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1.
Kidney Int ; 105(4): 717-730, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38154557

RESUMO

Some patients diagnosed with benign IgA nephropathy (IgAN) develop a progressive clinical course, not predictable by known clinical or histopathological parameters. To assess if gene expression can differentiate between progressors and non-progressors with assumed benign IgAN, we tested microdissected glomeruli from archival kidney biopsy sections from adult patients with stable clinical remission (21 non-progressors) or from 15 patients that had undergone clinical progression within a 25-year time frame. Based on 1 240 differentially expressed genes from patients with suitable sequencing results, we identified eight IgAN progressor and nine non-progressor genes using a two-component classifier. These genes, including APOL5 and ZXDC, predicted disease progression with 88% accuracy, 75% sensitivity and 100% specificity on average 21.6 years before progressive disease was clinically documented. APOL lipoproteins are associated with inflammation, autophagy and kidney disease while ZXDC is a zinc-finger transcription factor modulating adaptive immunity. Ten genes from our transcriptomics data overlapped with an external genome wide association study dataset, although the gene set enrichment test was not statistically significant. We also identified 45 drug targets in the DrugBank database, including angiotensinogen, a target of sparsentan (dual antagonist of the endothelin type A receptor and the angiotensin II type 1 receptor) currently investigated for IgAN treatment. Two validation cohorts were used for substantiating key results, one by immunohistochemistry and the other by nCounter technology. Thus, glomerular mRNA sequencing from diagnostic kidney biopsies from patients with assumed benign IgAN can differentiate between future progressors and non-progressors at the time of diagnosis.


Assuntos
Glomerulonefrite por IGA , Adulto , Humanos , Glomerulonefrite por IGA/diagnóstico , Glomerulonefrite por IGA/tratamento farmacológico , Glomerulonefrite por IGA/genética , Estudo de Associação Genômica Ampla , Glomérulos Renais/patologia , Perfilação da Expressão Gênica/métodos , Regulação da Expressão Gênica
2.
Bus Soc ; 63(4): 869-919, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38529203

RESUMO

While today it is universally acknowledged that COVID-19 has generated immense challenges for businesses and societies worldwide, public perceptions varied significantly at the time of the pandemic's initial appearance, even among democratic societies with comparable media systems. The growing scholarship on grand societal challenges in management and organization studies, however, tends to neglect the initial social construction of issues as complex, uncertain, evaluative, and widespread. We address this shortcoming by exploring the initial communicative enactment of COVID-19 in the media-based public discourse in Switzerland, Germany, and the United Kingdom. By applying a social problem work lens, we identify three mechanisms that explain the maturation of COVID-19 into a grand challenge, further showing how these are contextually dependent on differences in discourse quality. We add to research on grand challenges, issue maturation, and framing dynamics by theorizing how issues become constructed and acknowledged as grand challenges in the first place.

3.
Brief Bioinform ; 22(2): 1656-1678, 2021 03 22.
Artigo em Inglês | MEDLINE | ID: mdl-32055842

RESUMO

Drug development involves a deep understanding of the mechanisms of action and possible side effects of each drug, and sometimes results in the identification of new and unexpected uses for drugs, termed as drug repurposing. Both in case of serendipitous observations and systematic mechanistic explorations, confirmation of new indications for a drug requires hypothesis building around relevant drug-related data, such as molecular targets involved, and patient and cellular responses. These datasets are available in public repositories, but apart from sifting through the sheer amount of data imposing computational bottleneck, a major challenge is the difficulty in selecting which databases to use from an increasingly large number of available databases. The database selection is made harder by the lack of an overview of the types of data offered in each database. In order to alleviate these problems and to guide the end user through the drug repurposing efforts, we provide here a survey of 102 of the most promising and drug-relevant databases reported to date. We summarize the target coverage and types of data available in each database and provide several examples of how multi-database exploration can facilitate drug repurposing.


