bluuebunny/crossref_metadata_2025 huggingface dataset:
Adjuvant therapy in renal cell carcinoma: Tyrosine kinase inhibitor versus immune checkpoint inhibitor
Authors: Zhou Qingbo , Liu Jianjiang , Xie Shaoqin
Published: May 2024

Background:

To date, no meta-analysis has been conducted to compare the effectiveness and safety of adjuvant tyrosine kinase inhibitors (TKIs) and adjuvant immunotherapies (IMTs) in renal cell carcinoma (RCC) patients using reconstructed individual patient data (IPD). This study aims to fill that gap by assessing the efficacy and safety profiles of these treatments in such patients.

Methods:

This study employed a systematic approach for identifying relevant literature from the PubMed and EMBASE databases. We included articles published in English from the inception of these databases until November 11, 2023, focusing specifically on appropriate phase III randomized controlled trials (RCTs). To reconstruct survival curves, we utilized a semiautomated tool, WebPlotDigitizer, in conjunction with a novel shiny application integrated with R software. For adverse events (AEs), the summary measures were incidences, expressed as a 95% confidence interval (CI), calculated using a random-effects model with a logit transformation.

Results:

The analysis included 8 RCTs with a total of 9119 patients. Compared to adjuvant TKIs, adjuvant IMTs showed a similar disease-free survival (DFS) (hazard ratio [HR] 1.03, 95% CI [0.98–1.09], P = .281). However, the overall survival (OS) rates between the 2 groups couldn’t be directly compared due to unmatched control groups in the IMT and TKI studies. Against placebo, adjuvant IMTs demonstrated superior DFS (HR 0.82, 95% CI [0.71–0.94], P = .004) but comparable OS (HR 0.79, 95% CI [0.59–1.06], P = .120). Against placebo, adjuvant TKIs showed superior DFS (HR 0.85, 95% CI [0.79–0.92], P < .0001) and marginally better OS (HR 0.89, 95% CI [0.80–0.996], P = .042). Regarding severe AEs and discontinuation rates due to AEs, adjuvant IMTs had a significantly lower incidence of severe AEs (25% [320/1282] vs 59% [2192/3716], odds ratio [OR] 0.23, 95% CI [0.20–0.27], P < .0001) and a markedly better discontinuation rate (39% [499/1282] vs 52% [2068/4018], OR 0.60, 95% CI [0.53–0.68], P < .0001) compared to TKIs.

Conclusion:

This paper presents a thorough analysis of DFS, OS, and treatment-related AEs across various groups in RCC patients, offering a valuable resource for clinicians in everyday practice. Our findings indicate that while adjuvant IMTs and adjuvant TKIs demonstrate similar DFS, IMTs are notably superior in terms of safety and compliance.
Lipoprotein(a) level predicts the development of nonalcoholic fatty liver disease in Korean adults: A retrospective longitudinal study
Authors: Nam Ji Sun , Park Kahui , Baik Su Jung , Park Jong Suk
Published: May 2024

Nonalcoholic fatty liver disease (NAFLD) is a highly prevalent condition in the general population. Although recent studies have demonstrated a link between NAFLD and lipoprotein(a), a low-density lipoprotein-like particle synthesized in the liver, its precise physiological role and mechanism of action remain unclear. This study aimed to investigate the relationship between lipoprotein(a) levels and development of NAFLD and hepatic fibrosis in Korean adults. A total of 1501 subjects who underwent abdominal ultrasonography at least twice as part of a health checkup program were enrolled. Biochemical and ultrasonography results were analyzed longitudinally, and the degree of hepatic fibrosis was calculated in subjects with NAFLD using serum biomarkers, such as fibrosis-4 (FIB-4). During the 3.36-year follow-up period, 352 patients (23.5%) were diagnosed with NAFLD. The subjects were categorized into 4 groups based on their lipoprotein(a) levels. Remarkably, the incidence of NAFLD decreased as the lipoprotein(a) levels increased. Following logistic regression analysis and adjustment for various risk factors, the odds ratio for the development of NAFLD was 0.625 (95% CI 0.440–0.888; P = .032) when comparing the highest to the lowest tertile of lipoprotein(a). However, no significant association was observed between the occurrence of hepatic fibrosis and lipoprotein(a) levels in subjects with NAFLD. Lipoprotein(a) levels have been identified as a significant predictor of NAFLD development. Additional large-scale studies with extended follow-up periods are required to better understand the effect of lipoprotein(a) on NAFLD and hepatic fibrosis.
Inhibited hypoxia-inducible factor by intraoperative hyperglycemia increased postoperative delirium of aged patients: A review
Authors: Han Yutong , Ji Bing , Leng Yulin , Xie Chunguang
Published: May 2024

The underlying mechanism of postoperative delirium (POD) in elderly people remains unclear. Perioperative hyperglycemia (POHG) is an independent risk indicator for POD, particularly in the elderly. Under cerebral desaturation (hypoxia) during general anesthesia, hypoxia-inducible factor (HIF) is neuroprotective during cerebral hypoxia via diverse pathways, like glucose metabolism and angiogenesis. Hyperglycemia can repress HIF expression and activity. On the other hand, POHG occurred among patients undergoing surgery. For surgical stress, hypothalamic-pituitary-adrenal activation and sympathoadrenal activation may increase endogenous glucose production via gluconeogenesis and glycogenolysis. Thus, under the setting of cerebral hypoxia during general anesthesia, we speculate that POHG prevents HIF-1α levels and function in the brain of aged patients, thus exacerbating the hypoxic response of HIF-1 and potentially contributing to POD. This paper sketches the underlying mechanisms of HIF in POD in elderly patients and offers novel insights into targets for preventing or treating POD in the same way as POHG.
Assessing the readability, reliability, and quality of artificial intelligence chatbot responses to the 100 most searched queries about cardiopulmonary resuscitation: An observational study
Authors: Ömür Arça Dilek , Erdemir İsmail , Kara Fevzi , Shermatov Nurgazy , Odacioğlu Mürüvvet , İbişoğlu Emel , Hanci Ferid Baran , Sağiroğlu Gönül , Hanci Volkan
Published: May 2024

