematic review and network meta-analysis, we searched five databases and registries until 2 March 2024 for eligible randomized controlled trials (RCTs). The primary outcome was weight change. We did a pairwise meta-analysis to compare GLP-1RAs and placebo, followed by a drug-wise network meta-analysis (NMA) to compare GLP-1RAs against each other. RESULTS: We screened 770 records to include 12 RCTs with 883 participants. The evidence suggests that GLP-1RAs reduced weight (mean difference -4.21 kg, 95% confidence interval [CI] -7.08 to -1.35) and body mass index (BMI; mean difference -2.11 kg/m2, 95% CI -3.60 to -0.62). The evidence on waist circumference, body fat percentage and adverse events (AEs) was very uncertain. The results remained consistent with subgroup analyses for coexisting type 2 diabetes. Longer therapy duration led to a greater reduction in weight and BMI. In the NMA, semaglutide led to the greatest weight reduction, followed by exenatide, liraglutide and lixisenatide. CONCLUSIONS: The evidence suggests that GLP-1RAs reduce most weight-related outcomes in adolescents, with semaglutide being the most efficacious. There is uncertain evidence on body fat and serious AEs, probably due to fewer studies and low incidence, respectively. Larger RCTs with head-to-head comparisons, pragmatic design, adiposity-related outcomes, and economic evaluation can further guide the use and choice of GLP-1RAs.

Prevalence of Acute on Chronic Liver Failure in Autoimmune Hepatitis, Treatment Response and Mortality Burden Assessment: A Region-Predominant Systematic Review and Meta-Analysis.

Acute-on-chronic liver failure (ACLF) is a global health problem. Little scientific evidence exists on its prevalence in autoimmune hepatitis. Treatment response and mortality outcomes have also been reported differently. The study was conducted to estimate the overall prevalence of ACLF among patients with autoimmune hepatitis (AIH) and determine the associated treatment response and mortality. We scrutinized wide literature in Scopus, PubMed, Embase, Web of Science, and Cochrane, and assessed published articles completely, studies performed and reported from around the globe, until December 07, 2023, according to the PROSPERO registered protocol (CRD42023412176). Studies (retrospective and prospective cohort study type) that stated the ACLF development among established AIH cases were considered. Features of the study, duration of follow-up, and numeric patient information were retrieved from the studies included. The research paper quality was checked for risk of bias. Random effect meta-analysis with metaregression and subsection scrutinies were performed with R. The main outcome was the collective prevalence of ACLF in the AIH patients, whereas treatment response and mortality in AIH-associated ACLF were secondary outcomes. Six studies were involved with confirmed diagnoses in 985 AIH patients for the data synthesis. The pooled prevalence of ACLF in the explored patients was 12% (95% CI: 8-17) ( P =0.01). Heterogeneity was found to be high in the present meta-analysis ( I2 =72%; P < 0.01). For the secondary endpoint analysis, the pooled prevalence of complete remission at 1-year follow-up was 71% (0.52; 0.85), and mortality from the ACLF-AIH patient population was 32% (95% CI: 18-50). Sensitivity analysis showed no influence on the overall estimations of the pooled prevalence of ACLF by omitting studies one by one. One in 10 AIH patients likely present with ACLF. The response to treatment is seen in two-thirds of patients, and mortality is high.

A meta-analysis and mapping of global mpox infection among children and adolescents.

Monkeypox (mpox) is a significant health concern affecting children and adolescents globally. This systematic review and meta-analysis aims to synthesise the available evidence on the proportion of children and adolescents affected by the mpox virus. A comprehensive search was conducted in seven electronic databases (PubMed, Scopus, Web of Science, EMBASE, ProQuest, EBSCOHost, and Cochrane) to identify the original reports on mpox cases in children and adolescents till 15 January 2023. Descriptive reports on probable or laboratory-confirmed mpox in children and adolescents (0-17 years old) were considered eligible. Studies not providing separate data for the above age group and case-control studies were excluded. The primary outcome was pooled proportion of mpox cases among children and adolescents. Proportion meta-analysis and heterogeneity between studies were determined using a restricted maximum likelihood estimator, and a random-effects model was fitted to the data. Sensitivity analysis and subgroup analysis were also conducted. A drapery plot was also provided as a complementary figure to the forest plot. The protocol was prospectively registered with PROSPERO (CRD42023392475). A total of 440 studies were identified, of which 37 were included in the review and 25 in the meta-analysis (62,701 participants with 3306 children and adolescents). The pooled proportion of children and adolescents was 0.46 (95% CI: 0.30-0.63, I2 :100%). The proportion of children and adolescents was significantly lower (p < 0.001) in the ongoing pandemic 0.04 (95% CI: 0.00-0.32) than before 2022 0.62 (95% CI: 0.49-0.74). The meta-regression showed that the higher the study's sample size, the lower the proportion of children among the mpox cases. Both overall and subgroup heterogeneity were high. Adolescents and children below 5 years are commonly affected by the ongoing pandemic. In conclusion, the high proportion of children affected by the mpox virus highlights the need for increased research and targeted interventions to prevent and control the spread of the virus in this population.

