The NuRD complex cooperates with DNMTs to maintain silencing of key colorectal tumor suppressor genes

Many tumor suppressor genes (TSGs) are silenced through synergistic layers of epigenetic regulation including abnormal DNA hypermethylation of promoter CpG islands, repressive chromatin modifications and enhanced nucleosome deposition over transcription start sites. The protein complexes responsible for silencing of many of such TSGs remain to be identified. Our previous work demonstrated that multiple silenced TSGs in colorectal cancer cells can be partially reactivated by DNA demethylation in cells disrupted for the DNA methyltransferases 1 and 3B (DNMT1 and 3B) or by DNMT inhibitors (DNMTi). Herein, we used proteomic and functional genetic approaches to identify additional proteins that cooperate with DNMTs in silencing these key silenced TSGs in colon cancer cells. We discovered that DNMTs and the core components of the NuRD (Mi-2/nucleosome remodeling and deacetylase) nucleosome remodeling complex, chromo domain helicase DNA-binding protein 4 (CHD4) and histone deacetylase 1 (HDAC1) occupy the promoters of several of these hypermethylated TSGs and physically and functionally interact to maintain their silencing. Consistent with this, we find an inverse relationship between expression of HDAC1 and 2 and these TSGs in a large panel of primary colorectal tumors. We demonstrate that DNMTs and NuRD cooperate to maintain the silencing of several negative regulators of the WNT and other signaling pathways. We find that depletion of CHD4 is synergistic with DNMT inhibition in reducing the viability of colon cancer cells in correlation with reactivation of TSGs, suggesting that their combined inhibition may be beneficial for the treatment of colon cancer. Since CHD4 has ATPase activity, our data identify CHD4 as a potentially novel drug target in cancer.

Cellular Senescence in Intervertebral Disc Aging and Degeneration: Molecular Mechanisms and Potential Therapeutic Opportunities

Closely associated with aging and age-related disorders, cellular senescence (CS) is the inability of cells to proliferate due to accumulated unrepaired cellular damage and irreversible cell cycle arrest. Senescent cells are characterized by their senescence-associated secretory phenotype that overproduces inflammatory and catabolic factors that hamper normal tissue homeostasis. Chronic accumulation of senescent cells is thought to be associated with intervertebral disc degeneration (IDD) in an aging population. This IDD is one of the largest age-dependent chronic disorders, often associated with neurological dysfunctions such as, low back pain, radiculopathy, and myelopathy. Senescent cells (SnCs) increase in number in the aged, degenerated discs, and have a causative role in driving age-related IDD. This review summarizes current evidence supporting the role of CS on onset and progression of age-related IDD. The discussion includes molecular pathways involved in CS such as p53-p21CIP1, p16INK4a, NF-κB, and MAPK, and the potential therapeutic value of targeting these pathways. We propose several mechanisms of CS in IDD including mechanical stress, oxidative stress, genotoxic stress, nutritional deprivation, and inflammatory stress. There are still large knowledge gaps in disc CS research, an understanding of which will provide opportunities to develop therapeutic interventions to treat age-related IDD.

Fibrinogen fragments and platelet dysfunction in uremia

BACKGROUND

The uremic state is characterized by subnormal platelet aggregation. Fibrinogen fragments, usually absent in normal human blood, but present in uremic plasma, may play a role in uremic platelet dysfunction.

METHODS

To examine this hypothesis, we investigated the availability and function of fibrinogen receptors [glycoprotein (GP) IIb-IIIa] on uremic and normal platelets, as well as the effect of fragments obtained from chymotrypsin digestion of human fibrinogen on normal platelets. The availability of fibrinogen receptors was examined using anti-GP IIb-IIIa antibodies and flow cytometry, whereas receptor function was assessed by the receptor's ability to mediate fibrinogen binding and platelet aggregation.

RESULTS

Platelet aggregation and the availability of GP IIb-IIIa were lower in uremic patients when compared with normal controls. Flow cytometric analysis showed that fibrinogen fragments decreased the binding of anti-CD61, an activation-independent anti-GP IIIa monoclonal antibody, to resting normal platelets. These fragments also reduced the binding of PAC-1, an activation-dependent anti-GP IIb-IIIa monoclonal antibody, to adenosine diphosphate (ADP)-activated normal platelets. In addition, the binding of radiolabeled fibrinogen to activated normal platelets and platelet aggregation in response to ADP were both decreased by fibrinogen fragments.

