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1.
Neurourol Urodyn ; 43(4): 902-914, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38385648

ABSTRACT

BACKGROUND AND AIMS: Recurrent urinary tract infection (rUTI) has significant negative consequences for a wide variety of quality of life (QoL) domains. Without adequate validation and assessment of the unique insights of people living with rUTI, clinical results cannot be fully understood. The Recurrent UTI Impact Questionnaire (RUTIIQ), a novel patient-reported outcome measure of rUTI psychosocial impact, has been robustly developed with extensive patient and clinician input to facilitate enhanced rUTI management and research. This study aimed to confirm the structural validity of the RUTIIQ, assessing its strength and bifactor model fit. METHODS: A sample of 389 adults experiencing rUTI (96.9% female, aged 18-87 years) completed an online cross-sectional survey comprising a demographic questionnaire and the RUTIIQ. A bifactor graded response model was fitted to the data, optimizing the questionnaire structure based on item fit, discrimination capability, local dependence, and differential item functioning. RESULTS: The final RUTIIQ demonstrated excellent bifactor model fit (RMSEA = 0.054, CFI = 0.99, SRMSR = 0.052), and mean-square fit indices indicated that all included items were productive for measurement (MNSQ = 0.52-1.41). The final questionnaire comprised an 18-item general "rUTI QoL impact" factor, and five subfactor domains measuring "personal wellbeing" (three items), "social wellbeing" (four items), "work and activity interference" (four items), "patient satisfaction" (four items), and "sexual wellbeing" (three items). Together, the general factor and five subfactors explained 81.6% of the common model variance. All factor loadings were greater than 0.30 and communalities greater than 0.60, indicating good model fit and structural validity. CONCLUSIONS: The 18-item RUTIIQ is a robust, patient-tested questionnaire with excellent psychometric properties, which capably assesses the patient experience of rUTI-related impact to QoL and healthcare satisfaction. Facilitating standardized patient monitoring and improved shared decision-making, the RUTIIQ delivers the unique opportunity to improve patient-centered care.


Subject(s)
Quality of Life , Urinary Tract Infections , Adult , Humans , Female , Male , Quality of Life/psychology , Cross-Sectional Studies , Surveys and Questionnaires , Patient Reported Outcome Measures , Psychometrics/methods , Reproducibility of Results
2.
BJUI Compass ; 5(2): 240-252, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38371201

ABSTRACT

Objectives: To confirm the structural validity of the Recurrent Urinary Tract Infection Symptom Scale (RUTISS), determining whether a bifactor model appropriately fits the questionnaire's structure and identifying areas for refinement. Used in conjunction with established clinical testing methods, this patient-reported outcome measure addresses the urgent need to validate the patient perspective. Patients and methods: A clinically and demographically diverse sample of 389 people experiencing recurrent UTI across 37 countries (96.9% female biological sex, aged 18-87 years) completed the RUTISS online. A bifactor graded response model was fitted to the data, identifying potential items for deletion if they indicated significant differential item functioning (DIF) based on sociodemographic characteristics, contributed to local item dependence or demonstrated poor fit or discrimination capability. Results: The final RUTISS comprised a 3-item symptom frequency section, a 1-item global rating of change scale and an 11-item general 'rUTI symptom and pain severity' subscale with four sub-factor domains measuring 'urinary symptoms', 'urinary presentation', 'UTI pain and discomfort' and 'bodily sensations'. The bifactor model fit indices were excellent (root mean square error of approximation [RMSEA] = 0.041, comparative fit index [CFI] = 0.995, standardised root mean square residual [SRMSR] = 0.047), and the mean-square fit statistics indicated that all items were productive for measurement (mean square fit indices [MNSQ] = 0.64 - 1.29). Eighty-one per cent of the common model variance was accounted for by the general factor and sub-factors collectively, and all factor loadings were greater than 0.30 and communalities greater than 0.60. Items indicated high discrimination capability (slope parameters > 1.35). Conclusion: The 15-item RUTISS is a patient-generated, psychometrically robust questionnaire that dynamically assesses the patient experience of recurrent UTI symptoms and pain. This brief tool offers the unique opportunity to enhance patient-centred care by supporting shared decision-making and patient monitoring.

