Furthermore, the SVM model could distinguish MDD patients with different suicidality gradients . In conclusion, we have identified that disrupted brain connections were present in MDD patients with different suicidality gradient. These findings provided useful information about the pathophysiological mechanisms of MDD patients with suicidality.Suicidal behavior is a major concern for patients who suffer from major depressive disorder (MDD). However, dynamic alterations and dysfunction of resting-state networks (RSNs) in MDD patients with suicidality have remained unclear. Thus, we investigated whether subjects with different severity of suicidal ideation and suicidal behavior may have different disturbances in brain RSNs and whether these changes could be used as the diagnostic biomarkers to discriminate MDD with or without suicidal ideation and suicidal behavior. Then a multicenter, cross-sectional study of 528 MDD patients with or without suicidality and 998 healthy controls was performed. We defined the probability of dying by the suicide of the suicidality components as a ‘suicidality gradient’. We constructed ten RSNs, including default mode (DMN), subcortical (SUB), ventral attention (VAN), and visual network (VIS). The network connections of RSNs were analyzed among MDD patients with different suicidality gradients and healthy controls using ANCOVA, chi-squared tests, and network-based statistical analysis. And support vector machine (SVM) model was designed to distinguish patients with mild-to-severe suicidal ideation, and suicidal behavior. We found the following abnormalities with increasing suicidality gradient in MDD patients: within-network connectivity values initially increased and then decreased, and one-versus-other network values decreased first and then increased. Besides, within- and between-network connectivity values of the various suicidality gradients are mainly negatively correlated with HAMD anxiety and positively correlated with weight. We found that VIS and DMN-VIS values were affected by age ( Major depressive disorder (MDD) is a common psychiatric disorder characterized by an inability to experience pleasure/reward (anhedonia) , affecti. Furthermore, previous studies aver that cortical thickness of ten regions within fronto-temporal-parietal system act as top-ranked classifiers that could differentiate suicide attempts from SI in MDD patients [Neuroimaging and behavioral studies have recently centered on network-based structural and functional alterations of individuals at risk of suicide. Previous studies postulated that fronto-limbic system is the central circuit underlying the suicidal process under depressive conditions –15. MDD patients . In addipatients . These fBased on prior studies, we hypothesized that suicidal gradient in MDD patients might arise from disturbances in macroscale brain RSNs and altered brain connections may represent powerful diagnostic biomarkers to discriminate MDD with or without SI and SB. First, the current study mapped the dynamic trajectory of large-scale RSNs roles and their clinical significance with dynamic network-based analysis in MDD patients with suicidality gradient. Second, common and specific network connections associated with different suicidal gradients were identified in MDD patients. Third, the support vector machine (SVM) model was used to explore the role of these abnormal neuroimaging characteristics as objective diagnostic biomarkers in classifying MDD patients with different suicidal gradients. Depression shows gender specificity in which the incidence rate of MDD is approximately twofold higher in women than in men . TherefoAmong the previously mentioned MDD patients, 169 individuals had a medication history; nevertheless, they had refrained from taking medication for a duration of at least three weeks at the time of enrollment. Based on a 17-item HAMD suicide item score, MDD patients were categorized into five categories: a score of 0 was defined as MDD without suicidal ideation (MDDNSI); score of +1 was defined as MDD with mild suicidal ideation (MDDmSI); score of +2 was defined as MDD with moderate suicidal ideation (MDDmoSI); score of +3 was defined as MDD with severe suicidal ideation (MDDSSI); and score of +4 was defined as MDD with SB (MDDSB). HCs were randomly divided into HC and verification groups. Detailed information on all subjects is shown in Table A total of 528 MDD patients and 998 HCs were recruited from the REST-meta-MDD consortium  and the All study sites obtained approval from their local institutional review boards and ethics committees. Also, these research protocols were approved by the Ethics Committee of Henan Provincial Mental Hospital Affiliated with Xinxiang Medical University . All participants, their legal guardians, or their legally authorized representatives provided informed consent prior to their involvement in the study.Scan acquisition was completed within 1 week of assessments. Resting-state fMRI and structural T1-weighted MRI brain scans were acquired at each of the 24 participating study sites (see STable These networks comprise the auditory network (AUD), the cingulo-opercular network (CON), the dorsal and ventral attention network (DAN and VAN), the default mode network (DMN), the fronto-parietal network (FPN), the salience network (SAN), the sensorimotor network (SMN), the subcortical network (SUB), and the visual network (VIS). Network connectivity between all pairs of 10 RSNs, as well as between each RSN and all other RSNs  were computed.A power atlas  was usedp < 0.05 for all tests. In addition, a one-way analysis of variance (ANOVA) test was used to analyze continuous variables, with post hoc least significance difference (LSD) tests for pair-wise comparisons. Chi-squared tests were also used for categorical variables. Notably, each network metric ) was compared across groups using generalized linear model (GLM) analysis adjusted for age, gender, education, and study site as covariables. All p values were adjusted for multiple comparisons  using FDR correction.Group comparisons of demographic characteristics and network metrics across MDD subgroups were undertaken using analysis of covariance (ANCOVA) and significance levels were set at p < 0.001.The current study first generated a 226 * 226 connectivity matrix for each subject. Network-based statistical analysis (NBS) method was then used to identify common and differential connections of networks between healthy control (HC) and disease groups, as well as various disease subgroups. Each connection identified by NBS with Bonferroni correction satisfied Due to the potential effects of age and sex in dynamic network analysis, Wilcoxon rank sum tests were used to compare the abnormality of network and clinical variables in sex and age. Specifically, all patients were split into younger (age: 18–37) and older (age: 38–65) participants or females and males to obtain sex- and age-related alterations in networks and clinical variables, separately.The current study computed Pearson’s correlation between network variables and clinical data.SVM was used in the current study to classify MDD subgroups and HCs in MATLAB based on a library (LIBSVM) . The curAll described analyses were repeated using another set of healthy subjects that included 499 subjects to validate whether network role construction could be replicated and whether selected functional connections could be used for classification.p < 0.001) and subscales scores including anxiety (p = 0.0003), weight (p < 0.0001), retardation (p < 0.0001), and sleep (p = 0.0001), compared with those of MDNSI subjects, indicating that MDD patients R1–2 with suicidality had severer depression compared with MDNSI patients. Furthermore, there were no statistically significant differences in additional clinical characteristics upon enrollment, including total disease duration and frequency of episodes among the subgroups of individuals with MDD.Demographic information and characterization of all study subjects are outlined in Table  R1–3 and pairwise BNC in HC group and suicidality-related MDD patients Fig. . SpecifiTo further map abnormal network connections with significant group differences in within-, between- or one versus other networks of ten RSNs in MDD patients, the current study first established increased and decreased network connections in the suicidality-related MDD patients compared with the HC group as shown in Fig. To understand the clinical significance of abnormal WNC and BNC in MDD subgroups, the current study conducted Pearson’s correlation between FC strength within- and between networks and clinical variables including HAMD total scores and subfactor scores, including HAMD-Anxiety, HAMD-Weight, HAMD-Retardation, and HAMD-Sleep in MDD patients after controlling for covariables of age, gender, education, and study site. Correlation patterns showed group-level associations of WNC and BNC with depressive severity in MDD subgroup patients and established that distinctive network basis was associated with different symptom dimensions in MDD patients with or without suicidality Fig. . These nThe SVM model was used to explore the role of abnormal FC as an objective diagnostic biomarker in MDD patients. Mean FCIs from 31 pairs of network connections were used as input features to the linear support vector classifier (SVC). AUC showed that these FCIs demonstrated a higher capacity to discriminate MDD patients with SB from the HC group (AUC = 0.96). The use of the SVM-trained model as a classifier demonstrated that the SVM-trained model showed better power in separating MDD patients with SI or SB from MDDNSI patients . Furthermore, FCIs also showed greater potential to discriminate suicidality gradient-related MDD patients  except for MDDmSI from MDDmoSI patients AUC = 0.73). Detailed information is described in Fig. 3. DetailWilcoxon rank sum tests were used to determine the potential effects of age and sex on large-scale brain networks and clinical variables in females and males, or in younger and older participants, separately. The current study established that age and sex had significantly different impacts on the two variables Fig. . SpecifiThe current study repeated these analyses to validate current findings in independent cohorts that included new 499 HCs and the original 528 MDD patients. More females and lower educational years were found in MDD subgroup patients compared with the new HC group. In addition, large-scale network roles analysis showed similar network dynamics in MDD subgroups compared with the HC validation group . These findings indicate that the use of large-scale network connection approaches to identify more robust diagnostic neuroimaging biomarkers may vary depending on whether the prediction goal pertains to diagnosis. Therefore, the established key features of large-scale network dynamics are crucial for early recognition and timely diagnosis of individuals with suicidality in depression and achieve much greater progress towards understanding and preventing suicide, as well as reducing patients’ risk of morbidity from suicide ideation and attempts and their risks of suicide death. In clinical translational practice, measured imbalanced network links in the current study served as functional endophenotypes to particularly characterize depressive patients who tend to disguise real suicide intent without apparent symptoms. In addition, the current study used this endophenotype to guide informed treatment and monitor if medications target these networks.Several previous studies have established the effects of age and gender on large-scale network dynamics in healthy and depressive disorders –62. In mThe current study had some limitations. First, this was a cross-sectional study involving multiple centers. A longitudinal study should be undertaken to validate these findings. Second, the suicidality gradient in depression was assessed using HAMD suicidal factor scores, which may limit findings. Therefore, the use of improved suicidality assessment instruments is necessary to precisely evaluate the severity of suicide in MDD patients in future studies. Third, future studies are needed to establish whether these abnormal networks are long-lasting and how they may interact with environmental and genetic factors.In conclusion, the current study demonstrated that the dynamic trajectory of network roles at a large-scale level was associated with suicidality gradient in MDD patients. Abnormal overlapping network connections were used as neuroimaging biomarkers in the diagnostic identification of subjects who are vulnerable to suicide under depressive conditions. The current study achieved much greater progress towards understanding the pathologic mechanism of suicide and precisely preventing suicidal occurrence via targeting these circuits with effective medical or physical instruments.supplemental material