Assuntos
Bases de Dados Factuais , Reposicionamento de Medicamentos , Biologia Computacional/métodos , Sistemas de Liberação de Medicamentos , Inquéritos e Questionários
4.
Clin Infect Dis ; 72(10): 1838-1842, 2021 05 18.
Artigo em Inglês | MEDLINE | ID: mdl-33091118

RESUMO

An effective response to the coronavirus disease 2019 (COVID-19) pandemic requires a better understanding of the biology of the infection and the identification of validated biomarker profiles that would increase the availability, accuracy, and speed of COVID-19 testing. Here, we describe the strategic objectives and action lines of the European Alliance of Medical Research Infrastructures (AMRI), established to improve the research process and tackle challenges related to diagnostic tests and biomarker development. Recommendations include: the creation of a European taskforce for validation of novel diagnostic products, the definition and promotion of criteria for COVID-19 samples biobanking, the identification and validation of biomarkers as clinical endpoints for clinical trials, and the definition of immune biomarker signatures at different stages of the disease. An effective management of the COVID-19 pandemic is possible only if there is a high level of knowledge and coordination between the public and private sectors within a robust quality framework.


Assuntos
Pesquisa Biomédica , COVID-19 , Bancos de Espécimes Biológicos , Biomarcadores , Teste para COVID-19 , Humanos , Pandemias , SARS-CoV-2
5.
Cancer Cell Int ; 21(1): 690, 2021 Dec 20.
Artigo em Inglês | MEDLINE | ID: mdl-34930263

RESUMO

BACKGROUND: Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal cancer and one of the most common cancers. While survival for localized ccRCC is good, the survival of metastatic disease is not, and thirty percent of patients with ccRCC develop metastases during follow-up. Although current scoring methods accurately identify patients at low progression risk, a small subgroup of those patients still experience metastasis. We therefore aimed to identify ccRCC progression biomarkers in "low-risk" patients who were potentially eligible for adjuvant treatments or more intensive follow-up. METHODS: We assembled a cohort of ccRCC patients (n = 443) and identified all "low-risk" patients who later developed progressing tumors (n = 8). Subsequently, we performed genome-wide expression profiling from formalin-fixed samples obtained at initial surgery from these "low-risk" patients and 16 matched patients not progressing to recurrence with metastasis. The patients were matched for Leibovich sore, creatinine, age, sex, tumor size and tumor stage. Key results were confirmed with qPCR and external data from The Cancer Genome Atlas. RESULTS: Principal component analysis indicated that systematic transcriptomic differences were already detectable at the time of initial surgery. One thousand one hundred sixty-seven genes, mainly associated with cancer and immune-related pathways, were differentially expressed between progressors and nonprogressors. A search for a classifier revealed that overexpression of AGAP2-AS1, an antisense long noncoding RNA, correctly classified 23 of 24 samples, years (4.5 years average) in advance of the discovery of metastasis and without requiring larger gene panels. Subsequently, we confirmed AGAP2-AS1 gene overexpression by qPCR in the same samples (p < 0.05). Additionally, in external data from The Cancer Genome Atlas, overexpression of AGAP2-AS1 is correlated with overall unfavorable survival outcome in ccRCC, irrespective of other prognostic predictors (p = 2.44E-7). CONCLUSION: AGAP2-AS1 may represent a novel biomarker identifying high-risk ccRCC patients currently classified as "low risk" at the time of surgery.

6.
Adm Sci Q ; 65(3): 565-605, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32903518

RESUMO

Based on an in-depth, qualitative case study about a conflict between governmental authorities from the United States and Switzerland over the regulation of Swiss banks, we introduce indirect compellence as a novel triadic and indirect mechanism through which coercion leads to institutional change. Hostage-taking being a prototypical example, indirect compellence is typified by a coercive actor who takes a third party hostage to gain influence over a targeted actor. In our case, it meant that U.S. authorities (coercers) compelled Swiss policy makers (targets) to erode the famed Swiss banking secrecy rules by threatening the targets to otherwise enforce U.S. law extraterritorially against Swiss banks and bankers (hostages). Our constructivist and target-centered perspective explains this type of coercive pressure in detail, and it also suggests that targeted policy makers judge and respond to it contingent on their political ideologies. Our study contributes to research on power and influence in institutional environments and to research on global business regulation and transnational governance. Most generally, it also expands scholarly understanding of triadic relationships. In contrast to Simmelian perspectives' focus on triads in which the third party is in a powerful brokerage position and frequently benefits as a tertius gaudens, our study suggests that the third party can also become a rather powerless tertius miserabilis who suffers rather than benefits from others' conflict.