CONCLUSIONS

These findings suggest that fibrinogen fragments impair platelet function by occupying fibrinogen receptors prior to cell activation, thus preventing the binding of intact fibrinogen to platelets after subsequent stimulation. These observations also suggest a plausible mechanism by which endogenous fibrinogen fragments present in uremic plasma may contribute to platelet dysfunction.

Some ecological and physiological studies on bacteria isolated from salt-affected soils of Egypt

Members of Bacillaceae, Rhizobiaceae, actinomycetes and others were isolated from cultivated and non-cultivated saline soils. The high population of bacteria and actinomycetes were almost coincided with the relatively high levels of organic matter whatever the degree of soil salinity. Bacillus stearothermophilus and B. subtilis were more frequently isolated than other Bacillus species. Most of Rhizobium isolates were salt tolerant being able to grow in media containing 3% and 6% NaCl. The abilities of different bacterial isolates to attack citrus pectin, soluble and insoluble forms of cellulose were also tested.

JNK1 controls adult hippocampal neurogenesis and imposes cell-autonomous control of anxiety behaviour from the neurogenic niche

This corrects the article DOI: 10.1038/mp.2016.203.

Improved results demonstrated in the 2017 national audit of early syphilis management in the United Kingdom

The revised British Association of Sexual Health and HIV UK guidelines on the management of syphilis were published in 2015 and this audit measures performance against those standards and recommendations. Although not included in the guideline recommendations, an exploratory question on clinics’ HIV testing policy was also included. The audit was conducted over a two-month period in 2017 in genitourinary medicine (GUM) clinics across the UK of cases presenting in 2016. A total of 161 GUM clinics participated, and data were collected for 3017 cases. The standard for adherence to recommended treatment was met (97%, standard: 97%) and almost met for documented pre-treatment syphilis serology (95%, standard: 97%). Even though only 74% of patients had a documented action in relation to informing sexual contacts (standard: 97%), the standard for contacts seen and tested per index case within four weeks was met (0.9, standard: 0.6). Finally, those clinics with a formal policy on HIV testing after a syphilis diagnosis were twice as likely to test after the HIV window period, compared to clinics without a policy; a concurrent HIV diagnosis was made in 75 (3%) patients. More work is required to standardize documented delivery of effective partner notification and a formal policy on HIV testing appears to be effective.

Metastatic atypical renal tumour with metanephric characteristics treated with Sunitinib

Metanephric Adenoma (MA) is a rare and unclassifiable renal tumour with sparse reported clinical and morphological features. Generally MA's have a benign course without recurrence after nephrectomy, however a few cases received oncological treatment due to malignant progression.

We present a 42-year-old woman who years after an initial nephrectomy developed several processes and biopsy confirmed recurrence of MA. Sunitinib was given for only two weeks, as she developed side-effects and currently the patient undergoes control scans with only minimal growth of the processes.

This is the first case of MA treated with Tyrosin-Kinase-Inhibitor.

Extraction of sleep information from clinical notes of Alzheimer's disease patients using natural language processing

OBJECTIVES

Alzheimer's disease (AD) is the most common form of dementia in the United States. Sleep is one of the lifestyle-related factors that has been shown critical for optimal cognitive function in old age. However, there is a lack of research studying the association between sleep and AD incidence. A major bottleneck for conducting such research is that the traditional way to acquire sleep information is time-consuming, inefficient, non-scalable, and limited to patients' subjective experience. We aim to automate the extraction of specific sleep-related patterns, such as snoring, napping, poor sleep quality, daytime sleepiness, night wakings, other sleep problems, and sleep duration, from clinical notes of AD patients. These sleep patterns are hypothesized to play a role in the incidence of AD, providing insight into the relationship between sleep and AD onset and progression.