In recent few years, high-flow nasal oxygenation (HFNO) has been widely used for management of acute hypoxemic respiratory failure and during postextubation periods, including after endotracheal intubation general anesthesia (ETGA). However, HFNO generates positive pressure in the injured airway following removal of endotracheal tube may cause airway leaks. This is the first case report of severe airway leak syndrome following postextubation use of HFNO in surgical patients.This case report describes a 75-year-old female with critical aortic stenosis who underwent an emergency Bentall procedure. HFNO (flow rate of 45 L/min) was applied after weaning from mechanical ventilation and removal of the endotracheal tube.At 6 hours after HFNO application, subcutaneous emphysema in the neck bilaterally and face was noted, and the emphysema extended into the supraclavicular regions.The HFNO cannula was removed soon after and the patient was re-intubated with an endotracheal tube the following day due to progressive respiratory insufficiency. Unfortunately, the patient general condition deteriorated, as the subcutaneous air collections progressed into deep tissue infections of the neck, mediastinal abscesses, and left-sided empyema. Patient received surgical interventions repeatedly to drain the mediastinal abscess and empiric antimicrobial therapy was given.The patient passed away about 2 months later due to uncontrollable sepsis.Air leaks in the upper airway can occur during the use of post-extubation HFNO use, and the resulting subcutaneous emphysema can progress to severe intrathoracic infections in surgical patients who have a sternotomy wound. Therefore, HFNO-induced subcutaneous emphysema should be treated more aggressively in open thoracic or sternotomy surgeries to prevent the development of intrathoracic sepsis. HFNO is currently used to prevent hypoxic events during anesthesia induction, procedural sedation and as an alternative to respiratory support in critically ill patients.,2 A large-scale multi-center clinical trial further demonstrated that HFNO is not inferior to standard noninvasive mechanical ventilation for preventing reintubation and respiratory failure within 72 hours post endotracheal tube removal in high-risk critically ill adults. Compared with conventional oxygen therapy, HFNO also significantly reduces reintubation rates and rates of respiratory support escalation immediately after endotracheal general anesthesia (ETGA) in adult surgical patients. Therefore, HFNO is recommended over conventional oxygen therapy for the management of acute hypoxemic respiratory failure and for postextubation periods in emergency departments, hospital wards, intermediate or step-down units, and intensive care units. Although clinical studies did not find major complications in postextubation use of HFNO,,6 positive pressure in the upper airway from high gas flow may cause air-leaks into the subcutaneous tissues from the injured airway mucosa.,8 This case report describes a patient who was successfully weaned from invasive mechanical ventilatory support day 1 after a Bentall procedure, but developed extensive subcutaneous emphysema and pneumomediastinum within few hours after switching from endotracheal intubation to HFNO.Specially equipped high-flow nasal oxygenation (HFNO) provides a high flow rates (up to 70 L/min) of warm and humidified mixed oxygen/gas to generate continuous positive pressure in the upper airways, wash-out of dead space in the nasopharyngeal cavity, increase alveolar recruitment and functional residual capacity, reduce work of breathing and respiratory muscle fatigue, enhance airway secretion clearance, and improve hypercapnia post endotracheal tube extubation.A 75-year-old woman with a medical history of chronic hypertension and aortic stenosis developed progressive shortness of breath and orthopnea a few days before surgery. She presented to the emergency department with hypotension and low peripheral oxygen saturation. An echocardiographic study showed calcified and severely stenotic aortic valves with a mean transvalvular pressure gradient of 60 mm Hg and left ventricle dysfunction. The proximal aortic root was dilated to a diameter of 10 cm. Acute cardiac failure was evidenced by elevated serum levels of B-type natriuretic peptide (>500 pg/mL) and pulmonary edema on chest radiography. An urgent Bentall procedure, including graft replacement of the ascending aorta and aortic valves was performed under ETGA and cardiopulmonary bypass. An endotracheal tube was inserted smoothly on the first attempt using a video laryngoscope without complications.The whole surgical procedure was completed within 10 hours. After successfully weaning off cardiopulmonary bypass in the operating room, the patient was transferred to intensive care unit for postoperative care under mechanical ventilatory support. Mechanical ventilation was switched from pressure control and pressure support mode when the patient had regained consciousness and had shown effort of spontaneous respiration the morning after her operation. Following a successful spontaneous breathing trial for an hour, the endotracheal tube was removed and HFNO  was applied with 40% fraction of inspired oxygen at a flow rate of 45 L/min via a nasal cannula . The patient settled comfortably with HFNO, and adequate peripheral oxygen saturation was maintained. Six hours later, the patient claimed to have insidious attacks of sharp pain and swelling in the neck and face. Subcutaneous crepitus was detected at the neck bilaterally, extending to the lower jaw and the upper chest. HFNO was discontinued and the patient was put on a non-rebreathing mask for oxygen supplementation. A portable chest radiography taken at bedside confirmed the presence of subcutaneous emphysema in the neck and supraclavicular regions with no signs of pneumothorax or pneumomediastinum  who were treated with HFNO after endotracheal tube removal. Two of these patients developed pneumothoraxes and one developed pneumomediastinum at 4 to 5 hours after HFNO use. Air leak problems in these pediatric patients were diagnosed by routine chest radiographies rather the presence of subcutaneous emphysema or hypoxic events. There was another case of an adult female with hemophagocytic lymphohistiocytosis who received endotracheal intubation and mechanical ventilatory support due to acute respiratory failure. HFNO therapy was applied at a flow rate of 40 L/min after weaning from mechanical ventilation. Four days later, the patient developed dyspnea and hypoxemia. A series of radiological studies were performed to investigate and found pneumothorax, subcutaneous emphysema, and massive pneumomediastinum. After HFNO cessation, the patient respiratory conditions improved. Air-leak syndrome during postoperative HFNO use after ETGA in surgical patients have not been reported in the literature.It is generally believed that positive airway pressure generated by HFNO in the upper airway and trachea can squeeze air into subcutaneous tissues via micro-tears in the airway mucosa. However, our case progressed rapidly to intrathoracic sepsis and empyema due to gram negative nosocomial pathogen infections and she eventually expired because of uncontrollable sepsis. We speculated that the sternotomy wound might have precipitated the invasion of nosocomial organisms into the mediastinal subcutaneous air collection. Hence, more aggressive empirical antimicrobial treatment should be considered early stages subcutaneous emphysemas are found in surgical patients with a sternotomy or thoracotomy wound.We reported the first fatal air-leak complication following use of postextubation HFNO in a patient with a sternotomy after cardiac surgery. While most of the other case reports were associated with pneumothorax due to distal airway or lung tissue tears, the leak in our case was most likely located in the upper trachea, as the air-leak was not detected before removal of the cuffed endotracheal tube nor after tracheal re-intubation, and pneumothorax was also not found in our case. The initial clinical signs of air-leak syndrome in our patient were focal pain and detection of subcutaneous emphysema as opposed to being clinically asymptomatic or presence of hypoxia at the late stage in other cases. Therefore, detection of emphysema underneath the neck or facial subcutaneous tissues could be an early sign of upper airway leak when HFNO is applied after tracheal extubation. The outcomes of subcutaneous emphysema due to airway leak is usually self-limiting and requires mainly conservative management.In conclusion, the use of postextubation HFNO is generally safe after ETGA, but air-leak syndrome may still happen in unrecognized airway mucosal injuries, as continuous positive pressure is generated by the HFNO. The presence of subcutaneous emphysema can be an early sign of airway leak following application of HFNO and subcutaneous emphysema should be treated more aggressively in open thoracic or sternotomy surgery to prevent the development of intrathoracic sepsis.Conceptualization: Yu-Yang Liao, Hsuan-Yin Wu, Chen-Fuh Lam, Yi-Ming Wang.Data curation: Yu-Yang Liao, Yi-Ming Wang.Supervision: Chen-Fuh Lam, Yi-Ming Wang.Validation: Hsuan-Yin Wu, Chen-Fuh Lam.Writing – original draft: Yu-Yang Liao, Hsuan-Yin Wu.Writing – review & editing: Chen-Fuh Lam, Yi-Ming Wang.


Dear EditorWe thank Lightner and colleagues for their study on surveillance pouchoscopy in ulcerative colitis patients. The authors reported that neoplasia following ileal pouch-anal anastomosis (IPAA) is rare. They recommended pouch surveillance with random biopsies of the anal transition zone (ATZ) for patients with a personal or family history of colorectal neoplasia (CRN)It is unknown whether routine surveillance improves outcomes of pouch neoplasia, since pouch neoplasia is usually diagnosed after symptom development. As such, all patients in this study had a negative surveillance pouchoscopy in the 2 years prior to pouch carcinoma detectionWe question whether random biopsies lead to earlier detection of (pre)cancerous pouch lesions. The authors reported six pouch carcinomas and none were detected in random biopsies. Moreover, six of seven dysplastic lesions identified with random ATZ biopsies were not confirmed in follow-up biopsies and it could be questioned whether the initial lesions contained ‘true’ dysplasiaFinally, we disagree with the recommendation of pouch surveillance in patients with a family history of CRN. The authors reported a positive family history in only one of 13 patients and previous studies did not identify this as a risk factor for pouch neoplasia.In conclusion, we only advocate pouch surveillance with random ATZ biopsies in high-risk patients with prior CRN. Nevertheless, current data remain scarce and uniform, widely adopted pouch surveillance guidelines are needed to unify practice.Disclosure. The authors declare no conflicts of interest.