7.
Am J Physiol Renal Physiol ; 316(5): F1053-F1067, 2019 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-30838877

RESUMO

Renal cell cancer is among the most common forms of cancer in humans, with around 35,000 deaths attributed to kidney carcinoma in the European Union in 2012 alone. Clear cell renal cell carcinoma (ccRCC) represents the most common form of kidney cancer and the most lethal of all genitourinary cancers. Here, we apply omics technologies to archival core biopsies to investigate the biology underlying ccRCC. Knowledge of these underlying processes should be useful for the discovery and/or confirmation of novel therapeutic approaches and ccRCC biomarker development. From partial or full nephrectomies of 11 patients, paired core biopsies of ccRCC-affected tissue and adjacent ("peritumorous") nontumor tissue were both sampled and subjected to proteomics analyses. We combined proteomics results with our published mRNA sequencing data from the same patients and with published miRNA sequencing data from an overlapping patient cohort from our institution. Statistical analysis and pathway analysis were performed with JMP Genomics and Ingenuity Pathway Analysis (IPA), respectively. Proteomics analysis confirmed the involvement of metabolism and oxidative stress-related pathways in ccRCC, whereas the most affected pathways in the mRNA sequencing data were related to the immune system. Unlike proteomics or mRNA sequencing alone, a combinatorial cross-omics pathway analysis approach captured a broad spectrum of biological processes underlying ccRCC, such as mitochondrial damage, repression of apoptosis, and immune system pathways. Sirtuins, immunoproteasome genes, and CD74 are proposed as potential targets for the treatment of ccRCC.


Assuntos
Biomarcadores Tumorais/genética , Carcinoma de Células Renais/química , Carcinoma de Células Renais/genética , Perfilação da Expressão Gênica/métodos , Neoplasias Renais/química , Neoplasias Renais/genética , Proteômica/métodos , Adulto , Idoso , Biópsia com Agulha de Grande Calibre , Carcinoma de Células Renais/patologia , Linhagem Celular Tumoral , Estudos de Viabilidade , Feminino , Regulação Neoplásica da Expressão Gênica , Redes Reguladoras de Genes , Humanos , Neoplasias Renais/patologia , Masculino , Pessoa de Meia-Idade , Proteoma , Transdução de Sinais , Fixação de Tecidos , Transcriptoma
8.
Int J Mol Sci ; 19(3)2018 Mar 10.
Artigo em Inglês | MEDLINE | ID: mdl-29534467

RESUMO

Novel predictive tools for clear cell renal cell carcinoma (ccRCC) are urgently needed. MicroRNAs (miRNAs) have been increasingly investigated for their predictive value, and formalin-fixed paraffin-embedded biopsy archives may potentially be a valuable source of miRNA sequencing material, as they remain an underused resource. Core biopsies of both cancerous and adjacent normal tissues were obtained from patients (n = 12) undergoing nephrectomy. After small RNA-seq, several analyses were performed, including classifier evaluation, obesity-related inquiries, survival analysis using publicly available datasets, comparisons to the current literature and ingenuity pathway analyses. In a comparison of tumour vs. normal, 182 miRNAs were found with significant differential expression; miR-155 was of particular interest as it classified all ccRCC samples correctly and correlated well with tumour size (R² = 0.83); miR-155 also predicted poor survival with hazard ratios of 2.58 and 1.81 in two different TCGA (The Cancer Genome Atlas) datasets in a univariate model. However, in a multivariate Cox regression analysis including age, sex, cancer stage and histological grade, miR-155 was not a statistically significant survival predictor. In conclusion, formalin-fixed paraffin-embedded biopsy tissues are a viable source of miRNA-sequencing material. Our results further support a role for miR-155 as a promising cancer classifier and potentially as a therapeutic target in ccRCC that merits further investigation.