MATERIALS AND METHODS

A gold standard dataset is created from manual annotation of 570 randomly sampled clinical note documents from the adSLEEP, a corpus of 192 000 de-identified clinical notes of 7266 AD patients retrieved from the University of Pittsburgh Medical Center (UPMC). We developed a rule-based natural language processing (NLP) algorithm, machine learning models, and large language model (LLM)-based NLP algorithms to automate the extraction of sleep-related concepts, including snoring, napping, sleep problem, bad sleep quality, daytime sleepiness, night wakings, and sleep duration, from the gold standard dataset.

RESULTS

The annotated dataset of 482 patients comprised a predominantly White (89.2%), older adult population with an average age of 84.7 years, where females represented 64.1%, and a vast majority were non-Hispanic or Latino (94.6%). Rule-based NLP algorithm achieved the best performance of F1 across all sleep-related concepts. In terms of positive predictive value (PPV), the rule-based NLP algorithm achieved the highest PPV scores for daytime sleepiness (1.00) and sleep duration (1.00), while the machine learning models had the highest PPV for napping (0.95) and bad sleep quality (0.86), and LLAMA2 with finetuning had the highest PPV for night wakings (0.93) and sleep problem (0.89).

DISCUSSION

Although sleep information is infrequently documented in the clinical notes, the proposed rule-based NLP algorithm and LLM-based NLP algorithms still achieved promising results. In comparison, the machine learning-based approaches did not achieve good results, which is due to the small size of sleep information in the training data.

CONCLUSION

The results show that the rule-based NLP algorithm consistently achieved the best performance for all sleep concepts. This study focused on the clinical notes of patients with AD but could be extended to general sleep information extraction for other diseases.

Designer’s Confidence and Attitude towards Designing-for-Construction-Safety (DfCS) Implementation

The construction industry is known as a hazardous industry, which has been overwhelmed with accidents for a long time. One of the new strategies to reduce the number of accident in Malaysia is through emphasizing the safety responsibility on the parties involved during the design stage. This study investigated the confidence level of designing-for- construction-safety (DfCS) and the perceptions of the hindrance by focusing on the role of designers and its implementation among construction designers. The quantitative approach had been used, in which questionnaire survey forms were distributed via email and self-administered to forty (40) construction designers (i.e. civil and construction engineer, quantity surveyor, architect) in Johor. The findings have revealed that the respondents are confident of their ability to design for construction safety, though they are relatively less willing to implement the concept. This study demonstrates that significant effort is required to promote the benefits of DfCS in improving the safety performance of the construction industry so that it is widely accepted and implemented by the construction stakeholders.

Leveraging big data of immune checkpoint blockade response identifies novel potential targets

BACKGROUND

The development of immune checkpoint blockade (ICB) has changed the way we treat various cancers. While ICB produces durable survival benefits in a number of malignancies, a large proportion of treated patients do not derive clinical benefit. Recent clinical profiling studies have shed light on molecular features and mechanisms that modulate response to ICB. Nevertheless, none of these identified molecular features were investigated in large enough cohorts to be of clinical value.

MATERIALS AND METHODS

Literature review was carried out to identify relevant studies including clinical dataset of patients treated with ICB [anti-programmed cell death protein 1 (PD-1)/programmed death-ligand 1 (PD-L1), anti-cytotoxic T-lymphocyte antigen 4 (CTLA-4) or the combination] and available sequencing data. Tumor mutational burden (TMB) and 37 previously reported gene expression (GE) signatures were computed with respect to the original publication. Biomarker association with ICB response (IR) and survival (progression-free survival/overall survival) was investigated separately within each study and combined together for meta-analysis.

RESULTS

We carried out a comparative meta-analysis of genomic and transcriptomic biomarkers of IRs in over 3600 patients across 12 tumor types and implemented an open-source web application (predictIO.ca) for exploration. TMB and 21/37 gene signatures were predictive of IRs across tumor types. We next developed a de novo GE signature (PredictIO) from our pan-cancer analysis and demonstrated its superior predictive value over other biomarkers. To identify novel targets, we computed the T-cell dysfunction score for each gene within PredictIO and their ability to predict dual PD-1/CTLA-4 blockade in mice. Two genes, F2RL1 (encoding protease-activated receptor-2) and RBFOX2 (encoding RNA-binding motif protein 9), were concurrently associated with worse ICB clinical outcomes, T-cell dysfunction in ICB-naive patients and resistance to dual PD-1/CTLA-4 blockade in preclinical models.