Evolution of RANO in Assessing Brain Tumour Outcomes.

Assessing treatment response is extremely important in management of brain tumours. Response assessment in neuro-oncology (RANO) was introduced in 2008 for the purpose of making recommendations for it by addressing and countering the limitations in previously reported response criteriae. Subsequently, multiple RANO working groups have been formed to cater to different tumour types and to update their previous recommendations to counter the limitations in their criteria. Herein we have a summarized list of RANO criteria for adult brain tumours.

Photodynamic Therapy in Adult Intra-axial Brain Tumours.

The management of high-grade gliomas is challenging considering their infiltrative nature, involvement of the eloquent cortex, and high recurrence rate. Photodynamic therapy (PDT) is an emerging modality that selectively destroys tumour cells while preserving normal brain tissue. Its safety, and the concurrent use with surgery, radiation, and chemotherapy, is some of its appealing tenets. Here, we present a review of the literature regarding the mechanism, safety, and efficacy of PDT.

RAPNO efforts in Brain Tumour Outcomes.

Assessing treatment efficacy for brain tumours has evolved since its inception with the introduction of MacDonald's criteria, which pioneered the utility of imaging to determine an objective and quantifiable response to treatment. This criterion failed to distinguish pseudo response or progression from progression and did not account for non-enhancing disease therefore; the response assessment in neuro-oncology (RANO) working group was established to account for these limitations. Since, its commencement it has worked to determine response assessment for multiple tumours. As paediatric tumours exhibit heterogeneous and variable-enhancing characteristics, the response assessment in paediatric neuro-oncology (RAPNO) working group was formed to create separate criteria. Six response criteria have been published to date, and the article summarizes them.

Prognostic Value of BRAF Mutation in Glioblastoma.

With advances in molecular genetics, exploring targetable mutations for treating glioblastoma (GBM) patients, has become a centre of interest in modern day neuropathology. BRAF mutation has been extensively reported in several brain tumours. Recent studies report identification of BRAF mutation in GBM patients, especially isocitrate dehydrogenase wildtype glioblastomas (IDH-WT GBM), and its potential role in patient outcomes. Here we discuss the existing literature on the prognostic value of BRAF mutation in GBM.

Role of Machine Learning in Liquid Biopsy of Brain Tumours.

Liquid biopsy has multiple benefits and is used extensively in other fields of oncology, but its role in neuro-oncology has been limited so far. Multiple tumour-derived materials like circulating tumour cells (CTCs), tumour-educated platelets (TEPs), cell-free DNA (cfDNA), circulating tumour DNA (ctDNA), and miRNA are studied in CSF, blood (plasma, serum) or urine. Large and complex amounts of data from liquid biopsy can be simplified by machine learning using various algorithms. By using this technique, we can diagnose brain tumours and differentiate low versus highgrade glioma and true progression from pseudo-progression. The potential of liquid biopsy in brain tumours has not been extensively studied, but it has a bright future in the coming years. Here, we present a literature review on the role of machine learning in liquid biopsy of brain tumours.

The role of 18F-FDG PET/CT in Neurolymphomatosis: A Comprehensive Imaging Approach.

Neurolymphomatosis (NL) is an uncommon and rare neurologic disorder characterised by extranodal lymphoma, where the tumour cells invade the cranial nerves, nerve plexus, nerve root, spinal nerve roots, trunk nerves or peripheral nerves. MRI is the modality of choice, but is often challenging in detection of early recurrence, assessing residual disease and response evaluation. 18FFDG PET/CT has superior diagnostic performance compared with body CT in the evaluation of NL. 18F-FDG PET-CT is helpful in evaluation of disease extent and potential to guide biopsy. 18F-FDG PETCT is a highly sensitive technique for early localisation of NL than MRI or CT alone. Besides diagnostic and prognostic value in NL, it might be very helpful in response assessment.

Quality of life in survivors of pediatric medulloblastoma: a systematic review and meta-analysis.