Assuntos
Biomarcadores Tumorais/genética , Carcinoma de Células Renais/patologia , Neoplasias Renais/patologia , MicroRNAs/genética , Inclusão em Parafina/métodos , Fixação de Tecidos/métodos , Idoso , Biomarcadores Tumorais/metabolismo , Biomarcadores Tumorais/normas , Carcinoma de Células Renais/genética , Carcinoma de Células Renais/metabolismo , Feminino , Formaldeído , Humanos , Neoplasias Renais/genética , Neoplasias Renais/metabolismo , Masculino , MicroRNAs/metabolismo , MicroRNAs/normas , Pessoa de Meia-Idade , Inclusão em Parafina/normas , Fixação de Tecidos/normas
9.
Sci Prog ; 99(Pt 1): 59-67, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27120814

RESUMO

Genome-wide association study (GWAS) technology has been a primary method for identifying the genes responsible for diseases and other traits for the past 10 years. Over 2,000 human GWAS reports now appear in the scientific journals. The technology is continuing to improve, and has recently become accessible to researchers studying a wide variety of animals, plants and model organisms. Here, we present an overview of GWAS concepts: the underlying biology, the origins of the method, and the primary components of a GWAS experiment.


Assuntos
Estudo de Associação Genômica Ampla , Animais , Humanos , Fenótipo
10.
Nephrol Dial Transplant ; 29(6): 1177-85, 2014 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-24569495

RESUMO

BACKGROUND: We have previously described a transcriptomic classifier consisting of metzincins and related genes (MARGS) discriminating kidneys and other organs with or without fibrosis from human biopsies. We now apply our MARGS-based algorithm to a rat model of age-associated interstitial renal fibrosis. METHODS: Untreated Fisher 344 rats (n = 76) were sacrificed between 2 to 104 weeks of age. For gene expression studies, we used single colour (Cy3) Agilent Whole Rat Genome 4 × 44k microarrays; 4-5 animals of each sex were profiled at each of the following ages: 2, 5, 6, 8, 15, 21, 78 and 104 weeks. Intensity data were subjected to variance stabilization (www.Partek.com). Data were analysed with ANOVA and other statistical methods. RESULTS: Sixty MARGS were differentially expressed across age groups. More MARGS were differentially expressed in older males than in older females. Principal component analysis showed gene expression induced segregation of age groups by sex from 6 to 104 weeks of age. The expression level of MMP7 correlated best with fibrosis grade. Severity of fibrosis was determined in 20 animals at 78 and 104 weeks of age. Expression values of 15 of 19 genes of the original classifier present on the Agilent array, in conjunction with linear discriminant analysis, was sufficient to correctly classify these 20 samples into non-fibrosis and fibrosis. Overrepresentation of MMP2 protein and CD44 protein in fibrosis was confirmed by immunofluorescence. CONCLUSIONS: Based on these results and our previous work, the MARGS classifier represents a cross-organ and cross-species classifier of fibrosis irrespective of aetiology. This finding provides evidence for a common pathway leading to fibrosis and will help to design a PCR-based clinical test.


Assuntos
Envelhecimento/genética , Envelhecimento/patologia , Perfilação da Expressão Gênica/métodos , Rim/patologia , Rim/fisiologia , Transcriptoma/fisiologia , Algoritmos , Animais , Modelos Animais de Doenças , Feminino , Fibrose , Rim/fisiopatologia , Masculino , Metaloproteinase 2 da Matriz/metabolismo , Metaloproteinase 7 da Matriz/metabolismo , Análise em Microsséries , Reação em Cadeia da Polimerase , Análise de Componente Principal , Ratos , Ratos Endogâmicos F344
11.
Biomarkers ; 18(5): 436-45, 2013 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-23829492

RESUMO

CONTEXT: Correct gender assignment in humans at the molecular level is crucial in many scientific disciplines and applied areas. MATERIALS AND METHODS: Candidate gender markers were identified through supervised statistical analysis of genome wide microarray expression data from human blood samples (N = 123, 58 female, 65 male) as a training set. The potential of the markers to predict undisclosed tissue donor gender was tested on microarray data from 13 healthy and 11 cancerous human tissue collections (internal) and external datasets from samples of varying tissue origin. The abundance of some genes in the marker panel was quantified by RT-PCR as alternative analytical technology. RESULTS: We identified and qualified predictive, gender-specific transcript markers based on a set of five genes (RPS4Y1, EIF1AY, DDX3Y, KDM5D and XIST). CONCLUSION: Gene expression marker panels can be used as a robust tissue- and platform-independent predictive approach for gender determination.


