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Tracking-seq reveals the heterogeneity of off-target effects in CRISPR-Cas9-mediated genome editing.Nature Biotechnology Jul 2024The continued development of novel genome editors calls for a universal method to analyze their off-target effects. Here we describe a versatile method, called...
The continued development of novel genome editors calls for a universal method to analyze their off-target effects. Here we describe a versatile method, called Tracking-seq, for in situ identification of off-target effects that is broadly applicable to common genome-editing tools, including Cas9, base editors and prime editors. Through tracking replication protein A (RPA)-bound single-stranded DNA followed by strand-specific library construction, Tracking-seq requires a low cell input and is suitable for in vitro, ex vivo and in vivo genome editing, providing a sensitive and practical genome-wide approach for off-target detection in various scenarios. We show, using the same guide RNA, that Tracking-seq detects heterogeneity in off-target effects between different editor modalities and between different cell types, underscoring the necessity of direct measurement in the original system.
PubMed: 38956324
DOI: 10.1038/s41587-024-02307-y -
Scientific Reports Jul 2024The monocyte distribution width (MDW) has emerged as a promising biomarker for accurate and early identification of patients with potentially life-threatening...
Understanding the value of monocyte distribution width (MDW) in acutely ill medical patients presenting to the emergency department: a prospective single center evaluation.
The monocyte distribution width (MDW) has emerged as a promising biomarker for accurate and early identification of patients with potentially life-threatening infections. Here we tested the diagnostic performance of MDW in adult patients requiring hospital admission for community-acquired infections and sepsis, evaluated sources of heterogeneity in the estimates of diagnostic accuracy, and assessed the meaning of MDW in a patient population presenting to the emergency department (ED) for acute non-infectious conditions. 1925 consecutive patients were categorized into three groups: non-infection (n = 1507), infection (n = 316), and sepsis/septic shock (n = 102). Diagnostic performance for infection or sepsis of MDW alone or in combination with components of SOFA was tested using AUC of ROC curves, sensitivity, and specificity. The relationship between MDW and different pathogens as well as the impact of non-infectious conditions on MDW values were explored. For the prediction of infection, the AUC/ROC of MDW (0.84) was nearly overlapping that of procalcitonin (0.83), and C-reactive protein (0.89). Statistical optimal cut-off value for MDW was 21 for predicting infection (sensitivity 73%, specificity 82%) and 22 for predicting sepsis (sensitivity 79%, specificity 83%). The best threshold to rule out infection was MDW ≤ 17 (NPV 96.9, 95% CI 88.3-100.0), and ≤ 18 (NPV 99.5, 95% CI 98.3-100.0) to rule out sepsis. The combination of MDW with markers of organ dysfunction (creatinine, bilirubin, platelets) substantially improved the AUC (0.96 (95% CI 0.94-0.97); specificity and sensitivity of 88% and 94%, respectively). In conclusion, MDW has a good diagnostic performance in diagnosing infection and sepsis in patients presenting in ED. Its use as an infection marker even increases when combined with other markers of organ dysfunction. Understanding the impact of interactions of non-infectious conditions and comorbidities on MDW and its diagnostic accuracy requires further elucidation.
Topics: Humans; Emergency Service, Hospital; Male; Female; Middle Aged; Prospective Studies; Aged; Sepsis; Monocytes; Biomarkers; Adult; ROC Curve; Acute Disease; Aged, 80 and over; Community-Acquired Infections; Sensitivity and Specificity
PubMed: 38956252
DOI: 10.1038/s41598-024-65883-8 -
Nature Genetics Jul 2024Mismatch repair (MMR)-deficient cancer evolves through the stepwise erosion of coding homopolymers in target genes. Curiously, the MMR genes MutS homolog 6 (MSH6) and...
Mismatch repair (MMR)-deficient cancer evolves through the stepwise erosion of coding homopolymers in target genes. Curiously, the MMR genes MutS homolog 6 (MSH6) and MutS homolog 3 (MSH3) also contain coding homopolymers, and these are frequent mutational targets in MMR-deficient cancers. The impact of incremental MMR mutations on MMR-deficient cancer evolution is unknown. Here we show that microsatellite instability modulates DNA repair by toggling hypermutable mononucleotide homopolymer runs in MSH6 and MSH3 through stochastic frameshift switching. Spontaneous mutation and reversion modulate subclonal mutation rate, mutation bias and HLA and neoantigen diversity. Patient-derived organoids corroborate these observations and show that MMR homopolymer sequences drift back into reading frame in the absence of immune selection, suggesting a fitness cost of elevated mutation rates. Combined experimental and simulation studies demonstrate that subclonal immune selection favors incremental MMR mutations. Overall, our data demonstrate that MMR-deficient colorectal cancers fuel intratumor heterogeneity by adapting subclonal mutation rate and diversity to immune selection.