The natural amino acid asparagine (Asn) is required by cells to sustain function and proliferation. Healthy cells can synthesize Asn through asparagine synthetase (ASNS) activity, whereas specific cancer and genetically diseased cells are forced to obtain asparagine from the extracellular environment. ASNS catalyzes the ATP-dependent synthesis of Asn from aspartate by consuming glutamine as a nitrogen source. Asparagine Synthetase Deficiency (ASNSD) is a disease that results from biallelic mutations in the ASNS gene and presents with congenital microcephaly, intractable seizures, and progressive brain atrophy. ASNSD often leads to premature death. Although clinical and cellular studies have reported that Asn deprivation contributes to the disease symptoms, the global metabolic effects of Asn deprivation on ASNSD-derived cells have not been studied. We analyzed two previously characterized cell culture models, lymphoblastoids and fibroblasts, each carrying unique ASNS mutations from families with ASNSD. Metabolomics analysis demonstrated that Asn deprivation in ASNS-deficient cells led to disruptions across a wide range of metabolites. Moreover, we observed significant decrements in TCA cycle intermediates and anaplerotic substrates in ASNS-deficient cells challenged with Asn deprivation. We have identified pantothenate, phenylalanine, and aspartate as possible biomarkers of Asn deprivation in normal and ASNSD-derived cells. This work implies the possibility of a novel ASNSD diagnostic via targeted biomarker analysis of a blood draw. ASNS gene occupies 35 kb within chromosome 7q21.3 and is composed of a total of 13 exons glucose to analyze central carbon metabolism, [U-13C]aspartate to assess the specific fate of the ASNS reaction, and [U-13C]glutamine to assess TCA cycle turnover. Additionally, the significant decrements in lactate and central metabolism suggest that in vivo [2H7]glucose metabolic imaging may potentially be utilized to assess the effects of Asn deprivation on brain metabolism [In summary, our findings demonstrate that Asn deprivation leads to a broad-based disruption of the metabolic profiles of patient cells deficient for ASNS. We have identified potential metabolic signatures of Asn deprivation in healthy and ASNSD cells. This observation is of high interest for ASNSD and metabolic research as it warrants future work to establish the relevance of these metabolic signatures and their potential roles as diagnostic and prognostic biomarkers in an in vivo and clinical setting. While our results indicate a certain global metabolic insult caused by Asn deprivation in ASNS deficient cells, further work must be done to discern pathway-specific changes using isotopomer tracer and metabolic flux analysis. The research reported here warrants future studies on ASNSD cell models to assess the utilization of [U-tabolism .


Conversely, no statistically significant difference in oral microbiota composition was observed, thus further revealing a close relationship between ICI response and gut microbiota diversity in NSCLC patients. Extracellular vesicles (EVs) were broadly classified into three main categories based on their biosynthetic or secretory processes: exosomes, microvesicles/particles/extracellular bodies, and apoptotic vesicles  due to their association with both nutritional and inflammatory status. vesicles . With tharcinoma . A modelarcinoma . In addiarcinoma . Gao et Using Multi-Omics to Develop New Strategies for Improving Prognosis and Immunotherapy Outcomes in Cancer” serves as a platform for sharing innovative strategies developed through multi-omics to enhance the effectiveness of immunotherapies and improve patient outcomes. These studies integrate data from various layers, providing valuable insights into the molecular structure of tumors and expanding the scope of cancer biology. Although clinical applications of these techniques are still in the early stages, we believe that several of these new approaches will not only advance our understanding of tumor biology but also significantly shape the future of precision cancer therapies.The Research Topic “


Escherichia coli bacteremia. Larvae of Strongyloides stercoralis were also observed in stool smears after a centrifugation concentration method. This diagnosis was confirmed by qPCR detection of Strongyloides spp. using the Allplex GI-Helminth (I) Assay (Seegene) (The definitive diagnosis was disseminated strongyloidiasis with concurrent Seegene)  in the tS. stercoralis is a soil-transmitted nematode that is endemic in tropical and subtropical countries, especially in areas with inadequate sanitary conditions, and it is recognized as a neglected tropical disease  in the gut, resulting in autoinfection. This unique property allows infection to persist for decades (chronic strongyloidiasis) and cause overwhelming infection if people become immunosuppressed later in life, leading to Strongyloides Hyperinfection Syndrome (SHS) or disseminated infection (Strongyloides infection in patients treated with dexamethasone needs to be considered to avoid precipitating SHS and disseminated strongyloidiasis (nfection , 7. Concnfection , so asym


Plant genotype influences interactions among associated bacteria and fungi;Plant-growth-promoting bacterial communities lead to outcomes exceeding the sum of individual effects; andEnvironmental conditions impact how microbes in communities interact.Soils are home to a wide variety of microorganisms. The collective genome of these organisms is vast, and so individual strains perform some functions that few others can. In addition to the consumption of specific metabolites, many soil microbes excrete unique compounds into their direct environment in soils, at root surfaces, and inside plants as endophytes. The ensuing localized build-up of compounds impacts other organisms by exerting a variety of functions: promoting growth, activating signal transduction, suppressing cellular functions, or changing the physicochemical environment. Microorganisms share soils with plants, whose roots exude cocktails of organic compounds ,2 that fOryza rufipogon wild rice and male parent Oryza sativa cultivated rice had significantly different bacterial and fungal communities than either of the parental lines. Similarly, sorghum lines have different rhizo- and endosphere bacterial communities that contribute to plant performance to different degrees under low nitrogen stress conditions [Plant breeding has focused largely on improved agronomic traits, such as yield and disease resistance, invariably losing some parental traits not selected for. Rhizomicrobiome analysis of modern cultivars versus ancestral accessions has revealed significant differences in the bacterial and fungal communities of rice . The pronditions . Cultivanditions .A unique three-way interaction has been reported among plants, their endophytes, and the associated rhizomicrobial community. Fungal endophytes of Tall Fescue are not only associated with improved biomass yield and stress tolerance, but also with soil fungal community composition and increased diversity . These sStreptomyces [Physicochemical conditions are well known to affect the growth of individual microbial cultures. Invariably, shifts in environmental conditions also impact the fitness of individual species and strains. Farda et al. reviewed the literature on actinomycetes in caves . The scaptomyces . Tarin eptomyces .Various microbial strains isolated from soils have been shown to benefit crop production through mechanisms such as nutrient acquisition or suppression of pathogens. Wang et al. present an analysis of how the consortia of disease-suppressing microorganisms bring about enhanced protection when compared to individual strains . They goThe contributions to this Special Issue all point to the complexity of specific interactions that lead to shifts in microbial communities under specific conditions. Much remains to be done to unravel the specific components of these interactions.


Environmental transmission of bacteria, including multidrug-resistant organisms (MDROs), persists within hospitals despite routine cleaning. In prior work, we identified discordance between 16S profiles of room surfaces and culture of MDROs, suggesting unique environments for MDRO persistence within rooms. To build on this work, we used culture-enriched metagenomic sequencing to identify a broad range of viable taxa on surfaces with strain-level assignment and resistome profiling. Additionally, we evaluated the role of room proximity on sharing bacterial taxa and resistance genes between rooms.We selected three intensive care unit (ICU) rooms at the Hospital of the University of Pennsylvania with varying proximity and sampled 12 surfaces per room divided into three composite samples (Table 1). Sampling was repeated for 3 consecutive days. Samples underwent liquid media enrichment, DNA extraction and shotgun metagenomic sequencing. Strain-level assignment was performed with MetaPhlAn 4.0 and resistance genes assigned  via the Comprehensive Antibiotic Resistance Database (CARD).Each composite sample represents approximately 350 square inches of surface areaWe identified 40 strain-level assignments, with 18 shared between rooms. Within individual patient rooms, we identified microenvironments of bacterial strains and resistance genes  and an increased probability of detecting cephalosporin resistance genes as distance increased from the patient’s bed and neared bathroom sites . Using mixed effects regression, we found that distance between patient rooms was associated with decreased similarity in microbiomes of the distant in-room sites , while an opposite pattern was observed in the bathroom sites  .Rooms that were closer had greater similarity of microbiomes at the distant in-room site. Focused interventions on this microenvironment within patient rooms may be highest yield in reducing room-to-room transmission of bacteria. Shared microbiota at the bathroom site may be linked to plumbing infrastructure, but further research is needed to support this hypothesis.All Authors: No reported disclosures