3.
bioRxiv ; 2023 Aug 24.
Article in English | MEDLINE | ID: mdl-37662366

ABSTRACT

We present the genome of the living fossil, Wollemia nobilis, a southern hemisphere conifer morphologically unchanged since the Cretaceous. Presumed extinct until rediscovery in 1994, the Wollemi pine is critically endangered with less than 60 wild adults threatened by intensifying bushfires in the Blue Mountains of Australia. The 12 Gb genome is among the most contiguous large plant genomes assembled, with extremely low heterozygosity and unusual abundance of DNA transposons. Reduced representation and genome re-sequencing of individuals confirms a relictual population since the last major glacial/drying period in Australia, 120 ky BP. Small RNA and methylome sequencing reveal conservation of ancient silencing mechanisms despite the presence of thousands of active and abundant transposons, including some transferred horizontally to conifers from arthropods in the Jurassic. A retrotransposon burst 8-6 my BP coincided with population decline, possibly as an adaptation enhancing epigenetic diversity. Wollemia, like other conifers, is susceptible to Phytophthora, and a suite of defense genes, similar to those in loblolly pine, are targeted for silencing by sRNAs in leaves. The genome provides insight into the earliest seed plants, while enabling conservation efforts.

4.
Genome Biol Evol ; 15(9)2023 09 04.
Article in English | MEDLINE | ID: mdl-37728212

ABSTRACT

Bats are exceptional among mammals for their powered flight, extended lifespans, and robust immune systems and therefore have been of particular interest in comparative genomics. Using the Oxford Nanopore Technologies long-read platform, we sequenced the genomes of two bat species with key phylogenetic positions, the Jamaican fruit bat (Artibeus jamaicensis) and the Mesoamerican mustached bat (Pteronotus mesoamericanus), and carried out a comprehensive comparative genomic analysis with a diverse collection of bats and other mammals. The high-quality, long-read genome assemblies revealed a contraction of interferon (IFN)-α at the immunity-related type I IFN locus in bats, resulting in a shift in relative IFN-ω and IFN-α copy numbers. Contradicting previous hypotheses of constitutive expression of IFN-α being a feature of the bat immune system, three bat species lost all IFN-α genes. This shift to IFN-ω could contribute to the increased viral tolerance that has made bats a common reservoir for viruses that can be transmitted to humans. Antiviral genes stimulated by type I IFNs also showed evidence of rapid evolution, including a lineage-specific duplication of IFN-induced transmembrane genes and positive selection in IFIT2. In addition, 33 tumor suppressors and 6 DNA-repair genes showed signs of positive selection, perhaps contributing to increased longevity and reduced cancer rates in bats. The robust immune systems of bats rely on both bat-wide and lineage-specific evolution in the immune gene repertoire, suggesting diverse immune strategies. Our study provides new genomic resources for bats and sheds new light on the extraordinary molecular evolution in this critically important group of mammals.


Subject(s)
Chiroptera , Neoplasms , Humans , Animals , Chiroptera/genetics , Phylogeny , Evolution, Molecular , Genomics , Longevity , Neoplasms/genetics , Neoplasms/veterinary
5.
BJUI Compass ; 4(3): 285-297, 2023 May.
Article in English | MEDLINE | ID: mdl-37025478