Assuntos
Perfilação da Expressão Gênica , RNA Mensageiro/sangue , Análise para Determinação do Sexo/métodos , Biomarcadores/sangue , RNA Helicases DEAD-box/sangue , RNA Helicases DEAD-box/genética , Feminino , Histona Desmetilases/sangue , Histona Desmetilases/genética , Humanos , Masculino , Antígenos de Histocompatibilidade Menor , Análise de Sequência com Séries de Oligonucleotídeos , Especificidade de Órgãos , RNA Longo não Codificante/sangue , RNA Longo não Codificante/genética , RNA Mensageiro/genética , Proteínas Ribossômicas/sangue , Proteínas Ribossômicas/genética , Transcriptoma
12.
Magn Reson (Gott) ; 4(1): 27-46, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37904801

RESUMO

Laser-induced magnetic dipole (LaserIMD) spectroscopy and light-induced double electron-electron resonance (LiDEER) spectroscopy are important techniques in the emerging field of light-induced pulsed dipolar electron paramagnetic resonance (EPR) spectroscopy (light-induced PDS). These techniques use the photoexcitation of a chromophore to the triplet state and measure its dipolar coupling to a neighboring electron spin, which allows the determination of distance restraints. To date, LaserIMD and LiDEER have been analyzed with software tools that were developed for a pair of two S=1/2 spins and that neglected the zero-field splitting (ZFS) of the excited triplet. Here, we explore the limits of this assumption and show that the ZFS can have a significant effect on the shape of the dipolar trace. For a detailed understanding of the effect of the ZFS, a theoretical description for LaserIMD and LiDEER is derived, taking into account the non-secular terms of the ZFS. Simulations based on this model show that the effect of the ZFS is not that pronounced in LiDEER for experimentally relevant conditions. However, the ZFS leads to an additional decay in the dipolar trace in LaserIMD. This decay is not that pronounced in Q-band but can be quite noticeable for lower magnetic field strengths in X-band. Experimentally recorded LiDEER and LaserIMD data confirm these findings. It is shown that ignoring the ZFS in the data analysis of LaserIMD traces can lead to errors in the obtained modulation depths and background decays. In X-band, it is additionally possible that the obtained distance distribution is plagued by long distance artifacts.

13.
Hypertens Res ; 46(1): 144-156, 2023 01.
Artigo em Inglês | MEDLINE | ID: mdl-36229534

RESUMO

Hypertensive nephropathy (HN) requires a kidney biopsy as diagnostic gold-standard but histological findings are unspecific and specific prognostic markers are missing. We aimed at identifying candidate prognostic markers based on glomerular protein signatures. We studied adult patients (n = 17) with eGFR >30 ml/min/1.73m2 and proteinuria <3 g/d from the Norwegian Kidney Biopsy Registry, including subjects non progressing (NP, n = 9), or progressing (P, n = 8) to end-stage renal disease (ESRD) within an average follow-up of 22 years. Glomerular cross-sections from archival kidney biopsy sections were microdissected and processed for protein extraction. Proteomic analyses were performed using Q-exactive HF mass spectrometer and relative glomerular protein abundances were compared between P and NP patients. Immunohistochemistry (IHC) was used to validate selected data. Amongst 1870 quality filtered proteins, 58 were differentially expressed in P and NP patients' glomeruli, with absolute fold changes (FC) ≥1.5, p ≤ 0.05. Supervised classifier analysis (K nearest neighbor) identified a set of five proteins, including Gamma-butyrobetaine dioxygenase (BBOX1, O75936) and Cadherin 16 (CDH16, O75309), overexpressed in P, and Eosinophil peroxidase (EPX, P11678), DnaJ homolog subfamily B member 1 (DNAJB1, P25685) and Alpha-1-syntrophin (SNTA1, Q13424), overexpressed in NP glomeruli, correctly classifying 16/17 kidney biopsy samples. Geneset Enrichment Analysis (GSEA), showed that metabolic pathways were generally enriched in P, and structural cell pathways in NP. Pathway analysis identified Epithelial Adherens Junction Signaling as most affected canonical pathway. IHC analysis confirmed overexpression of BBOX1 and Cadherin 16 in glomeruli from P patients. In conclusion, glomerular proteomic profiling can be used to discriminate P from NP HN patients.