Open Biology, titled ‘Advances in Quantitative Bioimaging’, proposes an overview of the latest advancements in quantitative bioimaging techniques and their wide-ranging applications. The articles cover various topics, including modern imaging methods that enable visualization on a nanoscale, such as super-resolution microscopy and single-particle analysis. These techniques offer unparalleled insights into complex molecular structures and dynamic cellular processes in situ, such as mapping nuclear pore proteins or tracking single histone deposition events throughout the cell cycle. The articles presented in this edition showcase cutting-edge quantitative imaging techniques coupled with advanced computational analysis capable of precisely measuring biological structures and processes. Examples range from correlating calcium release events to underlying protein organization in heart cells to pioneering tools for categorizing changes in microglia morphology under various conditions. This editorial highlights how these advancements are revolutionizing our understanding of living systems, while acknowledging challenges that must be addressed to fully exploit the potential of these emerging technologies, such as improving molecular probes, algorithms and correlation protocols.This special feature of  Recent progress in quantitative bioimaging technologies has empowered us to visualize complex molecular architectures, track individual proteins, compare cellular dynamics with nanoscale precision and single-molecule resolution. This leap forward holds significant potential for driving our understanding into uncharted territory by offering fresh mechanistic insights into living systems. In this special feature issue of . 2et al. discusses the power of combining super-resolution microscopy (SRM) with single-particle analysis (SPA). Several primary research articles in this special edition leverage advanced imaging methods to shed light on important cellular processes: Hurley et al. explore the relationship between calcium signalling events and the structural organization of calcium channels in cardiac muscle cells; Lando et al. use single-particle tracking to understand histone CENP-A molecule deposition in fission yeast; Ragaller et al. propose novel smart probes to measure membrane properties, which are crucial for understanding cellular processes. On the computational front, Martinez et al. have developed machine learning-based tools to characterize morphological alterations and behavioural shifts in microglia during neuroinflammation.This special edition features articles highlighting the ground-breaking applications of quantitative bioimaging techniques in various areas of biology. A review by Mendes et al., in their review entitled ‘Mapping molecular complexes with super-resolution microscopy and single-particle analysis’, discuss the combined power of SRM and SPA [Mendes  and SPA . SRM's aMiriam E. Hurley and her colleagues in their paper ‘Correlative super-resolution analysis of cardiac calcium sparks and their molecular origins in health and disease' have successfully linked calcium release events, referred to as ‘sparks’, with the nanoscale arrangement of calcium channels known as ryanodine receptors RyR2) in rat heart cells [ in rat hIn vivo assessment of mechanical properties during axolotl development and regeneration using confocal Brillouin microscopy’ by Riquelme-Guzmán et al. used confocal Brillouin microscopy to uncover tissue mechanical changes in vivo throughout development and regeneration in the highly regenerative axolotl, with a particular focus on limb and digit cartilage [The article ‘artilage . Probinget al., the authors used image analysis tools to examine the morphology and phagocytic behaviour of microglia in healthy and pathological conditions in vitro and in brain tissue [In the article titled ‘Characterization of microglia behaviour in healthy and pathological conditions with image analysis tools’ by Martinez n tissue . The autet al., in their work ‘Dissecting the mechanisms of environment sensitivity of smart probes for quantitative assessment of membrane properties', present smart probes—Pro12A, NR12S and NR12A—to assess membrane properties [The research presented in this special issue has important implications for various fields. For instance, Ragaller operties . In thei. 3The studies presented here highlight scientific progress made possible by advanced quantitative bioimaging techniques and image analysis. These tools allow us to better understand the intricate layers of cellular functions and expand our perception of how living systems operate across different scales. Over time, these advancements will help bridge the gap between experimental observation and theoretical vision, progressively tackling the formidable complexity intrinsic to biology.


Nitrospirota and Nitrospinota have received significant research attention due to their unique nitrogen metabolisms important to biogeochemical and industrial processes. These phyla are common inhabitants of marine and terrestrial subsurface environments and contain members capable of diverse physiologies in addition to nitrite oxidation and complete ammonia oxidation. Here, we use phylogenomics and gene-based analysis with ancestral state reconstruction and gene-tree–species-tree reconciliation methods to investigate the life histories of these two phyla. We find that basal clades of both phyla primarily inhabit marine and terrestrial subsurface environments. The genomes of basal clades in both phyla appear smaller and more densely coded than the later-branching clades. The extant basal clades of both phyla share many traits inferred to be present in their respective common ancestors, including hydrogen, one-carbon, and sulfur-based metabolisms. Later-branching groups, namely the more frequently studied classes Nitrospiria and Nitrospinia, are both characterized by genome expansions driven by either de novo origination or laterally transferred genes that encode functions expanding their metabolic repertoire. These expansions include gene clusters that perform the unique nitrogen metabolisms that both phyla are most well known for. Our analyses support replicated evolutionary histories of these two bacterial phyla, with modern subsurface environments representing a genomic repository for the coding potential of ancestral metabolic traits.The phyla  Bacteria and Archaea are presumed to have retained ancient traits due to the environments being analogous to early-Earth, in some cases isolated from the surface world on geologic timescales . Ge. GeNitroses Fig. . Gene clly Figs. , 8.Fig. Nitrospirota and Nitrospinota as direct relatives . In. InnxrABota Fig. . This susmatales . The verNitrospirota and Nitrospinota are markedly different than the later branching groups that have received much attention due to their ecological prominence, especially in the marine environment, and unique nitrogen-based metabolisms. Despite some differences in particular metabolic functions, the similar evolutionary histories of Nitrospirota and Nitrospinota demonstrate how multiple modes of evolution can shape closely related phyla that occupy similar ecological niches. These data demonstrate that gene loss, de novo origination, or lateral acquisition of new genes is a replicated pattern in later-branching clades of phyla whose extant subsurface-inhabiting members resemble ancestral lineages that initially evolved in a primordial habitat.Here we demonstrate that the ancestral metabolisms of early branching clades for the sister phyla Supplmental Methods and FiguresSupplemental Data 1Supplemental Data 2Supplemental Data 3Supplemental Data 4Supplemental Data 5Supplemental Data 6Supplemental Data 7


Burgeoning evidence demonstrates that effects of environmental exposures can be transmitted to subsequent generations through the germline without DNA mutations1,2. This phenomenon remains controversial because underlying mechanisms have not been identified. Therefore, understanding how effects of environmental exposures are transmitted to unexposed generations without DNA mutations is a fundamental unanswered question in biology. Here, we used an established murine model of male-specific transgenerational obesity to show that exposure to the obesogen tributyltin (TBT) elicited heritable changes in chromatin interactions (CIs) in primordial germ cells (PGCs). New CIs were formed within theIdegene encoding Insulin Degrading Enzyme in the directly exposed PGCs, then stably maintained in PGCs of the subsequent (unexposed) two generations. Concomitantly,IdemRNA expression was decreased in livers of male descendants from the exposed dams. These males were hyperinsulinemic and hyperglycemic, phenocopyingIde-deficient mice that are predisposed to adult-onset, diet-induced obesity. Creation of new CIs in PGCs, suppression of hepaticIdemRNA, increased fat mass, hyperinsulinemia and hyperglycemia were male-specific. Our results provide a plausible molecular mechanism underlying transmission of the transgenerational predisposition to obesity caused by gestational exposure to an environmental obesogen. They also provide an entry point for future studies aimed at understanding how environmental exposures alter chromatin structure to influence physiology across multiple generations in mammals.


Editorial on the Research TopicRecent advances in the assessment and management of thoracic traumaThoracic trauma presents a significant global public health challenge, comprising approximately 25% of all injuries and contributing to up to 50% of trauma-related fatalities . SurvivoHoepelman et al.). This initiative aimed to delve into the clinical outcomes and quality of life experienced by individuals after surgical rib fixation for flail chest injuries. The findings showed a significant trend, with low complication rates and a favourable one-year quality of life, as assessed with the EQ-5D-5l questionnaire. Nonetheless, it is pertinent to note that substantial variability was observed among patients in this context.The majority of the articles included in this compilation scrutinized outcomes following surgical stabilisation of rib fractures in distinct patient cohorts. A noteworthy endeavour was carried out by the NEXT study group, encompassing a prospective cohort study that spanned six institutions across Switzerland and the Netherlands (Zhang et al. embarked on an evaluation of outcomes following surgical stabilisation of rib fractures in elderly patients. Employing a single-centre, propensity score matching analysis, their investigation identified a nuanced dichotomy. Patients who underwent surgery exhibited a modestly prolonged hospital stay by an average of two days when compared with their counterparts receiving conservative treatment. Nevertheless, the surgical cohort demonstrated markedly improved rates of fracture healing and a shorter duration of analgesic regimens, delineating a balance between hospitalisation duration and therapeutic efficacy.Becker et al. contributed a matched pairs analysis by using data from the German trauma registry. Their study focused on determining the optimal timing for rib fracture surgery. The findings highlighted a distinct advantage for surgical stabilisation within the initial 48 h post-trauma, resulting in significantly shorter durations of intensive care unit and hospital stays compared to fixation performed between three and ten days following the injury.van Veelen et al., a unique perspective emerged as the authors explored outcomes after surgical fixation of chest wall fractures incurred during cardiopulmonary resuscitation efforts. It is worth mentioning that this retrospective, single-centre study included 19 patients, representing the largest reported cohort to undergo fracture fixation due to cardiopulmonary resuscitation. The authors reported a lack of complications associated with rib fixation, with only one infection observed following sternal fixation. Furthermore, the long-term follow-up demonstrated a favourable quality of life, as measured with the EQ-5D-5l questionnaire.Shifting our attention to the study by While the studies included in this Research Topic make substantial contributions to the evidence base, it is essential to acknowledge certain limitations. In the domain of thoracic trauma, the predominant body of research is characterized by retrospective observational studies and non-randomized prospective trials. Moreover, there is a pronounced heterogeneity in surgical techniques and outcome reporting, making comparisons between studies a challenging endeavour . RegardiWhile the studies featured in this Research Topic undeniably advance our understanding of the assessment and management of thoracic trauma, they also reveal a multitude of unanswered questions. Key areas requiring further research include the definition of optimal patient selection criteria for surgical stabilisation of rib fractures. Currently, it remains uncertain whether fixation should be extended to include a broader spectrum of non-flail chest fracture patterns. There is also a pressing need for comparative effectiveness studies examining different surgical techniques. The role of thoracoscopic visualization in fracture management is an interesting topic that also requires more comprehensive evaluation. Moreover, the absence of standardized protocols for perioperative analgesia and rehabilitation is conspicuous. In addition, there is a dearth of research into long-term, patient-centred outcomes, such as persistent disability and return to work. Formal cost-effectiveness analyses comparing surgical stabilisation to non-operative management are also relatively absent. To address these knowledge gaps effectively, it is necessary to conduct high-quality randomised controlled trials with standardised treatment protocols and well-defined outcomes. Multicentre studies can facilitate larger sample sizes, leading to improved generalizability. Overall, continued research is crucial in honing best practices for thoracic trauma care and ultimately enhancing outcomes for these patients. The studies presented in this Research Topic are indeed promising strides forward, but they highlight that a plethora of unanswered questions awaits exploration in future research.Thoracic trauma continues to exact a substantial toll on global health, contributing significantly to morbidity and mortality rates. The research shared in this Topic signifies prominent advancements, yet further investigations are imperative to delineate optimal practices more precisely. Persistent research efforts in this pivotal domain are warranted to mitigate the global public health repercussions of chest injuries and ultimately improve patient outcomes.