ABSTRACT

Objectives: This study aimed to develop and validate a tailored patient-reported outcome measure (PROM) evaluating the patient experience of recurrent urinary tract infection (rUTI) symptom severity. This measure was designed to supplement clinical testing methods, allowing full assessment of the patient experience of rUTI symptom burden, while enhancing patient-centred UTI management and monitoring. Subjects and Methods: The Recurrent Urinary Tract Infection Symptom Scale (RUTISS) was developed and validated using a three-stage methodology, in accordance with gold-standard recommendations. Firstly, a two-round Delphi study was conducted to gain insights from 15 international expert clinicians working in rUTI, developing an initial pool of novel questionnaire items, assessing content validity and making item refinements. Next, two phases of one-to-one semi-structured cognitive interviews were conducted with a diverse sample of 28 people experiencing rUTI to assess questionnaire comprehensiveness and comprehensibility, making refinements after each phase. Finally, a comprehensive pilot of the RUTISS was conducted with 240 people experiencing rUTI across 24 countries, providing data for psychometric testing and item reduction. Results: Exploratory factor analysis indicated a four-factor structure comprising: 'urinary pain and discomfort', 'urinary urgency', 'bodily sensations' and 'urinary presentation', together accounting for 75.4% of the total variance in data. Qualitative feedback from expert clinicians and patients indicated strong content validity for items, which was supported by high content validity indices in the Delphi study (I-CVI > 0.75). Internal consistency and test-retest reliability of the RUTISS subscales were excellent (Cronbach's α = 0.87-0.94 and ICC = 0.73-0.82, respectively), and construct validity was strong (Spearman's ρ = 0.60-0.82). Conclusion: The RUTISS is a 28-item questionnaire with excellent reliability and validity, which dynamically assesses patient-reported rUTI symptoms and pain. This new PROM offers a unique opportunity to critically inform and strategically enhance the quality of rUTI management, patient-clinician interactions, and shared-decision making by monitoring key patient-reported outcomes.

6.
Qual Life Res ; 32(6): 1745-1758, 2023 Jun.
Article in English | MEDLINE | ID: mdl-36740638

ABSTRACT

PURPOSE: Recurrent urinary tract infection (rUTI) is a highly prevalent condition associated with significant poor quality of life outcomes. A patient-reported outcome measure (PROM) of rUTI-associated psychosocial impact is urgently required to supplement clinical evaluation and validate the challenges experienced by patients. This study therefore developed and validated the Recurrent UTI Impact Questionnaire (RUTIIQ). METHODS: A rigorous four-stage methodology was followed: (I) concept elicitation through a qualitative survey of the experiences of people with rUTI (N = 1983); (II) Delphi expert screening of the RUTIIQ with expert rUTI clinicians (N = 15); (III) one-to-one cognitive interviews with people experiencing rUTI (N = 28) to evaluate the comprehensiveness and comprehensibility of the RUTIIQ, and (IV) full pilot testing of the RUTIIQ with people experiencing rUTI (N = 240) to perform final item reduction and psychometric analysis. RESULTS: Exploratory factor analysis demonstrated a five-factor structure comprising: 'patient satisfaction', 'work and activity interference', 'social wellbeing', 'personal wellbeing', and 'sexual wellbeing', collectively accounting for 73.8% of the total variance in pilot scores. Results from expert clinicians and patients indicated strong item content validity (I-CVI > .75). The internal consistency and test-retest reliability of the RUTIIQ subscales were excellent (Cronbach's α = .81-.96, ICC = .66-.91), and construct validity was strong (Spearman's ρ > .69). CONCLUSION: The RUTIIQ is a 30-item questionnaire with excellent psychometric properties, assessing the patient-reported psychosocial impact of living with rUTI symptoms and pain. This new instrument delivers the unique opportunity to enhance patient-centred care through standardised observation and monitoring of rUTI patient outcomes. TRIAL REGISTRATION: This study was pre-registered with ClinicalTrials.gov (identifier: NCT05086900).


Subject(s)
Quality of Life , Urinary Tract Infections , Humans , Psychometrics , Reproducibility of Results , Quality of Life/psychology , Urinary Tract Infections/drug therapy , Surveys and Questionnaires , Patient Reported Outcome Measures
7.
ACS Med Chem Lett ; 13(7): 1165-1171, 2022 Jul 14.
Article in English | MEDLINE | ID: mdl-35859878

ABSTRACT

We describe the synthesis of triazole-containing carboline derivatives and their utility as bromodomain and extra-terminal (BET) inhibitors. A convergent synthetic route permitted the detailed investigation of deuteration and fluorination strategies to reduce clearance while maintaining a favorable in vitro profile. This work led to the identification of a potent BET inhibitor, 2-{8-fluoro-3-[4-(2H3)methyl-1-methyl-1H-1,2,3-triazol-5-yl]-5-[(S)-(oxan-4-yl)(phenyl)methyl]-5H-pyrido[3,2-b]indol-7-yl}propan-2-ol (15), which demonstrated reduced clearance and an improved pharmacokinetic (PK) profile across preclinical species. Importantly, no major metabolite was observed when 15 was incubated with human hepatocytes (hHEP) for 2 h. This study culminated with the evaluation of 15 in a mouse triple-negative breast cancer (TNBC) tumor model where it demonstrated robust efficacy at low doses.