PubMed: 38956208
DOI: 10.1038/s41588-024-01777-9 -
Scientific Reports Jul 2024The 2D:4D digit ratio is commonly used as a surrogate possibly reflecting prenatal testosterone levels. Indirect evidence comes from studies investigating the...
The 2D:4D digit ratio is commonly used as a surrogate possibly reflecting prenatal testosterone levels. Indirect evidence comes from studies investigating the association between 2D:4D and human characteristics that likely relate to prenatal testosterone. In children, sex-typed play reveals large sex differences early in development and an influence of prenatal testosterone is likely. Findings on the association between 2D:4D and children's sex-typed play are heterogeneous and other influences on the development of sex-typed play have been suggested, most of all social influences like siblings, their sex and birth order. The current study examined the association between right and left 2D:4D, a proposed surrogate for prenatal testosterone exposure, which was assessed in right and left hands of N = 505 6-month-old children, and sex-typed play behavior, which was evaluated 3.5 years later using the Pre-School Activities Inventory (PSAI), and the influence of siblings. To capture differential effects of siblings' sex and birth order, dummy-coded variables were used reflecting having no siblings as well as older or younger sisters or brothers. Multiple regression models were used to investigate the association between PSAI scores and sex, right and left 2D:4D, being a singleton as well as having an older or younger sister or brother. It was shown that sex and having an older brother were significant predictors for sex-typed play. Effects were further disentangled by conducting separate regression analyses in boys and girls. In boys, a significant association between PSAI scores and having an older brother was revealed, in girls, no significant associations were found. Results are discussed highlighting the non-significant association between 2D:4D and children's sex-typed play, which weakens the applicability of 2D:4D as a surrogate reflecting influences of prenatal T. Further, the importance of social factors like siblings on children's sex-typed play is discussed.
Topics: Humans; Female; Male; Siblings; Fingers; Play and Playthings; Infant; Testosterone; Child, Preschool; Sex Characteristics; Pregnancy; Child; Prenatal Exposure Delayed Effects
PubMed: 38956189
DOI: 10.1038/s41598-024-65739-1 -
Scientific Reports Jul 2024Assessing programmed death ligand 1 (PD-L1) expression through immunohistochemistry (IHC) is the golden standard in predicting immunotherapy response of non-small cell...
Assessing programmed death ligand 1 (PD-L1) expression through immunohistochemistry (IHC) is the golden standard in predicting immunotherapy response of non-small cell lung cancer (NSCLC). However, observation of heterogeneous PD-L1 distribution in tumor space is a challenge using IHC only. Meanwhile, immunofluorescence (IF) could support both planar and three-dimensional (3D) histological analyses by combining tissue optical clearing with confocal microscopy. We optimized clinical tissue preparation for the IF assay focusing on staining, imaging, and post-processing to achieve quality identical to traditional IHC assay. To overcome limited dynamic range of the fluorescence microscope's detection system, we incorporated a high dynamic range (HDR) algorithm to restore the post imaging IF expression pattern and further 3D IF images. Following HDR processing, a noticeable improvement in the accuracy of diagnosis (85.7%) was achieved using IF images by pathologists. Moreover, 3D IF images revealed a 25% change in tumor proportion score for PD-L1 expression at various depths within tumors. We have established an optimal and reproducible process for PD-L1 IF images in NSCLC, yielding high quality data comparable to traditional IHC assays. The ability to discern accurate spatial PD-L1 distribution through 3D pathology analysis could provide more precise evaluation and prediction for immunotherapy targeting advanced NSCLC.