Editorial on the Research TopicArtificial intelligence and advanced technologies in neurological surgerySurgical treatment of neurologic disorders has always benefited from technologic advancements in operative techniques and equipment, imaging, predictive analytics, and many others. In recent years, almost all neurosurgical subspecialties have seen a substantial effort to develop, validate, and utilize artificial intelligence and machine learning models in a clinical manner . Unique In this research topic, we explore recent technologic advancements made in neurosurgery, including supervised machine learning models aimed at predicting postoperative survival in glioma patients, customized 3D printing and laser navigation applied to minimally invasive hematoma evacuation, an advanced cerebrospinal fluid (CSF) drainage method for use in posterior fossa tumor resection, and a novel endoscopic approach for treatment of oculomotor nerve palsy, all of which may help to inspire future work in similar topics of interest.Li et al. at an academic institution in China compared the accuracy of traditional statistical models and supervised machine learning models in predicting patient survival following resection for gliomas. Multivariate Cox proportional hazards regression, support vector machine (SVM), random survival forest (RSF), and tree and component gradient boosting (GB) models were evaluated using patient-specific clinical and biomarker variables and were subsequently compared in performance using concordance indexes. Predictably, the traditional Cox proportional hazards regression model performed poorly in both training and testing sets when compared to the supervised machine learning models, of which the GB models produced superior performance in predicting survival. Time-dependent survival performance was additionally assessed between tree GB and component GB models, which displayed good discrimination (area under the curve >0.8) at all evaluated time points. The authors of this study recognized many important patient variables found to influence survival based on these models, including functional status, tumor size, and resection type, which can be utilized to develop patient-specific perioperative plans with the goal of extending survival and limiting morbidity.At the forefront of advancements in neurosurgical outcomes analysis is artificial intelligence and machine learning. A retrospective cohort study conducted by Yuan et al. studied hypertension-induced intracerebral hematoma external drainage techniques based on two new methods in a retrospective analysis: three-dimensional (3D) printing and laser guidance for navigation during puncture and debridement. In the 3D printing method, computed tomography (CT) image reconstructions were utilized to plan endoscope entry and trajectory into hematomas, which were then 3D printed in combination with patient face molds for customized intraoperative guidance. Laser guidance additionally utilized Xper-CT scans and 3D reconstructed images to emit a continuous focus directed towards the hematoma throughout the duration of the procedure. In direct intraoperative and postoperative comparisons, patients treated with 3D printing assistance were found to have significantly shorter operative durations than those treated with laser navigation assistance. However, outcomes including hematoma clearance rate, Glasgow Coma Sale improvement, and hospitalization time were similar between the two groups. The authors noted advantages to both techniques, including real-time navigation feedback and customized care, but may come at increased costs or extended preoperative setup time. Minimally invasive techniques in neurosurgery can be further improved with advancements in imaging and navigation, such as 3D printing and laser guidance.Beyond predictive analytics, developments in imaging technology have been utilized to improve intraoperative techniques. Recent work done by Roethlisberger et al. In their recent work, the authors utilized image-guided ipsilateral trigonal ventriculostomy for cerebellar pressure control during retrosigmoid craniotomy for cerebellopontine angle (CPA) tumor resection, after which outcomes were evaluated in a cohort of 52 patients. Prior to durotomy, the authors performed ventriculostomy of the ipsilateral trigone of the lateral ventricle using CT or magnetic resonance image (MRI) guidance, advancing an external ventricular drain (EVD) to release CSF and decompress the cerebellum. In the prospectively evaluated cohort, cerebellar swelling was avoided in 98% of cases using this technique. However, authors reported an 8% incidence of postoperative intracerebral or intraventricular hemorrhage without clinical complications. Ultimately, the authors recommended consideration of this technique for large posterior fossa tumors but not for small lesions.Developments in image guidance technology have been additionally explored in cerebrospinal fluid (CSF) diversion approaches to reduce cerebellar contusion, such as in the study described by Wang et al. The authors of this work describe detailed anatomic landmarks encountered in their endoscopic approach, focusing on correct identification of the optic strut triangle, consisting of the internal carotid artery, optic nerve, and superior orbital fissure, in preparation for oculomotor nerve decompression. Hollowing of the optic strut by sequential drilling under endoscopic visualization achieved decompression of the optic and oculomotor nerves, resulting in rapid neurologic symptom improvement in 2 presented patient cases. Although still requiring further trials, the techniques described in this study may introduce alternatives to invasive approaches that arise with often extensive complications.New surgical methodologies for conditions previously lacking standardized treatment plans have been developed with the aid of technological advancements including endoscopic approaches. A novel transnasal endoscopic approach for treatment of traumatic oculomotor nerve palsy associated with superior orbital fissure fracture is described in a recent study by Advancements in clinical and intraoperative technology have enabled neurosurgeons to create patient-specific management plans and improve postoperative outcomes for a range of conditions. In this research topic, four original studies were included that demonstrate the breadth of developments made in artificial intelligence-based predictive analytics, intraoperative imaging and navigation technologies, and novel cranial approaches aimed at improving patient outcomes. Further incorporation of machine learning algorithms, reconstructive software, and minimally invasive technology into daily medical practice will allow future generations of surgeons to provide personalized care to patients based on unique comorbidities and anatomic variations.We certainly live in an era of rapid technologic advancement, but this also comes with great responsibility. As physicians and surgeons, it is our duty to question these technologies and understand their limitations before implementing them in our clinical practice. However, it is also our duty to embrace and use them when they can improve our patients’ lives. As our techniques and devices continue to evolve, we look forward to exploring the positive impacts made to neurosurgery and beyond.


The need for high quality evidence is recognized for optimizing practices of parenteral nutrition (PN). The purpose of the present systematic review is to update the available evidence and investigate the effect of standardized PN (SPN) vs. individualized PN (IPN) on protein intake, immediate morbidities, growth, and long-term outcome in preterm infants. A literature search was performed on articles published in the period from 1/2015 to 11/2022 in PubMed and Cochrane database for trials on parenteral nutrition in preterm infants. Three new studies were identified. All new identified trials were nonrandomized observational trials using historical controls. SPN may increase weight and occipital frontal circumference gain and lower the value of maximum weight loss. More recent trials suggest that SPN may easily increase early protein intake. SPN may reduce the sepsis incidence, but overall, no significant effect was found. There was no significant effect of standardization of PN on mortality or stage ≥2 necrotizing enterocolite (NEC) incidence. In conclusion SPN may improve growth through higher nutrient  intake and has no effect on sepsis, NEC, mortality, or days of PN. Parenteral Nutrition (PN) is a lifesaving therapy for preterm infants. PN is indicated when oral or enteral nutrition is not possible, insufficient, or contraindicated in order to avoid undernutrition and related adverse consequences. The nutrient stores of very low birth weight  and extremely low birth weight  preterm infants are low. Bridging PN ensures adequate fluid intake and nutrient supply for weight gain and possibly neurodevelopmental long-term outcome. VLBW infants are vulnerable to postnatal growth failure because the gut is immature, and provision of nutrients is challenging. The evidence showing the beneficial effects of enhanced PN to VLBW infants is accumulating. Providing amino acids and energy immediately after birth with PN is a standard practice to promote positive nitrogen retention . SP. SP18]. However, the currently available commercial SPN solutions may not be the optimum approach. Commercial SPN may need an additional amino acid supply to achieve recommended target intakes and consequently adequate growth defined as intrauterine growth velocity .Beyond improved nutrient intake, the umbrella aim in introduction of SPN is to improve patient safety  possibly at the cost of increased PN solution wastage . Due to However, SPN did not significantly prevent hospital associated complications . EspeciaStandard PN Solutions (SPN) Should Generally Be Used over Individualized PN Solutions (IPN) in the Majority of Preterm Infants, Including VLBW Premature Infants .Individually Tailored PN Solution should Generally Be Used When the Nutritional Requirements Cannot Be Met by the Available Range of Standard PN Formulations  .It has been estimated that the majority of preterm infants receiving PN via central catheters may actually be treated by SPN, although, the optimum composition is not known ,38. SPN Adequately Powered Randomized Controlled Trials Based on Up-To-Date Parenteral Nutrition Recommendations Are Required to Evaluate the Real Clinical Benefits of SPN vs. IPN .Strengths of the present review are its exhaustive search of the available literature, reproducibility, systematic assessment of evidence and grading of recommendations. However, there are important limitations. Neonatology is rapidly developing and changing. E.g., nutritional recommendations changed several times within the last 20 years. Using historical controls rather than contemporaneous controls carries a high risk of bias and grossly limits the level of evidence. Improvements in nutritional status may rather be a consequence of increased nutritional awareness than a consequence of new developed PN approaches. The observed effects may have been noticed by chance and adequately powered, randomized controlled trials based on up-to-date parenteral nutrition recommendations are urgently required to evaluate the real clinical benefits of SPN bags. Given current parenteral nutrition recommendations a considerable proportion of infants of the reported trials are undernourished. In addition, the composition of SPN and IPN nutritional regimens and consequently the observed nutritional status, varied across and within the different studies, limiting the validity of the results of the meta-analyses. In the clinical experience of the authors, one SPN does not fit all preterm infants. The smaller the infants are, the more often adjustments are required, commercial SPN bags are more expensive than hospital pharmacy produced SPN bags, and finally commercial SPN bags still require pharmacy-based adjustments .We conclude that SPN may improve growth through higher nutrient  intake and has no effect on sepsis, NEC, mortality, or days of PN. These observations may have been noticed by chance and adequately powered randomized controlled trials are required to evaluate the real clinical benefits of SPN.