8.
Sci Data ; 9(1): 300, 2022 06 14.
Article in English | MEDLINE | ID: mdl-35701428

ABSTRACT

Most psychiatric disorders are chronic, associated with high levels of disability and distress, and present during pediatric development. Scientific innovation increasingly allows researchers to probe brain-behavior relationships in the developing human. As a result, ambitions to (1) establish normative pediatric brain development trajectories akin to growth curves, (2) characterize reliable metrics for distinguishing illness, and (3) develop clinically useful tools to assist in the diagnosis and management of mental health and learning disorders have gained significant momentum. To this end, the NKI-Rockland Sample initiative was created to probe lifespan development as a large-scale multimodal dataset. The NKI-Rockland Sample Longitudinal Discovery of Brain Development Trajectories substudy (N = 369) is a 24- to 30-month multi-cohort longitudinal pediatric investigation (ages 6.0-17.0 at enrollment) carried out in a community-ascertained sample. Data include psychiatric diagnostic, medical, behavioral, and cognitive phenotyping, as well as multimodal brain imaging (resting fMRI, diffusion MRI, morphometric MRI, arterial spin labeling), genetics, and actigraphy. Herein, we present the rationale, design, and implementation of the Longitudinal Discovery of Brain Development Trajectories protocol.


Subject(s)
Brain , Connectome , Mental Health , Adolescent , Brain/diagnostic imaging , Brain/physiology , Child , Diffusion Magnetic Resonance Imaging , Humans
9.
Am J Hum Genet ; 109(4): 631-646, 2022 04 07.
Article in English | MEDLINE | ID: mdl-35290762

ABSTRACT

Studies of de novo mutation (DNM) have typically excluded some of the most repetitive and complex regions of the genome because these regions cannot be unambiguously mapped with short-read sequencing data. To better understand the genome-wide pattern of DNM, we generated long-read sequence data from an autism parent-child quad with an affected female where no pathogenic variant had been discovered in short-read Illumina sequence data. We deeply sequenced all four individuals by using three sequencing platforms (Illumina, Oxford Nanopore, and Pacific Biosciences) and three complementary technologies (Strand-seq, optical mapping, and 10X Genomics). Using long-read sequencing, we initially discovered and validated 171 DNMs across two children-a 20% increase in the number of de novo single-nucleotide variants (SNVs) and indels when compared to short-read callsets. The number of DNMs further increased by 5% when considering a more complete human reference (T2T-CHM13) because of the recovery of events in regions absent from GRCh38 (e.g., three DNMs in heterochromatic satellites). In total, we validated 195 de novo germline mutations and 23 potential post-zygotic mosaic mutations across both children; the overall true substitution rate based on this integrated callset is at least 1.41 × 10-8 substitutions per nucleotide per generation. We also identified six de novo insertions and deletions in tandem repeats, two of which represent structural variants. We demonstrate that long-read sequencing and assembly, especially when combined with a more complete reference genome, increases the number of DNMs by >25% compared to previous studies, providing a more complete catalog of DNM compared to short-read data alone.


Subject(s)
Genomics , High-Throughput Nucleotide Sequencing , Female , Humans , Mutation/genetics , Nucleotides , Sequence Analysis, DNA , Software
10.
Cancer Res ; 82(7): 1174-1192, 2022 04 01.
Article in English | MEDLINE | ID: mdl-35180770

ABSTRACT

Triple-negative breast cancer (TNBC) is an aggressive form of breast cancer with poor patient outcomes, highlighting the unmet clinical need for targeted therapies and better model systems. Here, we developed and comprehensively characterized a diverse biobank of normal and breast cancer patient-derived organoids (PDO) with a focus on TNBCs. PDOs recapitulated patient tumor intrinsic properties and a subset of PDOs can be propagated for long-term culture (LT-TNBC). Single cell profiling of PDOs identified cell types and gene candidates affiliated with different aspects of cancer progression. The LT-TNBC organoids exhibit signatures of aggressive MYC-driven, basal-like breast cancers and are largely comprised of luminal progenitor (LP)-like cells. The TNBC LP-like cells are distinct from normal LPs and exhibit hyperactivation of NOTCH and MYC signaling. Overall, this study validates TNBC PDOs as robust models for understanding breast cancer biology and progression, paving the way for personalized medicine and tailored treatment options. SIGNIFICANCE: A comprehensive analysis of patient-derived organoids of TNBC provides insights into cellular heterogeneity and mechanisms of tumorigenesis at the single-cell level.