Topics: Humans; Carcinoma, Non-Small-Cell Lung; B7-H1 Antigen; Lung Neoplasms; Imaging, Three-Dimensional; Fluorescent Antibody Technique; Immunohistochemistry; Microscopy, Confocal; Biomarkers, Tumor
PubMed: 38956114
DOI: 10.1038/s41598-024-65187-x -
Translational Psychiatry Jul 2024The Addictions Neuroclinical Assessment (ANA) is a neurobiologically-informed framework designed to understand the etiology and heterogeneity of Alcohol Use Disorder... (Observational Study)
Observational Study
The Addictions Neuroclinical Assessment (ANA) is a neurobiologically-informed framework designed to understand the etiology and heterogeneity of Alcohol Use Disorder (AUD). Previous studies validated the three neurofunctional domains of ANA: Incentive Salience (IS), Negative Emotionality (NE) and Executive Function (EF) using secondary data. The present cross-sectional observational study assessed these domains in an independent, prospective clinical sample. Adults across the drinking spectrum (N = 300) completed the ANA battery, a standardized collection of behavioral tasks and self-report assessments. Factor analyses were used to identify latent factors underlying each domain. Associations between identified domain factors were evaluated using structural equation models. Receiver operating characteristics analyses were used to determine factors with the strongest ability to classify individuals with problematic drinking and AUD. We found (1) two factors underlie the IS domain: alcohol motivation and alcohol insensitivity. (2) Three factors were identified for the NE domain: internalizing, externalizing, and psychological strength. (3) Five factors were found for the EF domain: inhibitory control, working memory, rumination, interoception, and impulsivity. (4) These ten factors showed varying degrees of cross-correlations, with alcohol motivation, internalizing, and impulsivity exhibiting the strongest correlations. (5) Alcohol motivation, alcohol insensitivity, and impulsivity showed the greatest ability in classifying individuals with problematic drinking and AUD. Thus, the present study identified unique factors underlying each ANA domain assessed using a standardized assessment battery. These results revealed additional dimensionality to the ANA domains, bringing together different constructs from the field into a single cohesive framework and advancing the field of addiction phenotyping. Future work will focus on identifying neurobiological correlates and identifying AUD subtypes based on these factors.
Topics: Humans; Male; Female; Adult; Cross-Sectional Studies; Alcoholism; Executive Function; Neuropsychological Tests; Motivation; Middle Aged; Prospective Studies; Impulsive Behavior; Young Adult; Behavior, Addictive; Emotions; Factor Analysis, Statistical
PubMed: 38956031
DOI: 10.1038/s41398-024-02987-9 -
Indian Journal of Gastroenterology :... Jul 2024The guidelines recommend conventional cold snare polypectomy (C-CSP) for diminutive and small colorectal polyps (≤ 10 mm). However, it remains unclear whether CSP... (Review)
Review
BACKGROUND
The guidelines recommend conventional cold snare polypectomy (C-CSP) for diminutive and small colorectal polyps (≤ 10 mm). However, it remains unclear whether CSP with sub-mucosal injection (SI-CSP) achieves comparable efficacy to C-CSP for managing these lesions. This study compares SI-CSP with C-CSP for patients with diminutive and small colorectal polyps.
METHODS
An electronic literature search was conducted to retrieve articles comparing resection outcomes between SI-CSP and C-CSP in diminutive and small colorectal polyps (registration number INPLASY2023100096). Our primary outcomes of interest were the complete resection rate (CRR), complications (namely immediate bleeding, delayed bleeding and perforation) and polypectomy time. Mean differences with 95% confidence intervals (CI) were employed for continuous variables, while odds ratios (OR) with 95% CI were calculated for categorical variables. Data was analyzed using a random effects model and the I test was utilized to assess heterogeneity.
RESULTS
Eight studies involving 1470 patients with 2223 polyps were included in our analysis. The CRR was not significantly higher in the SI-CSP group, with an OR of 95% CI 0.50 (0.22, 1.15). The incidences of immediate bleeding (OR 95% CI 0.60 [0.26-1.40]) and delayed bleeding (OR 95% CI 0.88 [0.32-2.42]) did not differ significantly between the two groups. On average, the mean polypectomy time was 64.75 seconds shorter in the C-CSP group (95% CI, - 102.96 to - 26.53). Notably, no perforation events were reported in the included studies.
CONCLUSIONS
The use of SI-CSP was not superior to C-CSP in managing diminutive and small colorectal polyps and the procedure required significantly more time.