This study aimed to evaluate the readability, reliability, and quality of responses by 4 selected artificial intelligence (AI)-based large language model (LLM) chatbots to questions related to cardiopulmonary resuscitation (CPR). This was a cross-sectional study. Responses to the 100 most frequently asked questions about CPR by 4 selected chatbots (ChatGPT-3.5 [Open AI], Google Bard [Google AI], Google Gemini [Google AI], and Perplexity [Perplexity AI]) were analyzed for readability, reliability, and quality. The chatbots were asked the following question: “What are the 100 most frequently asked questions about cardio pulmonary resuscitation?” in English. Each of the 100 queries derived from the responses was individually posed to the 4 chatbots. The 400 responses or patient education materials (PEM) from the chatbots were assessed for quality and reliability using the modified DISCERN Questionnaire, Journal of the American Medical Association and Global Quality Score. Readability assessment utilized 2 different calculators, which computed readability scores independently using metrics such as Flesch Reading Ease Score, Flesch-Kincaid Grade Level, Simple Measure of Gobbledygook, Gunning Fog Readability and Automated Readability Index. Analyzed 100 responses from each of the 4 chatbots. When the readability values of the median results obtained from Calculators 1 and 2 were compared with the 6th-grade reading level, there was a highly significant difference between the groups (P < .001). Compared to all formulas, the readability level of the responses was above 6th grade. It can be seen that the order of readability from easy to difficult is Bard, Perplexity, Gemini, and ChatGPT-3.5. The readability of the text content provided by all 4 chatbots was found to be above the 6th-grade level. We believe that enhancing the quality, reliability, and readability of PEMs will lead to easier understanding by readers and more accurate performance of CPR. So, patients who receive bystander CPR may experience an increased likelihood of survival.
Assessment of vitamin D status and associated risk factors in high-altitude populations affected by multiple sclerosis: A case–control study
Authors: Alelyani Magbool , Gameraddin Moawia , Alshahrani Raghad , Alaslami Waad , Sarhan Ryoof , Alghamdi Shatha , Alkhathami Ali G. , Salih Suliman , Gareeballah Awadia , Hamad Zuhal , Alzain Amel F. , Omer Awatif M.
Published: May 2024

Several studies have suggested a correlation between serum vitamin D (VitD) level and multiple sclerosis (MS). MS has a known latitudinal distribution pattern, with greater incidence, prevalence, and mortality rates at higher latitudes. This study aims to assess levels of VitD and serum potassium in subjects with MS and the impact of gender and age as disease risk factors. A cross-sectional case-control study was conducted in a high-altitude region of Saudi Arabia. VitD deficiency was defined as serum 25 (OH)D level of ≤20 ng/mL and insufficiency as a serum level between >20 ng/mL and <30 ng/mL. Two hundred patients with MS volunteered for the study, and 160 healthy participants served as controls. VitD and serum potassium were measured in patients and controls. Student t test and regression analysis were used to analyze the data. The average MS patient age was 37.37 ± 10.8 years. Most (73.02%) MS patients suffered from deficient vitamin D, while insufficiency (20–29 ng/mL) was found in 12.17%. Only 6.35% had sufficient vitamin D (30–40 ng/mL). VitD was significantly decreased in MS patients compared to the healthy controls (17.036 vs 25.01 ng/mL, P < .001), while serum potassium was also decreased (4.278 vs 4.329 mmol/L, P = .269). Risk factors found to have a statistically significant association with MS included female gender (odd ratio [OR] = 1.72, 95% confidence interval: 1.016–2.915; P = .044) and patient age < 40 years (OR = 1.04, 95% confidence interval: 1.023–1.054; P = .044). VitD was significantly lower in MS patients. The prevalence of MS was higher among women and younger individuals in a high-altitude population in Saudi Arabia.
Exploring the role of eosinophil cationic protein (ECP) in schizophrenia: Insights and implications
Authors: Obeagu Emmanuel Ifeanyi
Published: May 2024

Schizophrenia, a multifaceted neuropsychiatric disorder characterized by disruptions in perception, cognition, and behavior, has been associated with neuroinflammatory processes. Emerging research has increasingly recognized the potential involvement of immune-related factors in the pathogenesis of schizophrenia, prompting investigations into biomarkers associated with inflammatory cascades. Among these biomarkers, Eosinophil Cationic Protein (ECP), traditionally known for its role in eosinophil-mediated immune responses, has garnered attention for its putative association with neuroinflammation in schizophrenia. This paper critically examines the current understanding of the role of ECP in schizophrenia. ECP, a cytotoxic protein released by eosinophils, has diverse immunomodulatory effects and has been identified in altered concentrations in individuals with schizophrenia. Studies have reported elevated levels of ECP in peripheral fluids of schizophrenia patients, suggesting a possible link between ECP dysregulation and the inflammatory milieu characteristic of the disorder. Moreover, the potential implications of ECP in neuroinflammatory processes relevant to schizophrenia pathophysiology are discussed. ECP’s role in modulating immune responses and its potential impact on neuronal function, synaptic plasticity, and neurotoxicity within the central nervous system (CNS) are considered, highlighting the potential contribution of ECP to the neuroinflammatory mechanisms underlying schizophrenia. In conclusion, while the precise role of ECP in schizophrenia pathogenesis warrants further elucidation, exploring its association with neuroinflammation holds promise in unraveling new biomarkers and therapeutic avenues for managing this complex psychiatric disorder.
A disulfidptosis-related classification and risk signature identifies immunotherapy biomarkers and predicts prognosis in gastric cancer: An observational study
Authors: Chen Ruyue , Jiang Lixin
Published: May 2024