Subject(s)
Triple Negative Breast Neoplasms , Cell Line, Tumor , Humans , Organoids/pathology , Precision Medicine , Proto-Oncogene Proteins c-myc/metabolism , Signal Transduction , Triple Negative Breast Neoplasms/pathology
11.
Cancer Discov ; 12(2): 450-467, 2022 02.
Article in English | MEDLINE | ID: mdl-34531253

ABSTRACT

An enhanced requirement for nutrients is a hallmark property of cancer cells. Here, we optimized an in vivo genetic screening strategy in acute myeloid leukemia (AML), which led to the identification of the myo-inositol transporter SLC5A3 as a dependency in this disease. We demonstrate that SLC5A3 is essential to support a myo-inositol auxotrophy in AML. The commonality among SLC5A3-dependent AML lines is the transcriptional silencing of ISYNA1, which encodes the rate-limiting enzyme for myo-inositol biosynthesis, inositol-3-phosphate synthase 1. We use gain- and loss-of-function experiments to reveal a synthetic lethal genetic interaction between ISYNA1 and SLC5A3 in AML, which function redundantly to sustain intracellular myo-inositol. Transcriptional silencing and DNA hypermethylation of ISYNA1 occur in a recurrent manner in human AML patient samples, in association with IDH1/IDH2 and CEBPA mutations. Our findings reveal myo-inositol as a nutrient dependency in AML caused by the aberrant silencing of a biosynthetic enzyme. SIGNIFICANCE: We show how epigenetic silencing can provoke a nutrient dependency in AML by exploiting a synthetic lethality relationship between biosynthesis and transport of myo-inositol. Blocking the function of this solute carrier may have therapeutic potential in an epigenetically defined subset of AML.This article is highlighted in the In This Issue feature, p. 275.


Subject(s)
Heat-Shock Proteins/genetics , Inositol/biosynthesis , Leukemia, Myeloid, Acute/drug therapy , Symporters/genetics , Animals , Developmental Biology , Humans , Mice
12.
Bioorg Med Chem Lett ; 51: 128376, 2021 11 01.
Article in English | MEDLINE | ID: mdl-34560263

ABSTRACT

We describe our efforts to introduce structural diversity to a previously described triazole-containing N1-carboline series of bromodomain and extra-terminal (BET) inhibitors. N9 carbolines were designed to retain favorable binding interactions that the N1-carbolines possess. A convergent synthetic route enabled modifications to reduce clearance, enhance physicochemical properties, and improve the overall in vitro profile. This work led to the identification of a potent BET inhibitor, (S)-2-{8-fluoro-5-[(3-fluoropyridin-2-yl)(oxan-4-yl)methyl]-7-[4-(2H3)methyl-1-methyl-1H-1,2,3-triazol-5-yl]-5H-pyrido[3,2-b]indol-3-yl}propan-2-ol (10), a compound with enhanced oral exposure in mice. Subsequent evaluation in a mouse triple-negative breast cancer tumor model revealed efficacy at 4 mg/kg of N9-carboline 10.


Subject(s)
Antineoplastic Agents/pharmacology , Carbolines/pharmacology , Drug Development , Proteins/antagonists & inhibitors , Triple Negative Breast Neoplasms/drug therapy , Administration, Oral , Animals , Antineoplastic Agents/administration & dosage , Antineoplastic Agents/chemistry , Carbolines/administration & dosage , Carbolines/chemistry , Cell Survival/drug effects , Dose-Response Relationship, Drug , Drug Screening Assays, Antitumor , Humans , Mammary Neoplasms, Experimental/drug therapy , Mammary Neoplasms, Experimental/pathology , Mice , Molecular Structure , Proteins/metabolism , Structure-Activity Relationship , Triple Negative Breast Neoplasms/pathology
13.
Bioorg Med Chem Lett ; 44: 128108, 2021 07 15.
Article in English | MEDLINE | ID: mdl-33991625