Arachis hypogaea is a segmental allotetraploid in the section Arachis of the genus Arachis along with the Section Rhizomataceae. Section Arachis has several diploid species along with Arachis hypogaea and A. monticola. The section Rhizomataceae comprises polyploid species. Several species in the genus are highly tolerant to biotic and abiotic stresses and provide excellent sets of genotypes for studies on differential gene expression. Though there were several studies in this direction, more studies are needed to identify more and more gene combinations. Next generation RNA-seq based differential gene expression study is a powerful tool to identify the genes and regulatory pathways involved in stress tolerance. Transcriptomic and proteomic study of peanut plants under biotic stresses reveals a number of differentially expressed genes such as R genes , pathogenesis related proteins  and defense related genes  that are the most consistently expressed genes throughout the studies reported so far. In most of the studies on biotic stress induction, the differentially expressed genes involved in the process with enriched pathways showed plant-pathogen interactions, phenylpropanoid biosynthesis, defense and signal transduction. Differential gene expression studies in response to abiotic stresses, reported the most commonly expressed genes are transcription factors , LEA proteins, chitinase, aquaporins, F-box, cytochrome p450 and ROS scavenging enzymes. These differentially expressed genes are in enriched pathways of transcription regulation, starch and sucrose metabolism, signal transduction and biosynthesis of unsaturated fatty acids. These identified differentially expressed genes provide a better understanding of the resistance/tolerance mechanism, and the genes for manipulating biotic and abiotic stress tolerance in peanut and other crop plants. There are a number of differentially expressed genes during biotic and abiotic stresses were successfully characterized in peanut or model plants (tobacco or Arabidopsis) by genetic manipulation to develop stress tolerance plants, which have been detailed out in this review and more concerted studies are needed to identify more and more gene/gene combinations.Peanut  Arachis hypogaea L.) is one of the most important legume crops economically worldwide and its seed a source of high quality edible oil, proteins, minerals and vitamins. It is widely cultivated across developing countries from semi-arid tropics to subtropical regions (st and 2nd respectively based on FAOSTAT data for the year 2020 (Peanut ( regions . China aear 2020 . ProductArabidopsis (135 Mb), rice (430 Mb), Medicago (904 Mb) and soybean (1.1 Gb). Large genome size and polyploidy nature  is quite large in size  in contry nature  hamper cArachis comprises many wild species at different ploidy levels that exhibit resistance/tolerance to several biotic and abiotic stresses, which makes it a rich resource of suitable genes for commercial applications. Some wild species were deployed in the experiments with the aim of transferring the genes for tolerance/resistance to different stresses from the related wild species to the cultivated peanut genotypes in crop improvement programs  is well-established and versatile technique with application to detects the enriched sequences in specific tissues at specific time points and used to characterize differential gene expression of plant responses to biotic and abiotic stresses . To inveRalstonia solanacearum , late leaf spot (LLS), rust, aflatoxin contamination and bacterial wilt disease by nacearum Figure 1nacearum . To manaCercospora arachidicola [Hori] and Phaeosariopsis personata [Berk & M. A. Curtis] respectively, are the major foliar fungal diseases in peanut, which cause complete defoliation of leaves leading to significant losses in plant productivity upto 50 to 70%  protein, transcription factors , peroxidases and genes related to secondary metabolites in the resistant variety upon pathogen invasion, while there was downregulation of genes including F-box, cytochrome p450, LRR protein kinase and terpene synthase that are associated with several biological processes in the susceptible variety. There is another recent report of DEGs of resistant and susceptible peanut cultivars to early leaf spot infection, which revealed the expression of resistance associated genes like CC-NB-LRR (NLR) type resistance gene, Phytoalexin deficient 4 (PAD 4) and polyphenol oxidase (PPO) that play important roles in mediating early leaf spot resistance  and late leaf spot (LLS) diseases also collectively known as ‘Tikka’ disease caused by 0 to 70% . Early l0 to 70% . Advance0 to 70% . Upon pa0 to 70% . Candidasistance . IdentifPheaosariopsis personata (Cercospora personata) is the most devastating disease in peanut and can lead to yield losses up to 70% under favorable conditions . Furthermore, they identified TDFs (transcript derived fragments) that are associated with defense, signal transduction and metabolism, and further reported several genes for proteins involved in hypersensitive cell death, cell wall fortification and defense mechanism. Differential gene expression analysis in wild type and mutant peanut cultivar against late leaf spot pathogen was also reported by There are several methods available to study differential gene expression during plant-pathogen interactions in peanut, such as Genefishing DEG kit, suppression subtractive hybridization (SSH), cDNA-AFLP and cDNA-microarray techniques . These ansferase . In an e pathway . Kumar aR-genes (381) associated with leaf spot disease was predicted by a RGA-PCR based technique , receptor like proteins (RLPs) and receptor like cytoplasmic kinases (RLCKs), which co-ordinate and initiate protection responses against the invading pathogen , as potential resistance (R) genes play important roles in recognition and activation of disease resistance responses and the identification of putative peanut echnique . Furtherpathogen . Recentlpathogen .Puccinia arachidis that often occurs along with leaf spot disease also because of its rain fed nature, which leads to further yield losses. There are several studies on quantitative trait locus (QTL) in cultivated peanut to identify molecular marker or genetic map for rust resistance  technique, which is based on next-generation sequencing (NGS) for genotyping and this resulted in the identification of six candidate genes for rust resistance  protein were significantly upregulated in the resistant genotype revealing their important roles in plant defense mechanism. These findings will be helpful in understanding the molecular mechanism of peanut plant defense against the rust pathogen and may assist the breeders in the development of resistant varieties through molecular approaches.Rust is another serious foliar disease of peanut caused by sistance , but thesistance . RecentlAspergillus flavus is an opportunistic saprophytic fungal pathogen that infects a number of seed crops   and microarray technology. Furthermore, they identified sixty two genes in the resistant cultivar that were upregulated in response to Aspergillus infection including defense related genes like PR10 protein, defensin, calmodulin, metallothionein like protein, Cu/Zn superoxide dismutase etc. and a large number of hypothetical proteins as the complete genome sequence was not available at that point of time. A similar study has reported the identification of Aspergillus resistance genes in peanut cultivars by comparing transcriptome profiles in resistant and susceptible peanut genotypes using microarray technique  and identified hub genes positively associated with resistance to A. flavus in peanut. Their analysis also revealed that upregulation of genes encoding pathogenesis-related protein (PR10), MAPK kinase, 1-aminocyclopropane-1-carboxylate oxidase (ACO1), a serine/threonine kinase, cytochrome P450, pectin esterase, SNARE protein SYP121, pentatricopeptide repeat (PPR) protein and disease resistance response proteins in the esistant peanut cultivar that play major roles in resistance to infection from A. flavus. These studies provide new insights into the molecular mechanism of peanut defense against aflatoxin contamination and further the safety and management of peanut products for human consumption.on etc.)  and prodon etc.) . Peanut nditions  that cauechnique . Their rchnology . This grRalstonia solanacearum) is the most devastating soil borne disease in peanut (Arachis hypogaea L.) leading to significant yield losses because of reduced plant stand on the field at the seedling stage of the crop. Molecular mechanism of peanut response to R. solanacearum remains unnknown and needs to be studied in detail. In an attempt to explore the molecular mechanism of bacterial wilt resistance in peanut using Genefishing DEG kit, several differentially expressed candidate genes encoding a cyclophilin, ADP-ribosylation factor, antibacterial peptide and disease resistance response proteins were identified by studying the differences in gene expression between inoculated and control peanut seeds  into six groups as resistant/susceptible response genes, which included PAMPs induced resistant/susceptible response genes and type III effectors (T3Es) induced resistant/susceptible response genes. Further more, KEGG enrichment pathway analysis of differentially expressed genes showed that MAPK signaling, plant-pathogen interaction, and plant hormone signal transduction pathways were upregulated. WRKY Transcription factors play an important role in plant disease resistance. Differential gene expression analysis of WRKY genes in cultivated peanut displayed different expression patterns in resistant and sensitive peanut cultivars infected with R. solanacearum. The identification of candidate WRKY genes with possible role in peanut resistance to R. solanacearum infection may contribute in the improvement of a resistant peanut variety , pathogenesis related proteins , defense related genes , glutathione S-transferase) and the genes involved in phenylpropanoid pathway are the most commonely expressed ones (Arabidopsis) through genetic manipulation and successfully developed biotic stress resistant plants  for functional characterization of genes that integrated into the corresponding genome. There are limited reports on differentially expressed peanut genes for further characterization using genetic engineering to develop stress tolerance plants. The transgenic plants that were developed for functional characterization of diffrentially expressed peanut genes are given in Several peanut genes, which were differentially expressed during biotic stress conditions were further characterized by transgenic approach. Presently, genetic engineering technique such as Cyclophillin (AdCyp) gene that was differentially expressed in wild peanut A. diogoi during late leaf spot infection was incorporated into tobacco genome under a constitutive promoter through the Agrobacterium method and this resulted in enhanced resistance to Ralstonia solanacearum and reduced susceptibility toward Phytophthora parasitica var. nicotianae. Further, the resistance phenomenon was associated with the up-regualtion of various defense related genes  genotype enhanced resistance to late leaf spot pathogen and this expression was associated with the co-expression of resistance-related genes, CC-NB-LRR and some protein kinases, while heterologous expression in tobacco enhanced its resistance against Phytophthora parasitica var. nicotianae, Alternaria alternata var. nicotianae and Rhizoctonia solani  like cell death and positively regulated defense response genes. Furthermore, ectopic expression of AdVPE in tobacco resulted in enhanced resistance against Phytophthora parasitica var. nicotianae, Alternaria alternata var. nicotianae and Rhizoctonia solani (AdZADH2) was also differentially upregulated in Arachis diogoi, a wild peanut upon challenge with the late leaf spot (LLS) pathogen. Transient over-expression of AdZADH2 under an estradiol inducible promoter (XVE) exhibited hypersensitive response (HR)-like cell death in tobacco leaf and the cell death was associated with the upregulation of antioxidative enzymes such as SOD, CAT and APX and pathogenesis-related (PR) proteins (Vacuolar processing enzymes (VPEs) are cysteine proteases exhibiting caspase-1-like activity, which mediate cell death and upregulated during pathogen infections . AdVPE wa solani . A novelproteins .R gene products, which can directly or indirectly recognize pathogen effector proteins and induce signaling pathways for resistance against the impending pathogen  in Nicotiana benthamiana and AhRLK1 overexpression in transgenic tobacco significantly enhanced resistance to R. solanacearum by triggering EDS1 and PAD4 in the R gene signaling pathway that possibly contributed to defense responses against the pathogen  protein was found to be upregulated in both approaches . Wang etranensis .Soil salinity is another major abiotic stress factor that affects plant growth and development reducing crop productivity. Peanut is considered to be a moderately salt sensitive species, which makes salinity a liming factor for peanut cultivation. In general, plants respond to salt stress by changing their gene expression, which leads to an increase in the concentrations of several metabolites to protect themselves against high salinity. Transcriptome study has become an important tool for studying the possible mechanism and elucidating signal pathways underlying salt stress tolerance in plants. However, limited information is available about the networks of gene expression regulation related to salt stress in peanut. A microarray study has been carried out in peanut roots under salt stress conditions, which revealed that metabolic pathway, biosynthesis of unsaturated fatty acids and plant-pathogen interaction were upregulated, while photosynthesis and phenylalanine metabolism were downregulated . TranscrTIP3 gene is significantly upregulated in response to salt stress. Furthermore, TIP3 overexpression in Arabidopsis resulted in enhanced seed germination under salt stress corroborating its important role in seed germination under salt stress.A comprehensive study of drought tolerance in cultivated peanut has been performed under salt stress environment and this concurrent stress application has detected several differentially expressed genes and transcription factors (TFs) such as MYB, WRKY, bHLH and AP2/ERF in response to salinity. Moreover, differentially expressed genes related to cell wall growth, antioxidant and peroxidase activity were significantly enriched while DEGs related to metabolic processes, oxidoreductase and catalytic activity were downregulated . AquaporPMP34 that encodes a peroxisomal nicotinamide adenine dinucleotide carrier, and Sodium/H+ antiporters (NHX7 and NHX8), and downregulated expression of proline dehydrogenase 2. This resulted in the accumulation of soluble sugars and proline to maintain the osmotic balance with an additional up-regulation of the aquaporin gene TIP2-1. Moreover, exogenous EBL application upregulated the expression of NHX7 and NHX8 to balance the ion concentrations across membranes with increased peroxidase activity to scavenge reactive oxygen species, and glutathione levels to improve salt tolerance in peanut.Brassinosteroids (BRs) are essential for plant growth and development, and play crucial roles in stress tolerance . HoweverLow temperature is a major environmental factor that limits plant growth, development and yield. Cold stress causes different degrees of damage to the peanut plant at the seedling, flowering, and all other growth stages. A transcriptome or differential gene expression analysis in response to cold or metal stress could provide a deeper insight into the transcriptional mechanism of plants and their protective role against damage. Differentially expressed peanut genes in response to different temperature regimes was carried out using suppression subtractive hybridization (SSH) for cultivated peanut seeds and this study identified genes that are involved in functional categories including metabolism, defense, stress response, signal transduction and transcriptional regulation .2H2, ERF, MYB, NAC and WRKY in response to cold stress, which could be crucial for peanut cold tolerance  are non-coding small RNAs that play important roles in various abiotic stresses by modulating gene expression. However, there is no report on the role of miRNAs in cultivated peanuts during cold stress. Very recently, cold-responsive miRNAs and candidate target genes were identified in peanut cold tolerant and sensitive varieties during cold stress using a deep sequencing method. Their analysis revealed several specific cold responsive microRNAs, which appear to mediate cold response. And, several transcription factors including WDRL, GRF and ARF, and genes such as  peanuts .EIL (EIN3-like), which reveals a link between ethylene signal transduction and Al resistance related genes in peanut (Aluminum (Al) is the most abundant metal element in the Earth’s crust, and has toxic effects on plant growth in acidic soils . The tarn peanut . An ultrn peanut . The samn peanut .Arachis accessions under drought, salt, cold and metal stress conditions will provide a better understanding of the tolerance mechanism, and will further provide reference for improving abiotic tolerant peanut cultivar through genetic manipulation.Differential gene expression study of peanut plants in response to abiotic stresses, reported by the most of the studies Table 3,Agrobacterium tumefaciens mediated genetic transformation. There are several reports on the characterization of differentially expressed genes in peanut and/or model plants to develop stress resistance plants. The list of transgenic plants deploying differentially expressed peanut genes is provided in Further characterization of differentially expressed genes during various abiotic stresses by genetic manipulation like transgenic approach would aid in developing stress tolerance peanut cultivars, which can help achieve increased crop productivity. Till today, different types of transgenic plants were generated by genetic engineering technique using AhERF019 in Arabidopsis resulted in enhanced tolerance to drought, heat, and salt stresses (LEA) gene was differentially expressed in wild peanut upon infection with late leaf spot pathogen and overexpression of AdLEA in tobacco resulted in enhanced tolerance of plants to dehydration, salinity and oxidative stress. Furthermore, AdLEA overexpressed tobacco plants maintained better photosynthetic efficiency under drought conditions implying that it could be a potential gene for genetic modification in crop plants  gene and overexpression of AdGolS3 gene in Arabidopsis resulted in increased raffinose production and tolerance to drought, salt and osmotic stresses  plays a significant role in regulating gene expression in plant responses to stresses and was identified from peanut EST sequences available in the NCBI database. Ectopic expression of stresses . Late Emp plants . In silistresses . A CBL-in plants .TIP3 was found differentially upregulated under salt stress condition in cultivated peanut. Furthermore, the ectopic expression of AhTIP3;1 contributed to improved seed germination under salt stress in Arabidopsis  was found upregulated during plant-microbe interaction in peanut and further, the overexpression of AhCytb6 gene in tobacco resulted in enhanced seed germination under N2 deficit and salt stress conditions  gene was observed to be upregulated  was found to be differentially expressed in the wild peanut after late leaf spot infection  stress in tobacco  are important endogenous non-coding RNAs with an average size of 21 to 23-nt in length that regulate gene expression in plants and animals by regulating mRNA expression post-transcriptionally . RNA polAspergillus flavus  under Al stress, root tips of Al-sensitive and Al-tolerant peanut cultivars were analyzed under Al stress condition. Further intergrated analysis of transcriptomics, sRNAs, and degradome data sets revealed differential expression of 89 miRNA-mRNA interactions that might be involved in PCD under Al stress . In respArachis species using differential expression analysis for stress tolerance. However, commercially cultivated transgenic plants were not developed in peanut so far using the identified genes. There could be several reasons for this. Since peanut is a crop of high commercial significance whose produce is of prime importance in human nutrition, it is not easy to get regulatory approvals from the respective Governmental authorities across the world for the deployment of transgenic plants for field- level cultivation. Probably, many major efforts were not made in peanut in this direction because of this reason. With the advent of genome editing technology for various plant systems, the future is very optimistic for developing genome edited crops including peanut for stress tolerance as genome-edited crops might get regulatory approvals more easily compared to transgenic plants.The biological stresses mainly comprise attack from pathogenic fungi, bacteria, viruses, nematode and insects, whereas the abiotic constraints include drought, salinity, cold, metal, waterlogging and temperature changes. To overcome these various stress environments, plants must be capable of tolerating these stress conditions by modulating their metabolism in the right direction. In this direction, the genetically modified crops are considered to be good candidates for sustainable food production. It is to be noted that there were several genes identified in Agrobacterium tumefaciens or Rhizobium rhizogenes mediated genetic transformation technique through either in vitro or in planta methods for improvement. Transgene expression is highly dependent on the promoter selection for gene expression followed by protein synthesis. Several promoters of various origins have been tested for transgene expression besides viral gene promoter CaMV35S in peanut. In the backdrop of this, no meaningful progress of gene editing technique that is gaining enormous attention recently has been made so far in peanut.Genome modifications allow improvements in stress and weed tolerance, plant breeding procedure, productivity, food quality and safety. However, introduction of genetically modified crops may adversely affect the environmental conditions exercising harmful effects on animals and humans and this has been the main concern of the environmentalists . There aThere are several powerful plant-targeted genome editing tools for functional and applied genetic manipulations that include engineered nucleases, such as Zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regulatory interspaced short palindromic repeats (CRISPR) systems .Recently developed prokaryotic immune system based CRISPR technology is a high-throughput genome editing tool that has been found to be very successful in a variety of plant species . The CRIBiotic stress tolerance where crop yield and quality are largely affected by biotic stresses like viral, fungal, bacterial and insects were improved by using CRISPSR/Cas9 system. For instance, wheat and rice have been made tolerant to their respective viral, bacterial and fungal diseases . Tomato,FAD2) gene in peanut. This gene codes for the desaturase that is responsible for the conversion of monounsaturated oleic acid into polyunsaturated linoleic acid. The knock out mutation in FAD2 resulted in high oleic acid content in peanut oil (AhNFR gene through hairy root transformation system and validated the function for nodule formation in peanut. Using the CRISPR/Cas9 system, AhFatB genes Arahy4E7QKU and ArahyL4EP3N were knocked out in peanut, and mutation at Arahy.4E7QKU displayed low palmitic acid and high oleic acid content significantly improving oil quality in peanut (Application of CRISPR/Cas9-based gene editing technique would provide genetic improvement in peanut cultivars against biotic and abiotic stresses. However, application of this breakthrough gene editing technology to peanut is still rare. Till date, there is limited report of CRISPAR/Cas9-based gene editing in peanut. This technique is used for knocking out fatty acid desaturase2 (anut oil . Shu et n peanut . PotentiArachis divided into various Sections is a boon to the investigators undertaking differential expression studies using the previously popular techniques like cDNA-AFLP and the highly efficient RNA-Seq studies using the Next Generation Sequencing technologies that became available recently. The goal of these studies is to understand molecular mechanisms during stress conditions and identify the genes responsible for stress tolerance in peanut plants. Depending on the availability of financial resources, the choice of the technology can be made. The primary advantage with the NGS technologies is that they give faster results on gene expression at whole genome level compared to the earlier technologies. The wild Arachis germplasm offers excellent material for the differential expression studies because of the availability of genotypes that are both susceptible and highly resistant to corresponding trait, be it biotic or abiotic stress tolerance. The alloploid species belonging to the Section Rhizomataceae are very highly tolerant to abioic stresses like high temperature and water limited conditions. Hence, the germplasm can be used for identifying tolerance genes within the tolerant genotype itself by comparing sets with and without treatments. Otherwise, a more efficient option would be to compare the resistant and susceptible genotypes at the same ploidy level with and without suitable treatments. Information from such studies could lead to novel genes that would actually decide the trait under consideration. The genes identified can be used in other related legume crop plants. This is particularly because of the possible colinearity of different related genomes in legumes. Hence, the opportunities are enormous when the investigator uses the material judiciously.The wild germplasm belonging to the genus DK: Conceptualization, Writing – original draft. PBK: Conceptualization, Writing – review & editing.