Assuntos
Hipertensão Renal , Proteômica , Adulto , Humanos , Glomérulos Renais/metabolismo , Hipertensão Renal/metabolismo , Progressão da Doença , Biópsia , Caderinas/metabolismo , Rim/patologia , Proteínas de Choque Térmico HSP40/metabolismo
14.
Physiol Rep ; 11(19): e15825, 2023 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-37813528

RESUMO

Hypertensive nephrosclerosis (HN) and Type 2 diabetic nephropathy (T2DN) are the leading causes of chronic kidney disease (CKD). To explore shared pathogenetic mechanisms, we analyzed transcriptomes of kidney biopsies from patients with HN or T2DN. Total RNA was extracted from 10 µm whole kidney sections from patients with HN, T2DN, and normal controls (Ctrl) (n = 6 for each group) and processed for RNA sequencing. Differentially expressed (log2 fold change >1, adjusted p < 0.05) genes (DEG) and molecular pathways were analyzed, and selected results were validated by immunohistochemistry (IHC). ELISA on serum samples was performed on a related cohort consisting of patients with biopsy-proven HN (n = 13) and DN (n = 9), and a normal control group (n = 14). Cluster analysis on RNA sequencing data separated diseased and normal tissues. RNA sequencing revealed that 88% (341 out of 384) of DEG in HN were also altered in T2DN, while gene set enrichment analysis (GSEA) showed that over 90% of affected molecular pathways, including those related to inflammation, immune response, and cell-cycle regulation, were similarly impacted in both HN and T2DN samples. The increased expression of genes tied to interleukin signaling and lymphocyte activation was more pronounced in HN, while genes associated with extracellular matrix organization were more evident in T2DN. Both HN and T2DN tissues exhibited significant upregulation of genes connected with inflammatory responses, T-cell activity, and partial epithelial to mesenchymal transition (p-EMT). Immunohistochemistry (IHC) further confirmed T-cell (CD4+ and CD8+ ) infiltration in the diseased tissues. Additionally, IHC revealed heightened AXL protein expression, a key regulator of inflammation and p-EMT, in both HN and T2DN, while serum analysis indicated elevated soluble AXL levels in patients with both conditions. These findings underline the shared molecular mechanisms between HN and T2DN, hinting at the potential for common therapeutic strategies targeting both diseases.


Assuntos
Diabetes Mellitus Tipo 2 , Nefropatias Diabéticas , Nefroesclerose , Humanos , Nefropatias Diabéticas/metabolismo , Nefroesclerose/genética , Nefroesclerose/complicações , Transição Epitelial-Mesenquimal , Transcriptoma , Diabetes Mellitus Tipo 2/complicações , Diabetes Mellitus Tipo 2/genética , Inflamação/genética , Inflamação/complicações
15.
Genome Biol ; 24(1): 245, 2023 10 26.
Artigo em Inglês | MEDLINE | ID: mdl-37884999

RESUMO

The Quartet Data Portal facilitates community access to well-characterized reference materials, reference datasets, and related resources established based on a family of four individuals with identical twins from the Quartet Project. Users can request DNA, RNA, protein, and metabolite reference materials, as well as datasets generated across omics, platforms, labs, protocols, and batches. Reproducible analysis tools allow for objective performance assessment of user-submitted data, while interactive visualization tools support rapid exploration of reference datasets. A closed-loop "distribution-collection-evaluation-integration" workflow enables updates and integration of community-contributed multiomics data. Ultimately, this portal helps promote the advancement of reference datasets and multiomics quality control.