ABSTRACT

We describe our efforts to identify structurally diverse leads in the triazole-containing N1-carboline series of bromodomain and extra-terminal inhibitors. Replacement of the N5 "cap" phenyl moiety with various heteroaryls, coupled with additional modifications to the carboline core, provided analogs with similar potency, improved pharmacokinetic properties, and increased solubility compared to our backup lead, BMS-986225 (2). Rapid SAR exploration was enabled by a convergent, synthetic route. These efforts provided a potent BET inhibitor, 3-fluoropyridyl 12, that demonstrated robust efficacy in a multiple myeloma mouse tumor model at 1 mg/kg.


Subject(s)
Antineoplastic Agents/pharmacology , Carbolines/pharmacology , Drug Development , Multiple Myeloma/diet therapy , Proteins/antagonists & inhibitors , Triazoles/pharmacology , Animals , Antineoplastic Agents/chemical synthesis , Antineoplastic Agents/chemistry , Carbolines/chemical synthesis , Carbolines/chemistry , Dose-Response Relationship, Drug , Humans , Mice , Molecular Structure , Multiple Myeloma/metabolism , Proteins/metabolism , Structure-Activity Relationship , Triazoles/chemical synthesis , Triazoles/chemistry
14.
Cancer Discov ; 11(9): 2300-2315, 2021 09.
Article in English | MEDLINE | ID: mdl-33893150

ABSTRACT

Hundreds of genes become aberrantly silenced in acute myeloid leukemia (AML), with most of these epigenetic changes being of unknown functional consequence. Here, we demonstrate how gene silencing can lead to an acquired dependency on the DNA repair machinery in AML. We make this observation by profiling the essentiality of the ubiquitination machinery in cancer cell lines using domain-focused CRISPR screening, which revealed Fanconi anemia (FA) proteins UBE2T and FANCL as unique dependencies in AML. We demonstrate that these dependencies are due to a synthetic lethal interaction between FA proteins and aldehyde dehydrogenase 2 (ALDH2), which function in parallel pathways to counteract the genotoxicity of endogenous aldehydes. We show DNA hypermethylation and silencing of ALDH2 occur in a recurrent manner in human AML, which is sufficient to confer FA pathway dependency. Our study suggests that targeting of the ubiquitination reaction catalyzed by FA proteins can eliminate ALDH2-deficient AML. SIGNIFICANCE: Aberrant gene silencing is an epigenetic hallmark of human cancer, but the functional consequences of this process are largely unknown. In this study, we show how an epigenetic alteration leads to an actionable dependency on a DNA repair pathway through the disabling of genetic redundancy.This article is highlighted in the In This Issue feature, p. 2113.


Subject(s)
Aldehyde Dehydrogenase, Mitochondrial/genetics , Fanconi Anemia Complementation Group Proteins/metabolism , Leukemia, Myeloid, Acute/genetics , Cell Line, Tumor , Humans , Ubiquitination
15.
World J Gastroenterol ; 27(14): 1465-1482, 2021 Apr 14.
Article in English | MEDLINE | ID: mdl-33911468