INTRODUCTION: Medulloblastoma (MB) is the most common malignant pediatric brain tumor. The mainstay of treatment is maximum surgical resection and craniospinal radiation, which may be followed by chemotherapy. The debilitating effect of the tumor and the intensive treatment approaches in MB lead to long-term neuropsychological, physical, and chronic medical problems. We conducted a systematic review to assess the quality of life (QoL) in the long-term survivors of MB and the factors leading to compromised QoL. METHODS: We utilized the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines for our review. A comprehensive literature search was performed using PubMed, Cochrane Library, Digital Commons Network, and Wiley Online Library databases to search for articles having quality of life, medulloblastoma, and pediatric survivors in title or abstract. We removed duplicates and screened through titles, and full texts. Twelve articles were included in our study. Articles using and reporting all domains of PaedsQL were included in the meta-analysis. The PaedsQL scores of survivors and their caregivers were compared. Subgroup analysis was conducted for craniospinal and proton radiotherapy groups. RESULTS: As compared to other posterior fossa tumors, MB survivors have the lowest QoL scores. There is a difference in the perception of QoL of survivors between caregivers and survivors themselves with survivors rating themselves higher in several domains. The overall PaedsQL scores were significantly different for both groups (p < 0.001). Subgroup analysis showed that the difference between those who were treated with craniospinal or proton radiation was not significant (p = 0.76). For the subscales, physical (p = 0.005), psychosocial (p = 0.0003), and school (p = 0.03) perceptions were significantly different for the survivors and their caregivers; however, psychosocial (p = 0.80) and emotional (p = 0.93) scales were not different for the survivors or caregivers. Patient characteristics related to a worse QoL included disease severity, metastatic disease, lesser family income, smaller current ventricle size, need for permanent hydrocephalus treatment, and lesser age at diagnosis. CONCLUSION: An analysis of various studies, using different measures of QoL, concludes that QoL is compromised in all pediatric survivors of MB; however, the perception of QoL of the survivors is better than objective or caretaker-rated QoL.

Quality of life in children operated for spina bifida; low- and middle-income country perspective.

INTRODUCTION: Spina bifida is a potentially disabling congenital condition and affects the quality of life (QOL). We aimed to assess clinical outcomes and QOL in children who underwent spina bifida repair at our hospital. METHODS: This was a retrospective cohort study on children who underwent spina bifida repair at our hospital over 10 years. Phone calls were made to parents of the children, and the Health Utility Index Mark 3 (HUI 3) score was used to assess QoL, and degree of disability. Demographics and clinical data were obtained from the medical chart review. Statistical analysis was done using SPSS (version 21). RESULTS: Eighty children with a median age of 1.1 months (IQR 0.03-2.0) at the time of presentation, were included in this study. The mean follow-up period was 6.04 ± 2.54 years and the median HUI-3 score was 0.64 (IQR: 0.40 - 0.96) on a scale of 0 (dead) to 1 (perfectly healthy). Based on the severity of disability, 12 (23.1%) children had mild disability, 4 (7.7%) had moderate disability, and 23 (44.2%) had severe disability. Factors including a leaking spina bifida and paraplegia at presentation; radiological findings of hydrocephalus and Chiari malformation, were associated with a significantly low QOL. Children who required CSF diversion (EVD/ VP shunt) during the repair or at a later stage also had significantly low QOL. CONCLUSION: In LMIC, children with myelomeningocele (MMC) born with lower limb weakness, hydrocephalus, Chiari malformation, and those presenting with leaking MMC, have a significantly low QoL at a mean follow-up of 6 years.

Exploring the 'January effect' at a university hospital in Pakistan: a retrospective cohort study investigating the impact of trainee turnover on patient care quality outcomes.

OBJECTIVE: There are reports of a potential rise in a teaching hospital's morbidity and mortality rates during the trainee turnover period, i.e., with the induction of new residents and house staffs, and the changeover of clinical teams. The published literature displays mixed reports on this topic with lack of reproducible observations. The current study was conducted to explore existence of any such phenomenon (January effect) in Pakistan. METHODS: This retrospective cohort study was conducted at Aga Khan University Hospital, Karachi, Pakistan. Five-year (2013-2018) record of all the patients in all age groups related to these outcomes was retrieved and recorded in specifically designed questionnaire. Different outcome measures were used as indicators of patient care and change in these outcomes at the time of new induction was related to possible January effect. RESULTS: During the five-year study period, more than 1100 new trainees were inducted into the post graduate medical education program (average of 237 per year) with more than 22,000 inpatient admissions (average of 45,469 per year). Some patterns were observed in frequencies of surgical site infections, medication errors, sentinel events, patient complaints, and adverse drug reactions. However, these were not consistently reproducible and could not be directly attributed to the trainee turnover. All other indicators did not show any pattern and were considered inconclusive. No effect of overlap was observed. CONCLUSIONS: Inconsistency in the patient care quality indicators do not favor existence of January effect in our study. Further research is recommended to establish our results.

Effect of post-operative infections on glioblastoma outcomes.

Glioblastoma multiforme (GBM) is the most aggressive primary brain tumour with a poor prognosis. The risk of developing a post-operative infection after craniotomy is the highest in GBM patients. Historical beliefs suggest that post-operative infections render a survival advantage in GBM patients, however recent clinical neurosurgical reports involving large multicentric patient cohorts do not support this claim. Nonetheless, the relationship has not been extensively studied which poses the need for further large, scaled studies to determine the association between post-operative infections and survival benefit in GBM patients.