Gastric cancer (GC) is one of the most prevalent types of cancer globally, often detected at advanced stages. However, its prognosis remains poor, necessitating the exploration of new biomarkers. Disulfidptosis, a recently identified form of programmed cell death, has not yet been investigated in relation to GC and its associated mechanisms. We analyzed and identified potential associations between disulfidptosis genes and GC clinical risk using TCGA (The Cancer Genome Atlas)-STAD (stomach adenocarcinoma) as the training set and GSE84433 as the validation set. In addition, we explored the prognostic value and potential biological mechanisms of disulfide genes in GC by consensus clustering, enrichment analysis, mutation histology analysis and immune infiltration analysis. Finally, we constructed a disulfidptosis-related risk signature (DRRS) to assess the association between risk class, survival prognosis, and immune infiltration. By utilizing data from 19 disulfidptosis-related genes, we successfully identified subgroups of C1 and C2 patients through consensus clustering. Notably, the 2 groups exhibited significant variations in terms of survival rates, immune scores, and immune cell infiltration. Subsequently, we developed a DRRS via LASSO (least absolute shrinkage and selection operator) regression analysis, incorporating PRICKLE1, NRP1, APOD, MISP3, and SERPINE1. This scoring system effectively distinguished individuals with high and low risks, as verified with a validation set. These findings strongly indicate a close association between disulfidptosis and the immune microenvironment of GC tumors. Moreover, the DRRS demonstrated commendable predictive capabilities for the survival outcomes of GC patients. In this study, we have identified the association between different subtypes of disulfidptosis and alterations in the GC immunotumour microenvironment. Furthermore, we have developed and verified the accuracy of the DRRS, a valuable tool for predicting survival, biological function, and immune infiltration in patients with GC. These findings contribute to a better comprehension of disulfidptosis and offer potential opportunities for innovative approaches in GC treatment.
Progressive increase in vascular access blood flow after percutaneous transluminal angioplasty in patients on hemodialysis
Authors: Koh Hyun Jin , Kim Seung-Jung , Lee Shina
Published: May 2024

Percutaneous transluminal angioplasty (PTA) is the gold standard for treating stenoses with dysfunctional vascular access. Recently, we found that vascular access blood flow (VABF) measured immediately after PTA increased over time without the need for additional procedures in the patients who underwent PTA. Therefore, this study was conducted to confirm an increase in VABF after PTA and identify the factors associated with it. Patients on chronic hemodialysis at a single institution were retrospectively reviewed and those with accesses that had a measurement of VABF immediately after PTA and within 1 month from PTA were included in the study. The relationship between clinical parameters and changes in VABF were analyzed using paired t-test and linear regression. A total of 47 PTA accesses (fistulas, 26; grafts,21) were included. The mean VABF on the day of PTA and the following measurement were 796.9 ± 329.1 mL/min and 1105.1 ± 410.3 mL/min, respectively. In the univariate analysis, the diameter of the balloon catheter used in the PTA and serum uric acid (SUA) level were significantly associated with an increase in VABF. Atrial fibrillation was a significant factor for the percentage change in vascular access. In the multivariate analysis, SUA level, balloon catheter diameter, and atrial fibrillation remained independent factors for changes in VABF and percentage change in VABF, respectively. The study identified progressive increases in the VABF after PTA without additional procedures. SUA level, balloon catheter diameter used in PTA, and atrial fibrillation were independently associated with changes in VABF.
Construction and validation of a necroptosis-related prognostic signature in acute myeloid leukemia
Authors: Pan Yu-Qing , Yang Kai , Zhang Xi , Li Yi-Xun , Guo Chong , Chen Zheng-Hui , Du Yan
Published: May 2024

Acute myeloid leukemia (AML), an uncommonly low 5-year survival and high mortality rate, is a potentially catastrophic diagnosed subtype of leukemia. The development of new prognostic markers is urgently needed to guide its treatment. Necroptosis is a newly defined biological process for regulating cell death, and previous studies have confirmed that the abnormality of the physical function can lead to multiple malignancies. Here, we performed necroptosis-related genes (NRGs) to build a predictive model in the Cancer Genome Atlas (TCGA)-AML patients, thus exploring the correlation between the NRG prognosis signature (NRG score) of this model and immune infiltration, pathway activity, clinical features, and immunotherapy. Besides, we computed the statistical measure Spearman rank correlation between the NRG score and the Log IC50 values of therapeutic agents. Subsequently, we divided the TCGA-AML cohort into 2 groups, one with high scores and the other with low scores depending on the model score. AML patients with high NRG scores exhibited a lower estimated overall survival (OS) rate than those with low NRG scores, which was confirmed in the validation set. The prognostic value of the constructed NRG signature to the AML, independent of other variables, was demonstrated by uni- and multivariate stepwise regression analysis. When comparing the infiltrating states of specialized cells associated with immune system from the 2 groups, B cells naive, Plasma cells, and monocytes represented significant differences among various subgroups of samples. Moreover, the 30 hallmark-related pathways related to necroptosis characteristics were remarkably different between the high/low NRG score groups. And patients showed remarkable NRG score distribution in clinical features of bone marrow lymphocyte, category, and FAB classifications. Besides, we found that the BIRB0796, VX680, Vorinostat, and Axitinib positively related with NRG score, whereas CI. 1040, PD. 0325901, Z.L LNle. CHO, and AZD6244 negatively correlated with the NRG score. These drugs may provide a reference for subsequent treatment.
Prognostic value of pretreatment platelet count, fibrinogen and d-dimer levels in osteosarcoma patients: A meta-analysis
Authors: Li Xianfeng , Ren Honghong , Peng Lipeng , Li Jie
Published: May 2024