ABSTRACT

BACKGROUND: Integrative multi-omic approaches have been increasingly applied to discovery and functional studies of complex human diseases. Short-term preoperative antibiotics have been adopted to reduce site infections in colorectal cancer (CRC) resections. We hypothesize that the antibiotics will impact analysis of multi-omic datasets generated from resection samples to investigate biological CRC risk factors. AIM: To assess the impact of preoperative antibiotics and other variables on integrated microbiome and human transcriptomic data generated from archived CRC resection samples. METHODS: Genomic DNA (gDNA) and RNA were extracted from prospectively collected 51 pairs of frozen sporadic CRC tumor and adjacent non-tumor mucosal samples from 50 CRC patients archived at a single medical center from 2010-2020. The 16S rRNA gene sequencing (V3V4 region, paired end, 300 bp) and confirmatory quantitative polymerase chain reaction (qPCR) assays were conducted on gDNA. RNA sequencing (IPE, 125 bp) was performed on parallel tumor and non-tumor RNA samples with RNA Integrity Numbers scores ≥ 6. RESULTS: PERMANOVA detected significant effects of tumor vs nontumor histology (P = 0.002) and antibiotics (P = 0.001) on microbial ß-diversity, but CRC tumor location (left vs right), diabetes mellitus vs not diabetic and Black/African Ancestry (AA) vs not Black/AA, did not reach significance. Linear mixed models detected significant tumor vs nontumor histology*antibiotics interaction terms for 14 genus level taxa. QPCR confirmed increased Fusobacterium abundance in tumor vs nontumor groups, and detected significantly reduced bacterial load in the (+)antibiotics group. Principal coordinate analysis of the transcriptomic data showed a clear separation between tumor and nontumor samples. Differentially expressed genes obtained from separate analyses of tumor and nontumor samples, are presented for the antibiotics, CRC location, diabetes and Black/AA race groups. CONCLUSION: Recent adoption of additional preoperative antibiotics as standard of care, has a measurable impact on -omics analysis of resected specimens. This study still confirmed increased Fusobacterium nucleatum in tumor.


Subject(s)
Colorectal Neoplasms , Microbiota , Anti-Bacterial Agents/therapeutic use , Colorectal Neoplasms/genetics , Colorectal Neoplasms/surgery , Humans , RNA, Ribosomal, 16S/genetics , Transcriptome
16.
Genome Res ; 30(9): 1258-1273, 2020 09.
Article in English | MEDLINE | ID: mdl-32887686

ABSTRACT

Improved identification of structural variants (SVs) in cancer can lead to more targeted and effective treatment options as well as advance our basic understanding of the disease and its progression. We performed whole-genome sequencing of the SKBR3 breast cancer cell line and patient-derived tumor and normal organoids from two breast cancer patients using Illumina/10x Genomics, Pacific Biosciences (PacBio), and Oxford Nanopore Technologies (ONT) sequencing. We then inferred SVs and large-scale allele-specific copy number variants (CNVs) using an ensemble of methods. Our findings show that long-read sequencing allows for substantially more accurate and sensitive SV detection, with between 90% and 95% of variants supported by each long-read technology also supported by the other. We also report high accuracy for long reads even at relatively low coverage (25×-30×). Furthermore, we integrated SV and CNV data into a unifying karyotype-graph structure to present a more accurate representation of the mutated cancer genomes. We find hundreds of variants within known cancer-related genes detectable only through long-read sequencing. These findings highlight the need for long-read sequencing of cancer genomes for the precise analysis of their genetic instability.


Subject(s)
Breast Neoplasms/genetics , Genomic Structural Variation , Whole Genome Sequencing/methods , Cell Line, Tumor , DNA Copy Number Variations , DNA Methylation , DNA, Neoplasm , Female , Humans , Nanopores , Organoids , RNA-Seq
17.
Cell ; 182(1): 145-161.e23, 2020 07 09.
Article in English | MEDLINE | ID: mdl-32553272

ABSTRACT

Structural variants (SVs) underlie important crop improvement and domestication traits. However, resolving the extent, diversity, and quantitative impact of SVs has been challenging. We used long-read nanopore sequencing to capture 238,490 SVs in 100 diverse tomato lines. This panSV genome, along with 14 new reference assemblies, revealed large-scale intermixing of diverse genotypes, as well as thousands of SVs intersecting genes and cis-regulatory regions. Hundreds of SV-gene pairs exhibit subtle and significant expression changes, which could broadly influence quantitative trait variation. By combining quantitative genetics with genome editing, we show how multiple SVs that changed gene dosage and expression levels modified fruit flavor, size, and production. In the last example, higher order epistasis among four SVs affecting three related transcription factors allowed introduction of an important harvesting trait in modern tomato. Our findings highlight the underexplored role of SVs in genotype-to-phenotype relationships and their widespread importance and utility in crop improvement.