CONCLUSION

Our study highlights the potential of large-scale meta-analyses in identifying novel biomarkers and potential therapeutic targets for cancer immunotherapy.

Risk factors of non-alcoholic fatty liver disease

This case control study was carried out in Mymensingh Medical College Hospital, Mymensingh, Bangladesh and Dhaka Medical College Hospital, Dhaka, Bangladesh from November 2010 to October 2011 to find out the risk factors of non-alcoholic fatty liver disease. A total of 90 participants (45 cases and 45 controls) were included. A higher proportion of patients with age >45 years were found in case group compared to control (51.1% vs. 15.6%). The mean age was significantly higher in case group 49.8±12.6 years. Males demonstrated their predominance in both case (62.2%) and control (68.9%) groups, although the two groups did not differ in terms of sex distribution. Body mass index demonstrates that 26.7% of patients in case group were of normal weight, 46.7% overweight and 26.7% obese. In the control group, two-thirds (68.9%) of the patients were of normal weight and 24.4% overweight and 7.8% obese. Diabetes and hypertension were significantly present in the case group than those in control counterparts 75.6% vs. 15.6% and 86.7% vs. 15.6 % respectively. The mean fasting blood glucose, ALT, total cholesterol and triglycerides were significantly higher in case group compared to control group 7.8±1.3 vs. 5.4±2.5mmol/L (p<0.001); 39.1±12.4 vs. 30.3±14.1IU/L, (p=0.002); 239.9±14.3 vs. 183.3±11.4mg/dl, (p<0.001) and 183.6±12.5 vs. 133.5±16.0mg/dl, (p<0.001) respectively. However, no significant difference was observed between the case and the control groups in terms of HDL cholesterol (35.9±1.2 vs. 38.0±1.1mg/dl, p=0.203). Majority of the patients in case group (88.9%) exhibited increased echogenicity of liver on ultrasonogram as opposed to 15.6% in the control group.

Treatment outcome of national guideline based antitubercular chemotherapy in tubercular ascites patients

Adenosine De Aminase (ADA) is increased in tuberculous ascitic fluid due to the stimulation of T-cells by mycobacterial antigens. The treatment for abdominal tuberculosis including ascites as a presentation is a matter of controversy around the world. The study is aim at to see the outcome of antitubercular chemotherapy in selected tubercular ascites patients. This hospital based prospective study was done in 24 cases of adult (>13 years) tubercular ascites admitted in a tertiary hospital Dhaka, over one year. Increased ADA level (>37iu/L) in ascitic fluid evaluated after the colorimetric method of Galanti and Giusti and other supportive investigations were done for diagnosing tuberculosis. Patients were under treatment of ATT cat-1 for six months as per national guide line. Outcome was seen as predefined criteria as treatment completed, cured, improved and not improved. Total number of patient is 24. Of which range of age is 13-70 years and mean±SD (33.2±14.77) with male female ratio is 0.85:1. Ninety six percent patients presented with abdominal pain, 23(96%) with fever, 22 (91%) with anorexia. Abdominal tenderness in 22(91%), ascites on 24(100%), hepatomegaly on 2(8%). Hundred percent patients were evaluated after completion of treatment. Twenty three (96%) patients improved and 1(4%) not improved. There is effectiveness of standard chemotherapy suggested by national guideline. Outcome of the patients were highly satisfactory with short regimen of antitubercular chemotherapy.