Background:

Previous studies explored the prognostic value of pretreatment platelet count, fibrinogen, and d-dimer level in patients with several types of cancer, however, a comprehensive conclusion has not been reached in osteosarcoma patients.

Methods:

PubMed, Web of Science, Embase, and CNKI databases were systematically searched for eligible studies up to May 09, 2023, and pooled hazard ratios (HRs) with corresponding 95% confidence intervals (CIs) were calculated to assess the prognostic impact of these indicators in osteosarcoma patients.

Results:

Twelve studies from China consisting of 1682 patients were finally included. Our findings revealed that an elevated level of pretreatment platelet or d-dimer was associated with a worse outcome of overall survival (platelet: HR = 1.63, 95% CI: 1.18–2.26, P = .003; d-dimer: HR = 2.29, 95% CI: 1.58–3.31, P < .001).

Conclusion:

Based on current evidence, pretreatment platelet count and d-dimer level could be good prognostic biomarkers for Chinese osteosarcoma patients. However, future validation is also needed.
Multifocal Papillary Thyroid Carcinomas With Discordant Molecular Drivers
Authors: Rivera Jonathan P. , Yeh Yi-Chen , Chen Paul Chih-Hsueh , Hang Jen-Fan
Published: May 2024

Multifocal papillary thyroid carcinomas (PTCs) are common and the majority of the tumors harbor mutual BRAF p.V600E mutation. This study aimed to investigate a contemporary series of multifocal PTCs with discordant molecular drivers. Consecutive thyroidectomies diagnosed with multifocal PTCs ≥0.5 cm between 2019 and 2023 were reviewed. Immunohistochemistry (IHC) for BRAF VE1 was performed for all tumors. Cases with discordant BRAF IHC results or morphologic discrepancy were identified, and BRAF IHC-negative tumors were subjected to RAS Q61R IHC and/or targeted RNA next-generation sequencing. A total of 770 patients with a main PTC ≥0.5 cm were identified; 255 (33.1%) had multifocal disease, and 142 (18.4%) had at least another PTC ≥0.5 cm. Among them, 13 cases (9.2%, 13/142) had discordant molecular drivers. Twelve cases had one or more BRAF-positive PTCs accompanied by a BRAF-negative PTC (3 with CCDC6::RET fusion, 1 with NCOA4::RET fusion, 1 with ACBD5::RET fusion, 2 with ETV6::NTRK3 fusion, 1 with TG::FGFR1 fusion, 1 with LMTK2::BRAF fusion, 1 with AGK::BRAF fusion and RAS p.Q61R mutation, 1 with RAS p.Q61R mutation, and 1 without detectable molecular drivers). The last case had tumors with discordant fusion drivers (VIM::NTRK3 and TNS1::BRAF). Most cases showed tumors that were morphologically distinct (92.3%, 12/13) and occurred in the contralateral lobes (76.9%, 10/13). Notably, we identified 4 cases (30.8%) that presented as collision tumors and 6 cases (46.2%) that showed lymph node metastases, including 2 with simultaneous involvement by tumors with discordant molecular drivers, as novel findings. In summary, a subset (9.2%) of multifocal PTCs had discordant molecular drivers and 84.6% of them were a combination of BRAF-positive and kinase gene fusion-associated PTCs, most with distinct morphologies. Almost half of the cases had nodal metastasis and a third of them showed simultaneous involvement by tumors with discordant molecular drivers. The results highlight the clinical importance of identifying such cases, given the potentially different treatments.
Impact of enhanced adherence counselling on viral re-suppression among adolescents and young persons with persistent viremia
Authors: Wasilwa Anne , Amadi Emmanuel , Ramadhani Habib O. , Lascko Taylor , Ndaga Angela , Makokha Violet , Abuya Kepha , Oneya Daniel , Nyabiage Lennah , Ng’eno Caroline
Published: May 2024

Objective:

Kenya ART guidelines recommend three sessions of enhanced adherence counselling (EAC) following detectable viral load. The objective of this study was to assess completion of EAC sessions and factors associated with viral re-suppression amongst adolescents and young persons (AYPs) with persistent viremia in Western Kenya.

Methods:

A retrospective analysis of routinely collected data abstracted from viral load registers was done. AYP with persistent viremia (consecutive viral load ≥1000 copies/ml) between October 2017 to September 2019 were followed for 12 months; those with more than one follow-up viral load results were analyzed. EAC was satisfactory if at least three sessions attended, barriers identified and addressed. Morisky scores 0 and at least 1 indicated optimal and sub-optimal adherence, respectively. Logistic regression models were used to assess predictors of viral load suppression (VLS).