Subject(s)
Crops, Agricultural/genetics , Gene Expression Regulation, Plant , Genomic Structural Variation , Solanum lycopersicum/genetics , Alleles , Cytochrome P-450 Enzyme System/genetics , Ecotype , Epistasis, Genetic , Fruit/genetics , Gene Duplication , Genome, Plant , Genotype , Inbreeding , Molecular Sequence Annotation , Phenotype , Plant Breeding , Quantitative Trait Loci/genetics
18.
G3 (Bethesda) ; 10(5): 1617-1628, 2020 05 04.
Article in English | MEDLINE | ID: mdl-32132169

ABSTRACT

Analysis of patient-derived DNA samples has identified hundreds of variants that are likely involved in neuropsychiatric diseases such as autism spectrum disorder (ASD) and schizophrenia (SCZ). While these studies couple behavioral phenotypes to individual genotypes, the number and diversity of candidate genes implicated in these disorders highlights the fact that the mechanistic underpinnings of these disorders are largely unknown. Here, we describe a RNAi-based screening platform that uses C. elegans to screen candidate neuropsychiatric risk genes (NRGs) for roles in controlling dendritic arborization. To benchmark this approach, we queried published lists of NRGs whose variants in ASD and SCZ are predicted to result in complete or partial loss of gene function. We found that a significant fraction (>16%) of these candidate NRGs are essential for dendritic development. Furthermore, these gene sets are enriched for dendritic arbor phenotypes (>14 fold) when compared to control RNAi datasets of over 500 human orthologs. The diversity of PVD structural abnormalities observed in these assays suggests that the functions of diverse NRGs (encoding transcription factors, chromatin remodelers, molecular chaperones and cytoskeleton-related proteins) converge to regulate neuronal morphology and that individual NRGs may play distinct roles in dendritic branching. We also demonstrate that the experimental value of this platform by providing additional insights into the molecular frameworks of candidate NRGs. Specifically, we show that ANK2/UNC-44 function is directly integrated with known regulators of dendritic arborization and suggest that altering the dosage of ARID1B/LET-526 expression during development affects neuronal morphology without diminishing aspects of cell fate specification.


Subject(s)
Autism Spectrum Disorder , Caenorhabditis elegans Proteins , Animals , Autism Spectrum Disorder/genetics , Caenorhabditis elegans/genetics , Caenorhabditis elegans/metabolism , Caenorhabditis elegans Proteins/genetics , Caenorhabditis elegans Proteins/metabolism , Humans , RNA Interference , Transcription Factors/genetics
20.
ACS Chem Neurosci ; 10(3): 1091-1098, 2019 03 20.
Article in English | MEDLINE | ID: mdl-30335349

ABSTRACT

Abnormal hippocampal activity has been linked to impaired cognitive performance in Alzheimer's disease and schizophrenia, leading to a hypothesis that normalization of this activity may be therapeutically beneficial. Our work suggests that one approach for hippocampal normalization may be through activation of the M4 muscarinic acetylcholine receptor. We used a brain penetrant M4 muscarinic acetylcholine receptor selective activator, PT-3763, to show dose-dependent attenuation of field potentials in Schaffer collateral (CA3-CA1) and recurrent associational connections (CA3-CA3) ex vivo in hippocampal slices. In vivo, systemic administration of PT-3763 led to attenuation of glutamate release in CA3 as measured by amperometry and to a dose-dependent decrease in population CA1 pyramidal activity as measured by fiber photometry. This decrease in population activity was also evident with a localized administration of the compound to the recorded site. Finally, PT-3763 reversed scopolamine-induced deficit in Morris water maze. Our results suggest that M4 muscarinic acetylcholine receptor activation may be a suitable therapeutic treatment in diseases associated with hyperactive hippocampal activity.


Subject(s)
Alzheimer Disease , Hippocampus/physiology , Muscarinic Agonists/pharmacology , Receptor, Muscarinic M4/agonists , Receptor, Muscarinic M4/physiology , Schizophrenia , Alzheimer Disease/drug therapy , Animals , Dose-Response Relationship, Drug , Hippocampus/drug effects , Male , Maze Learning/drug effects , Maze Learning/physiology , Mice , Muscarinic Agonists/chemistry , Muscarinic Agonists/therapeutic use , Organ Culture Techniques , Rats , Rats, Long-Evans , Rats, Sprague-Dawley , Schizophrenia/drug therapy
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