The transforming mutation E17K/AKT1 is not a major event in B-cell-derived lymphoid leukaemias

Despite the major role of the AKT/PKB family of proteins in the regulation of many growth and survival mechanisms in the cell, and the increasing evidence suggesting that AKT disruption could play a key role in many human malignancies, no major mutations of AKT genes had been reported, until very recently when Carpten et al reported a novel transforming mutation (E17K) in the pleckstrin homology domain of the AKT1 gene in solid tumours. Several laboratories are now screening for this mutation in different malignancies, and, recently, the mutation was described by Malanga et al in 1.9% of lung cancer patients. Considering the importance of the PI3K/AKT pathway in mediating survival and antiapoptotic signals in the B-cell types of chronic lymphocytic leukaemia (CLL) and acute lymphoblastic leukaemia (ALL), we sequenced the AKT1 exon 3 for the above mentioned mutation in 87 specimens, representing 45 CLLs, 38 ALLs and 4 prolymphocytic leukaemia (PLL) cases, which are all of B-cell origin. Our results show that the mutation E17K/AKT1 was not detected in the pleckstrin homology domain of AKT1 of the investigated cases. We conclude that this mutation is not a major event in B-cell-derived lymphoid leukaemias.

A 47 Years Lady with Intrathoracic Lipoma

A case of a 47 years old female who presented to Mymensingh Medical College Hospital, Medicine Unit-5, complaining of severe dyspnea and occasional leg swelling. Chest X-ray, USG of chest and chest CT scan revealed a right sided giant intrathoracic mass extending across the posterior mediastinum into the left chest cavity. CT guided FNAC of right lung revealed lipoma.

Intra-operative implantation errors during hemiarthroplasty

BACKGROUND

Hemiarthroplasty with Austin Moore endoprosthesis is an established treatment modality for displaced intracapsular femoral neck fractures in elderly patients above 60years.Technical errors in implantation of the un-cemented Austin Moore are common, and have been associated with complications that may culminate in early prosthetic failure requiring revision surgery.

OBJECTIVE

To analyse the frequency of technical errors experienced by surgeons during implantation of uncemented Austin Moore endoprosthesis with the view to improving technique and minimizing early prosthetic failure.

MATERIALS AND METHODS

This is a 5year retrospective analysis of radiographs of patients who had hemiarthroplasty with un-cemented Austin Moore endoprosthesis conducted at NKST rehabilitation hospital Mkar in Benue State, North- Central Nigeria with particular reference to intraoperative errors associated with early failure of the prosthesis. Data was analysed using SPSS version 21.

RESULTS

A total of 48 patients were operated by 3 orthopaedic surgeons and 35patients met the required criteria for the study.Twenty five intraoperative errors in implantation were identified in 16(45.7%) patients. The commonest intraoperative error was inadequate length of the neck remnant in 13(37.1%) patients followed by inadequate calcar seating in 3 (8.6%) patients, incorrect prosthetic head size in 2(5.7%) patients, intraoperative periprosthetic fracture 2(5.7%) patients and inadequate proximal metaphyseal fill in 1(2.9%) patient.

CONCLUSION

Hemiarthroplasty is a technically demanding procedure frequently associated with intraoperative implantation errors. Adequate pre-operative planning, Careful patient selection, proper training of surgeons as well as attention to detail is vital and may minimize technical errors during implantation and consequent early prosthetic failure.

Clinical Information Retrieval: A Literature Review

Clinical information retrieval (IR) plays a vital role in modern healthcare by facilitating efficient access and analysis of medical literature for clinicians and researchers. This scoping review aims to offer a comprehensive overview of the current state of clinical IR research and identify gaps and potential opportunities for future studies in this field. The main objective was to assess and analyze the existing literature on clinical IR, focusing on the methods, techniques, and tools employed for effective retrieval and analysis of medical information. Adhering to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we conducted an extensive search across databases such as Ovid Embase, Ovid Medline, Scopus, ACM Digital Library, IEEE Xplore, and Web of Science, covering publications from January 1, 2010, to January 4, 2023. The rigorous screening process led to the inclusion of 184 papers in our review. Our findings provide a detailed analysis of the clinical IR research landscape, covering aspects like publication trends, data sources, methodologies, evaluation metrics, and applications. The review identifies key research gaps in clinical IR methods such as indexing, ranking, and query expansion, offering insights and opportunities for future studies in clinical IR, thus serving as a guiding framework for upcoming research efforts in this rapidly evolving field. The study also underscores an imperative for innovative research on advanced clinical IR systems capable of fast semantic vector search and adoption of neural IR techniques for effective retrieval of information from unstructured electronic health records (EHRs).

Supplementary Information

The online version contains supplementary material available at 10.1007/s41666-024-00159-4.