Results:

Of 124 AYPs with persistent viremia, 118 (95.2%) had documented follow-up viral load results and 119 (96%) completed three EAC sessions. Overall, 55 (47%) clients re-suppressed during the study period. AYPs who had satisfactory EAC sessions had higher odds of achieving VLS [odds ratio (OR) = 3.7, 95% confidence interval (CI): 1.6–8.1]. Similarly, AYPs with an optimal adherence had eight times (OR = 8.1, 95% CI: 3.5–18.5) higher odds of achieving VLS, and those who were suppressed at 6 months post-ART initiation had higher odds of achieving VLS at 12-months (OR = 2.5, 95% CI: 1.1–5.8).

Conclusion:

Satisfactory EAC sessions and optimal ART adherence was strongly associated with viral re-suppression among AYPs with persistent viremia. Continued support to EAC intervention is critical to improve treatment outcome among AYP living with HIV.
Central Retinal Artery Occlusion after Peribulbar Injection of Triamcinolone Acetonide in Thyroid-associated Ophthalmopathy
Authors: Dai Baozhu , Jiang Yan , Dai Yan
Published: May 2024

Central retinal artery occlusion (CRAO) is a form of acute ocular ischemic syndrome that causes visual loss. Timely treatment is of great importance for visual recovery, but the prognosis is usually poor. By analyzing the pathogenesis, diagnosis, and treatment process of a CRAO case after peribulbar injection of triamcinolone acetonide in thyroid-associated ophthalmopathy (TAO), this study aims to investigate the association of CRAO with hemodynamics and orbital pressure, thereby providing references in safety improvement of diagnosis and treatment on TAO.
Rehabilitation of Severely Atrophic Maxilla with Le Fort I Advancement Surgery and Subperiosteal Implant in a Patient With Ectodermal Dysplasia
Authors: Ayhan Mustafa , Yey Özkeskin Sabahat Zeynep
Published: May 2024

Objectives:

In this case, the patient with ectodermal dysplasia lost his teeth and acquired maxillary insufficiency. The aim of this case is to advance the maxilla using Le Fort I surgery and make fixation with a subperiosteal implant.

Methods:

On the three-dimensional model, a surgical guide for Le Fort I osteotomy and subperiosteal implant design was planned. In the surgery, Le Fort I osteotomy was made according to the guide, and maxillary advancement was obtained, then a subperiosteal implant was fixated. Prosthetic rehabilitation was made after 1 month.

Results:

Maxillary repositioning is obtained according to virtual planning and subperiosteal implant is used for both fixation and prosthetic rehabilitation. Proper fixation is ensured and full arch prosthetic rehabilitation supported by a subperiosteal implant is performed.

Conclusion:

With this technique, in the rehabilitation of atrophic maxilla, sagittal insufficiency is corrected with Le Fort 1 surgery, whereas the patient’s treatment period is shortened by placing a subperiosteal implant at the same time.
‘Conga lines’ of Ediacaran fronds: insights into the reproductive biology of early metazoans
Authors: Delahooke Katie M. , Liu Alexander G. , Stephenson Nile P. , Mitchell Emily G.
Published: May 2024

Late Ediacaran strata from Newfoundland, Canada (~574–560 Ma) document near-census palaeocommunities of some of the earliest metazoans. Such preservation enables reproductive strategies to be inferred from the spatial distribution of populations of fossilized benthic organisms, previously revealing the existence of both propagule and stoloniferous reproductive modes among Ediacaran frondose taxa. Here, we describe ‘conga lines’: linear arrangements of more than three closely spaced fossil specimens. We calculate probabilistic models of point maps of 13 fossil-bearing bedding surfaces and show that four surfaces contain conga lines that are not the result of chance alignments. We then test whether these features could result from passive pelagic propagules settling in the lee of an existing frond, using computational fluid dynamics and discrete phase modelling. Under Ediacaran palaeoenvironmental conditions, preferential leeside settlement at the spatial scale of the conga lines is unlikely. We therefore conclude that these features are novel and do not reflect previously described reproductive strategies employed by Ediacaran organisms, suggesting the use of mixed reproductive strategies in the earliest animals. Such strategies enabled Ediacaran frondose taxa to act as reproductive generalists and may be an important facet of early metazoan evolution.
Multi-omics data integration reveals molecular mechanisms of carfilzomib resistance in multiple myeloma
Authors: Malyutina Alina , Sergeev Philipp , Huber Julia , Miettinen Juho J. , Bolomsky Arnold , Bao Jie , Parsons Alun O. , Muller André , Marella Nara , van Duin Mark , Ludwig Heinz , Tang Jing , Heckman Caroline A.
Published: May 2024

Multiple myeloma represents a complex hematological malignancy, characterized by its wide array of genetic and clinical events. The introduction of proteasome inhibitors, such as carfilzomib or bortezomib, into the therapeutic landscape has notably enhanced the quality of life and survival rates for patients suffering from this disease. Nonetheless, a significant obstacle in the long-term efficacy of this treatment is the inevitable development of resistance to PIs, posing a substantial challenge in managing the disease effectively. Our study investigates the molecular mechanisms behind carfilzomib resistance by analyzing multi-omics profiles from four multiple myeloma cell lines: AMO-1, KMS-12-PE, RPMI-8226 and OPM-2, together with their carfilzomib-resistant variants. We uncovered a significant downregulation of metabolic pathways linked to strong mitochondrial dysfunction in resistant cells. Further examination of patient samples identified key genes - ABCB1, RICTOR, PACSIN1, KMT2D, WEE1 and GATM - potentially crucial for resistance, guiding us towards promising carfilzomib combination therapies to circumvent resistance mechanisms. The response profiles of tested compounds have led to the identification of a network of gene interactions in resistant cells. We identified two already approved drugs, benidipine and tacrolimus, as potential partners for combination therapy with carfilzomib to counteract resistance. This discovery enhances the clinical significance of our findings.
Design of a multi-epitope camel mastitis vaccine candidate using a reverse vaccinology approach
Authors: murungi edwin , langat nathan , masila ednah , onywera ruth , ogali irene , gicheru nimmo , wesonga hezron , maichomo monicah
Published: May 2024