Liquid biopsy assays for minimal residual disease (MRD) are used to monitor and inform oncological treatment and predict the risk of relapse in cancer patients. To-date, most MRD assay development has focused on targeting somatic mutations. However, epigenetic changes are more frequent and universal than genetic alterations in cancer and circulating tumor DNA (ctDNA) retains much of these changes. Here, we review the epigenetic signals that can be used to detect MRD, including DNA methylation alterations and fragmentation patterns that differentiate ctDNA from noncancerous circulating cell-free DNA (ccfDNA). We then summarize the current state of MRD monitoring; highlight the advantages of epigenetics over genetics-based approaches; and discuss the emerging paradigm of assaying both genetic and epigenetic targets to monitor treatment response, detect disease recurrence, and inform adjuvant therapy. MRD does not cause clinical symptoms and is not detectable by traditional methods such as imaging  or abnormal blood serum protein levels. MRD assays must be sensitive enough to detect as little as 1 cancerous cell in a background of 1 million noncancerous cells. This extreme sensitivity makes MRD assay development complex, but overcoming this barrier imbues MRD assays with the potential for much earlier detection of cancer recurrence than traditional methods, and thus earlier intervention with adjuvant chemotherapy or second and third-line treatments.Detection of MRD indicates the failure of treatment to eliminate all cancerous cells which implies greater probability of future disease recurrence. Monitoring MRD signals during the remission period allows early detection of disease progression . Assayin22.1DNA methylation is a covalent modification of the DNA strand that, in mammals, occurs almost exclusively within the sequence context of cytosine followed by guanosine (CpG) dinucleotides. The genomic acquisition of DNA methylation is an essential developmental process with diverse roles including repressive associations at gene promoters and mobile genetic elements or, conversely, increased transcriptional activity when found within gene bodies [reviewed in Greenberg & Bourc’his ]. GenomeMost DNA methylation-based liquid biopsies target cancer-specific aberrations that separate cancer from its normal tissue counterpart. However, within healthy tissues DNA methylation exhibits highly cell type specific patterns across the genome . This un2.2The term “fragmentomics” describes the study of ccfDNA fragmentation patterns and the use of these patterns to decern biologically relevant information such as nucleosome positioning. Although few assays to-date utilize ccfDNA fragmentation patterns, numerous properties of ctDNA compared to healthy ccfDNA instill fragmentomics with the potential for use in oncological assays ; (ii) shAs for nucleosome positioning, ccfDNA fragmentation patterns downstream of transcription start sites have been shown to reflect differential nucleosome positioning between expressed and unexpressed genes . These cGoing forward, the most sensitive and universal MRD assays will likely combine these epigenomic approaches. Until recently, the combination of DNA methylation and fragmentomics in a single assay was not possible due DNA methylation detection relying on bisulfite conversion . Bisulfi3The marketplace for MRD liquid biopsy assays is new, but several MRD diagnostic tests have now received early regulatory approvals Table 1.While there are only a few somatic mutation-based MRD panels in the marketplace, there are a host currently in development and undergoing clinic trials. For example, Strata Oncology are also exploring a two-staged tumor-informed panel design in their Sentinel trial for cancer recurrence . BurningNotably, genetic mutations are not broadly shared across cancers and the two-stage solutions to this shortcoming are limited by tumor heterogeneity and the volume of a tissue biopsy. That is, because only a subset of a tumor is sequenced there is still a high probability that mutations will be missed. However, a multi-omics approach can augment this shortcoming. The greater frequency and universality of epigenetic changes makes them more sensitive and universal markers for evidence of cancer after curative intent treatment, and somatic mutation testing highlights actionable variants that can inform subsequent treatment. This promise of MRD assays that incorporate epigenetics with somatic mutation testing is being realized. Guardant Health has combined somatic mutations, DNA methylation and fragmentomics into their LUNAR panel, which they have progressed into clinical trials for both primary detection and MRD of early-stage colorectal cancer .Multiple companies are also progressing purely epigenetic-based MRD panel approaches. MethylGene is undertaking a clinical trial on multiple myeloma patients that will utilize DNA methylation sequencing of ctDNA for MRD detection . While GWhile most product development for MRD is concentrated around sequencing large panels of markers, simple DNA methylation-based PCR tests can also be highly efficacious. Colvera, developed by Clinical Genomics, is available as an LDT in the USA and has Medicare coverage for MRD and recurrence monitoring of colorectal cancer. This methylated ctDNA test detected 66.0% of recurrence, significantly higher than the 31.9% sensitivity of carcinoembryonic antigen (CAE), the current standard of care , and alsInterestingly, a simple well-designed PCR test can have adequate diagnostic power when compared to a large NGS panel. This is illustrated when comparing the rates of primary detection of colorectal cancer across the GRAIL-sponsored circulating cell-free genome atlas (CCGA)  study T (Trial i4Liquid biopsy is a powerful, multifaceted, and minimally invasive method for MRD detection and hence for monitoring therapeutic response, disease recurrence, or patient resistance to therapy. Although a relatively new field, liquid biopsy assays are showing promising results when compared to current standards of care. Two-staged somatic mutation approaches, where tumor sequencing informs MRD assay targets, allow clinicians to track actionable mutations and monitor for signs of treatment resistance. However, the time required to establish theses assays does not fit well with the patient journey, as clinicians need to know sooner than 5-6 weeks whether a patient is not responding to treatment. Therefore, epigenetic-based MRD assays are preferable at treatment onset, as epigenetic changes are typically more widespread and likely to be shared among a greater number of cancers than somatic mutations. With the recent advent of enzymatic methylation conversion, targeted sequencing approaches combining DNA methylation, fragmentomics and machine learning will likely come to predominate. However, DNA methylation-based PCR tests currently offer the most cost-effective solution within this niche. In fact, a compelling paradigm may be the combination of inexpensive serial testing with a DNA methylation-based assay, then following a positive MRD/recurrence result with a broad NGS-based somatic mutation panel to identify actionable mutations.AJ, JR, CM, KF, and WL wrote and revised this review. All authors contributed to the article and approved the submitted version.