PubMed: 38955995
DOI: 10.1007/s12664-024-01600-7 -
Neurocritical Care Jul 2024Spontaneous intracerebral hemorrhage (ICH) is the most devastating type of stroke, and it is associated with high morbidity and mortality. Patients with a spontaneous... (Review)
Review
Spontaneous intracerebral hemorrhage (ICH) is the most devastating type of stroke, and it is associated with high morbidity and mortality. Patients with a spontaneous ICH are routinely admitted to an intensive care unit (ICU). However, an ICU is a valuable and limited resource, and not all patients may require this level of care. The authors conducted a systematic review and meta-analysis evaluating the safety and outcome of admission to a step-down level of care or stroke unit (SU) compared to intensive care in adult patients with low-risk spontaneous ICH. PubMed, Embase, and the Cochrane Library were searched for randomized clinical trials and observational cohort studies. The Mantel-Haenszel method or inverse variance, as applicable, was applied to calculate an overall effect estimate for each outcome by combining the specific risk ratio (RR) or standardized mean difference. Risk of bias was analyzed using the Newcastle-Ottawa Scale. The protocol was registered in PROSPERO (CRD42023481915). The primary outcome examined was in-hospital mortality. Secondary outcomes were unfavorable short-term outcome, length of hospital stay, and (re)admission to the ICU. Five retrospective cohort studies involving 1347 patients were included in the qualitative analysis. Two of the studies had severity-matched groups. The definition of low-risk ICH was heterogeneous among the studies. Admission to an SU was associated with a similar rate of mortality compared to admission to an ICU (1.4% vs. 0.6%; RR 1.66; 95% confidence interval [CI] 0.24-11.41; P = 0.61), a similar rate of unfavorable short-term outcome (14.6% vs. 19.2%; RR 0.77; 95% CI 0.43-1.36; P = 0.36), and a significantly shorter mean length of stay (standardized mean difference - 0.87 days; 95% CI - 1.15 to - 0.60; P < 0.01). Risk of bias was low to moderate for each outcome. The available literature suggests that a select subgroup of patients with ICH may be safely admitted to the SU without affecting short-term outcome, potentially saving in-hospital resources and reducing length of stay. Further studies are needed to identify specific and reliable characteristics of this subgroup of patients.
PubMed: 38955932
DOI: 10.1007/s12028-024-02044-9 -
ACS Applied Materials & Interfaces Jul 2024Accurate detection of heterogeneous circulating tumor cells (CTCs) is critical as they can make tumor cells more aggressive, drug-resistant, and metastasizing. Although...
Accurate detection of heterogeneous circulating tumor cells (CTCs) is critical as they can make tumor cells more aggressive, drug-resistant, and metastasizing. Although the leukocyte membrane coating strategy is promising in meeting the challenge of detecting heterogeneous CTCs due to its inherent antiadhesive properties, it is still limited by the reduction or loss of expression of known markers. Bioorthogonal glycol-metabolic engineering is expected to break down this barrier by feeding the cells with sugar derivatives with a unique functional group to establish artificial targets on the surface of tumor cells. Herein, an engineered leukocyte biomimetic colorimetric sensor was accordingly fabricated for high-efficient detection of heterogeneous CTCs. Compared with conventional leukocyte membrane coating, the sensor could covalently bound to the heterogeneous CTCs models fed with AcManNAz in vitro through the synergy of bioorthogonal chemistry and metabolic glycoengineering, ignoring the phenotypic changes of heterogeneous CTCs. Meanwhile, a sandwich structure composed of leukocyte biomimetic layer/CTCs/MoS nanosheet was formed for visual detection of HeLa cells as low as 10 cells mL. Overall, this approach can overcome the dependence of conventional cell membrane biomimetic technology on specific cell phenotypes and provide a new viewpoint to highly efficiently detect heterogeneous CTCs.
PubMed: 38955781
DOI: 10.1021/acsami.4c06272 -
International Journal of Dermatology Jul 2024Primary cutaneous CD4+ small/medium T-cell lymphoproliferative disorder (PCSM-LPD) is an increasingly recognized entity with heterogeneous management strategies that may...
BACKGROUND
Primary cutaneous CD4+ small/medium T-cell lymphoproliferative disorder (PCSM-LPD) is an increasingly recognized entity with heterogeneous management strategies that may include radiotherapy.
OBJECTIVE
Our aim was to characterize treatment options for PCSM-LPD, with a focus on the role of radiotherapy.
METHODS
This is a retrospective review of 46 patients seen in the Cutaneous Lymphoma Program at the University of Texas MD Anderson Cancer Center, with a clinicopathologic review consistent with PCSM-LPD. All patients were biopsied and underwent observation, topical/intralesional steroids, and/or radiotherapy. Patients were confirmed to have residual disease prior to radiotherapy.
RESULTS
All patients achieved a complete response (CR). Sixteen patients (35%) received focal radiotherapy, with a CR in 15 (94%). The CR rate following ultra-low-dose radiotherapy (4 Gy in 1-2 fractions) was 92%. There was no grade 3 toxicity after radiotherapy. Thirty patients were managed without radiotherapy, with excision and observation or steroids.
CONCLUSION
Primary cutaneous CD4+ small/medium T-cell lymphoproliferative disorder has excellent outcomes, and management strategies may include observation following biopsy, steroids, or radiation. Ultra-low-dose radiotherapy results in excellent outcomes with limited toxicity and is effective for persistent lesions after steroidal therapy.
PubMed: 38955474
DOI: 10.1111/ijd.17352