Camel mastitis caused by a diverse array of pathogenic bacteria including Staphylococcus aureus and Streptococcus agalactiae is responsible for enormous socioeconomic losses in the arid and semi-arid regions of Africa where camels are an invaluable source livelihood and nutrition. Although S. aureus and S. agalactiae are environmental contaminants, the latter is an infectious zoonotic agent. The development of a safe, efficacious vaccine for camel mastitis is a compelling priority particularly against backdrop of climate change and antimicrobial resistance. We have sequenced and assembled the genomes of local strains of S. aureus, S. agalactiae, L. lactis, E. faecium and E. gallinarum isolated from milk samples of pastoralists camel herds in Kenya, analysed the subtracted proteomes for antigenic proteins using VaxiJen and ascertained the allergenicity, subcellular localisation and the number of transmembrane helices of the putative candidates using AllerTOP, PSORTb and DeepTMHMM. Furthermore, B-cell and T-cell epitopes uncovered in the antigenic protein sequences using Bepi-Pred-2.0, NetCTL 1.2 and NetMHCII 2.3 were used to design a potential vaccine candidate that exhibited adequate immunogenicity, stability and flexibility without toxicity and allergenicity. Collectively, we have delineated a potential multi-epitope vaccine for camel mastitis.
The principles of expected and realised genetic relatedness among individual honeybees
Authors: Strachan Laura , Bubnič Jernej , Petersen Gertje , Gorjanc Gregor , Obsteter Jana
Published: May 2024

Monitoring honeybee genetic variability is essential to manage global and local ge-netic diversity. Coefficients of relatedness are regularly used to measure genetic similar-ity within and between populations and their individuals. Although the haplo-diploid inheritance of honeybees is well understood, interpreting the various types of related-ness coefficients based on pedigree and genotype data is a challenge for researchers and practitioners in honeybee breeding. To demonstrate the principles of genetic relatedness in honeybees and its different individual-based estimators, we simulated three honeybee populations each containing 400 colonies over 10 years using the stochastic simulator SIMplyBee. We kept two populations closed and hybridised the third one by importing drones from one of the closed populations. We evaluated the relatedness between indi-viduals within a colony, between queens of the same population, and between queens of different populations. We calculated three types of relatedness: expected identity by descent using pedigree information, realised identity by descent using pedigree and genotype information, and identity by state using genotype information. Our results demonstrated an alignment of mean relatedness across different types when calculated using the same founder population, regardless of their data source. Identity by state relatedness varied significantly when calculated with different founder populations. Al-though this is an expected result, it shows that caution is needed when comparing values between studies using different populations with different allele frequencies. We expectedly showed increased relatedness over time in closed populations and decreased in the hybrid population. Our results underscore the significance of understanding the methodology for computing relatedness coefficients.
Model-based analysis of the circadian rhythm generation of bioluminescence reporter activity in duckweed
Authors: Horikawa Yu , Watanabe Emiri , Ito Shogo , Oyama Tokitaka
Published: May 2024

Bioluminescence monitoring techniques are widely used to study the gene expression dynamics in living plants. Monitoring the bioluminescence from a luciferase gene under the control of a circadian promoter is indispensable for examining plant circadian systems. The bioluminescence monitoring technique was successfully applied to physiological studies of circadian rhythms in duckweed plants. It has been reported that a luciferase gene under a constitutive promoter also exhibits a bioluminescent circadian rhythm in duckweed. However, the mechanisms underlying rhythm generation remain unknown. In this study, we performed a model-based analysis to evaluate the machinery that generates the bioluminescence rhythm. We hypothesized the rhythmic factor of three aspects regarding the bioluminescence intensities of luciferase in cells: luminescence efficiency, production rate, and degradation rate. Theoretically, if the latter two are involved in rhythm generation, the difference in luciferase stability affects the amplitude and phase relations of the bioluminescence rhythm. Luciferase stability is irrelevant to these rhythm properties if only the luminescence efficiency is involved. First, we simulated the bioluminescence rhythms of two luciferases with different stabilities associated with each of three rhythmic factors. Luciferase stability was set based on the reported values for Emerald-luciferase and Emerald-luciferase-PEST. We then experimentally examined the bioluminescence rhythms of reporters of these luciferases driven by theCAULIFLOWER MOSAIC VIRUS 35Spromoter in the duckweedLemna japonica. Their circadian properties matched those obtained from the simulation of the luminescence efficiency. This supports the view that cells in duckweed show circadian changes in physiological conditions associated with the luciferase enzyme reaction.
Evolution of theCdk4/6–Cdkn2system in invertebrates
Authors: Yuki Shiori , Sasaki Shunsuke , Yamamoto Yuta , Murakami Fumika , Sakata Kazumi , Araki Isato
Published: May 2024