Editorial on the Research TopicRecent advances in hypospadiologyHypospadias is one of the most common genital anomalies in men and displays a wide range of complex phenotypes. Multiple studies have reported a marked global increase in hypospadias cases over the past three decades, although the underlying basis for this remains unclear , 2. WhilBaray et al., developed an automated deep learning-based method for accurate PC measurement using 2D images, which could significantly improve patient assessment by surgeons and researchers alike. The novel pipeline they propose includes three key consecutive steps: penile localization, shaft segmentation, and angle measurement considering only the proximal and distal parts of the penile shaft. This method may overcome current limitations encountered by conventional approaches to measuring arc-type PC.Penile curvature (PC) is a key anatomical component of many hypospadias phenotypes and can have long-lasting effects on patients’ psychosexual health and quality of life. While several prior studies have attempted to establish criteria for evaluating PC, there is still no standardized method for doing so. Despite significant challenges with assessing PC in both clinical practice and research settings, numerous procedures are now being investigated that have potential to resolve longstanding issues. Zhou et al., one-stage correction of severe hypospadias was achieved using a free preputial tube graft in conjunction with urethral plate urethroplasty and a Buck's fascia integral covering (BFIC) to protect the neourethra and minimize fistula risk. Using an alternative approach, Li et al., report their experience with transverse preputial island flap urethroplasty (TPIFU) in a retrospective cohort study. In 136 patient who underwent single-stage TPIFU, re-operation to address postoperative complications was required in 39% of cases, the majority of which were due to urethrocutaneous fistulas .Among the wide spectrum of hypospadias anomalies, proximal cases include a subset of severe phenotypes that can significantly impact treatment protocols and post-operative results. In these instances, choice of surgical approach is heavily influenced by surgeon experience and personal preference in addition to patient anatomy . There is still considerable disagreement about the optimal method for treating proximal hypospadias, but surgeons are increasingly testing new approaches to achieve better patient outcomes. In a study by Tian et al., present the results of a retrospective cohort of 195 patients who underwent hypospadias repair and subsequently developed postoperative fistulas. Patients with recurrent fistulas after initial closure were compared with patients who achieved successful fistula closure, which revealed an association of catheter type used for drainage with local purulent discharge after surgery.Weidler et al., report their results from a multicenter collaboration evaluating the controversy surrounding optimal timing of surgery. In particular, their study focuses on decision making in individuals with differences in sexual development, as well as their caregivers and healthcare providers. Using a semi-structured interview, the authors evaluated potential determinants of successful outcomes in 110 participants. They identify several key themes including; (1) the nature/type of decision being made, (2) person involved in decision making, (3) timing of conversations about surgery, (4) barriers to decision-making surrounding surgery, (5) elements involved in these discussions, and (6) optimal approach to surgical decision-making. Priority was given to children and adolescents with disorders of sexual differentiation to ensure their involvement in all discussions. In summary, while many issues remain unresolved in the field of hypospadiology, novel approaches and improved understanding of surgical and patient-reported outcomes will be crucial to the continuing evolution of this challenging field.