The cell cycle is driven by cyclin-dependent kinases (Cdks). The decision whether the cell cycle proceeds is made during G1 phase, when Cdk4/6 functions. Cyclin-dependent kinase inhibitor 2 (Cdkn2) is a specific inhibitor of Cdk4/6, and their interaction depends on D84 in Cdkn2 and R24/31 in Cdk4/6. This knowledge is based mainly on studies in mammalian cells. Here, we comprehensively analyzedCdk4/6andCdkn2in invertebrates and found thatCdk4/6was present in most of the investigated phyla, but the distribution ofCdkn2was rather uneven among and within the phyla. The positive charge of R24/R31 in Cdk4/6 was conserved in all analyzed species in phyla with Cdkn2. The presence ofCdkn2and the conservation of the positive charge were statistically correlated. We also found thatCdkn2has been tightly linked toFas associated factor 1(Faf1) during evolution. We discuss potential interactions between Cdkn2 and Cdk4/6 in evolution and the possible cause of the strong conservation of the microsynteny.
Arabidopsis terminal nucleotidyl transferases govern secondary siRNA production at distinct steps
Authors: Vigh Maria Louisa , Thieffry Axel , Arribas-Hernández Laura , Brodersen Peter
Published: May 2024

In plants, RNA interference (RNAi) mediated by the endonucleolytic RNA-Induced Silencing Complex (RISC) defends against foreign RNA and regulates endogenous genes. Targeting of RISC to foreign RNA establishes amplification loops, wherein RNA-dependent RNA Polymerase 6 (RDR6) synthesizes double-stranded RNA (dsRNA) for secondary small interfering RNA (siRNA) biogenesis, using cleavage fragments of RNA targeted by RISC programmed with a primary siRNA as template. Secondary siRNA production from endogenous RISC targets requires a particular primary small RNA size or target site multiplicity. siRNA amplification in yeast and nematodes requires terminal nucleotidyl transferases (TNTases), but their roles in plants are unclear. Here, we demonstrate two functions of TNTases in siRNA amplification inArabidopsis thaliana. URT1 prevents initiation of microRNA-induced secondary siRNA formation through uridylation of 5’-cleavage fragments, sometimes redundantly with the exosome and the TNTase HESO1. Once initiated via RDR6 recruitment, HESO1 and other TNTases stimulate secondary siRNA formation by producing 2-nt 3’overhangs on RDR6-synthesized dsRNA to yield substrates for processing into siRNAs by DICER-LIKE4. These results define molecular mechanisms by which TNTases control siRNA amplification in plants.
PTGS is dispensable for the initiation of epigenetic silencing of an active transposon inArabidopsis
Authors: Trasser Marieke , Bohl-Viallefond Grégoire , Barragán-Borrero Verónica , Diezma-Navas Laura , Loncsek Lukas , Nordborg Magnus , Marí-Ordóñez Arturo
Published: May 2024

Transposable elements (TEs) are largely repressed in plants through transcriptional gene silencing (TGS), which is maintained by heritable epigenetic silencing marks such as DNA methylation. However, the mechanisms by which silencing is installed in the first place remains poorly understood in plants. Small interfering (si)RNAs and post-transcriptional gene silencing (PTGS) play a role in the initial response by reducing mRNA and protein levels of active TEs and are believed to mediate the initiation of TGS by guiding the first deposition of DNA methylation. To determine how this silencing installation works, we took advantage ofÉVADÉ (EVD), an endogenous retroelement in Arabidopsis, which can be used to recapitulate truede novosilencing with a well-established sequence of PTGS followed by a TGS phase. To test whether PTGS is a prerequisite for TGS, activeEVDcopies were introduced into RNA-DEPENDENT-RNA-POLYMERASE-6 (RDR6) mutants lacking an essential PTGS component.EVDactivity and silencing were monitored across several generations. Unexpectedly, even in the absence of PTGS, TGS and silencing ofEVDwere still achieved through installation of RNA-directed DNA methylation (RdDM) atEVDregulatory sequences without any prior DNA methylation at its coding sequence. Hence, our study shows that PTGS is dispensable forde novo EVDsilencing. Although we cannot rule out that PTGS might facilitate the initiation of TGS, or control TE activity until then, initiation of epigenetic silencing can take place in its absence.
The endolysosomal phospholipid bis(monoacylglycero)phosphate is synthesized via intra- and extracellular pathways
Authors: Bulfon Dominik , Breithofer Johannes , Grabner Gernot F. , Fawzy Nermeen , Pirchheim Anita , Wolinski Heimo , Kolb Dagmar , Hartig Lennart , Tischitz Martin , Zitta Clara , Bramerdorfer Greta , Lass Achim , Taschler Ulrike , Kratky Dagmar , Greimel Peter , Zimmermann Robert
Published: May 2024

Bis(monoacylglycero)phosphate (BMP) is a major phospholipid constituent of intralumenal membranes in late endosomes/lysosomes, where it regulates the degradation and sorting of lipid cargo. Recent observations suggest that the Batten disease - associated protein CLN5 functions as lysosomal BMP synthase. Here, we show that transacylation reactions catalyzed by cytosolic and secreted enzymes enhance BMP synthesis independently of CLN5. The transacylases identified in this study are capable of acylating the precursor lipid phosphatidylglycerol (PG), generating acyl-PG, which is subsequently hydrolyzed to BMP. Extracellularly, acyl-PG and BMP are generated by endothelial lipase in cooperation with other serum enzymes of the pancreatic lipase family. The intracellular acylation of PG is catalyzed by several members of the cytosolic phospholipase A2 group IV (PLA2G4) family. Overexpression of secreted or cytosolic transacylases was sufficient to correct BMP deficiency in HEK293 cells lackingCLN5. Collectively, our observations suggest that functionally overlapping pathways promote BMP synthesis in mammalian cells.
Spatiotemporally resolved transcriptome atlas of developing mouse placenta reveals mechanisms of embryonic lethality
Authors: Fu Yuting , Zeng Xiaoqi , Liu Yifang , Jia Shikai , Jiang Yujia , Tan Jia Ping , Yuan Yue , Xia Tianchang , Mei Yun , Wen Shan , Liu Xiaojing , You Yue , Pei Weike , Yang Chengshuo , Shao Sida , Cheng Saifeng , Tian Luyi , Liu Longqi , Wei Xiaoyu , Liu Xiaodong
Published: May 2024

Proper placentation is essential for embryonic growth and viability, yet the spatial organization and interactions of placental cell types remain incompletely understood. Here, we present a spatiotemporal transcriptomic atlas of the mouse placenta (STAMP) from embryonic days 9.5 to 18.5 at single-cell resolution. This atlas delineates major placental cell types and developmental trajectories. We observed labyrinth region expansion through branching morphogenesis, with trophoblast progenitor cells declining and terminally differentiated trophoblast cells increasing from E12.5 onward, and glycogen cells (GCs) transitioned from the junctional zone (JZ) to the maternal decidua. Furthermore, we found two novel GC subclusters with distinct spatial distributions and molecular features. Analysis of defective placentas revealed an increased number of GCs and altered macrophage distribution in the labyrinth layer. Transmission electron microscopy and glycogen content examination confirmed sluggish glycogen breakdown, while macrophage accumulation correlated with tissue remodeling and immune responses. Our spatial transcriptomic analysis elucidates mechanisms underlying placental abnormalities and embryonic lethality. This atlas enhances understanding of mouse placental development, aids in identifying developmental defects and pathogenic causes in dysfunctional placentas, and provides valuable insights for optimizingin vitroembryo culture conditions.
Ion channel inhibition by targeted recruitment of NEDD4-2 with divalent nanobodies
Authors: Morgenstern Travis J. , Darko-Boateng Arden , Afriyie Emmanuel , Shanmugam Sri Karthika , Zhou Xinle , Choudhury Papiya , Desai Meera , Kass Robert S. , Clarke Oliver B. , Colecraft Henry M.
Published: May 2024

Targeted recruitment of E3 ubiquitin ligases to degrade traditionally undruggable proteins is a disruptive paradigm for developing new therapeutics. Two salient limitations are that <2% of the ~600 E3 ligases in the human genome have been exploited to produce proteolysis targeting chimeras (PROTACs), and the efficacy of the approach has not been demonstrated for a vital class of complex multi-subunit membrane proteins— ion channels. NEDD4-1 and NEDD4-2 are physiological regulators of myriad ion channels, and belong to the 28-member HECT (homologous to E6AP C-terminus) family of E3 ligases with widespread roles in cell/developmental biology and diverse diseases including various cancers, immunological and neurological disorders, and chronic pain. The potential efficacy of HECT E3 ligases for targeted protein degradation is unexplored, constrained by a lack of appropriate binders, and uncertain due to their complex regulation by layered intra-molecular and posttranslational mechanisms. Here, we identified a nanobody that binds with high affinity and specificity to a unique site on the N-lobe of the NEDD4-2 HECT domain at a location physically separate from sites critical for catalysis— the E2 binding site, the catalytic cysteine, and the ubiquitin exosite— as revealed by a 3.1 Å cryo-electron microscopy reconstruction. Recruiting endogenous NEDD4-2 to diverse ion channel proteins (KCNQ1, ENaC, and CaV2.2) using a divalent (DiVa) nanobody format strongly reduced their functional expression with minimal off-target effects as assessed by global proteomics, compared to simple NEDD4-2 overexpression. The results establish utility of a HECT E3 ligase for targeted protein downregulation, validate a class of complex multi-subunit membrane proteins as susceptible to this modality, and introduce endogenous E3 ligase recruitment with DiVa nanobodies as a general method to generate novel genetically-encoded ion channel inhibitors.
Aging represses lung tumorigenesis and alters tumor suppression
Authors: Shuldiner Emily G. , Karmakar Saswati , Tsai Min K. , Hebert Jess D. , Tang Yuning J. , Andrejka Laura , Wang Minwei , Detrick Colin R. , Cai Hongchen , Tang Rui , Petrov Dmitri A. , Winslow Monte M.
Published: May 2024

Most cancers are diagnosed in persons over the age of sixty, but little is known about how age impacts tumorigenesis. While aging is accompanied by mutation accumulation — widely understood to contribute to cancer risk — it is also associated with numerous other cellular and molecular changes likely to impact tumorigenesis. Moreover, cancer incidence decreases in the oldest part of the population, suggesting that very old age may reduce carcinogenesis. Here we show that aging represses tumor initiation and growth in genetically engineered mouse models of human lung cancer. Moreover, aging dampens the impact of inactivating many, but not all, tumor suppressor genes with the impact of inactivating PTEN, a negative regulator of the PI3K/AKT pathway, weakened to a disproportionate extent. Single-cell transcriptomic analysis revealed that neoplastic cells from tumors in old mice retain many age-related transcriptomic changes, showing that age has an enduring impact that persists through oncogenic transformation. Furthermore, the consequences of PTEN inactivation were strikingly age-dependent, with PTEN deficiency reducing signatures of aging in cancer cells and the tumor microenvironment. Our findings suggest that the relationship between age and lung cancer incidence may reflect an integration of the competing effects of driver mutation accumulation and tumor suppressive effects of aging.