Assuntos
Multiômica , Software , Humanos , Controle de Qualidade
16.
Genome Biol ; 24(1): 270, 2023 Nov 27.
Artigo em Inglês | MEDLINE | ID: mdl-38012772

RESUMO

BACKGROUND: Genomic DNA reference materials are widely recognized as essential for ensuring data quality in omics research. However, relying solely on reference datasets to evaluate the accuracy of variant calling results is incomplete, as they are limited to benchmark regions. Therefore, it is important to develop DNA reference materials that enable the assessment of variant detection performance across the entire genome. RESULTS: We established a DNA reference material suite from four immortalized cell lines derived from a family of parents and monozygotic twins. Comprehensive reference datasets of 4.2 million small variants and 15,000 structural variants were integrated and certified for evaluating the reliability of germline variant calls inside the benchmark regions. Importantly, the genetic built-in-truth of the Quartet family design enables estimation of the precision of variant calls outside the benchmark regions. Using the Quartet reference materials along with study samples, batch effects are objectively monitored and alleviated by training a machine learning model with the Quartet reference datasets to remove potential artifact calls. Moreover, the matched RNA and protein reference materials and datasets from the Quartet project enables cross-omics validation of variant calls from multiomics data. CONCLUSIONS: The Quartet DNA reference materials and reference datasets provide a unique resource for objectively assessing the quality of germline variant calls throughout the whole-genome regions and improving the reliability of large-scale genomic profiling.


Assuntos
Benchmarking , Genoma Humano , Humanos , Reprodutibilidade dos Testes , Polimorfismo de Nucleotídeo Único , Células Germinativas , Sequenciamento de Nucleotídeos em Larga Escala/métodos
17.
Nat Biotechnol ; 2023 Sep 07.
Artigo em Inglês | MEDLINE | ID: mdl-37679545

RESUMO

Certified RNA reference materials are indispensable for assessing the reliability of RNA sequencing to detect intrinsically small biological differences in clinical settings, such as molecular subtyping of diseases. As part of the Quartet Project for quality control and data integration of multi-omics profiling, we established four RNA reference materials derived from immortalized B-lymphoblastoid cell lines from four members of a monozygotic twin family. Additionally, we constructed ratio-based transcriptome-wide reference datasets between two samples, providing cross-platform and cross-laboratory 'ground truth'. Investigation of the intrinsically subtle biological differences among the Quartet samples enables sensitive assessment of cross-batch integration of transcriptomic measurements at the ratio level. The Quartet RNA reference materials, combined with the ratio-based reference datasets, can serve as unique resources for assessing and improving the quality of transcriptomic data in clinical and biological settings.

18.
Nat Biotechnol ; 2023 Sep 07.
Artigo em Inglês | MEDLINE | ID: mdl-37679543

RESUMO

Characterization and integration of the genome, epigenome, transcriptome, proteome and metabolome of different datasets is difficult owing to a lack of ground truth. Here we develop and characterize suites of publicly available multi-omics reference materials of matched DNA, RNA, protein and metabolites derived from immortalized cell lines from a family quartet of parents and monozygotic twin daughters. These references provide built-in truth defined by relationships among the family members and the information flow from DNA to RNA to protein. We demonstrate how using a ratio-based profiling approach that scales the absolute feature values of a study sample relative to those of a concurrently measured common reference sample produces reproducible and comparable data suitable for integration across batches, labs, platforms and omics types. Our study identifies reference-free 'absolute' feature quantification as the root cause of irreproducibility in multi-omics measurement and data integration and establishes the advantages of ratio-based multi-omics profiling with common reference materials.

19.
J Phys Chem Lett ; 13(47): 10958-10964, 2022 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-36399541

RESUMO

Distance determination with pulsed EPR has become an important technique for the structural investigation of biomacromolecules, with double electron-electron resonance spectroscopy (DEER) as the most important method. GdIII-based spin labels are one of the most frequently used spin labels for DEER owing to their stability against reduction, high magnetic moment, and absence of orientation selection. A disadvantage of GdIII-GdIII DEER is the low modulation depth due to the broad EPR spectrum of GdIII. Here, we introduce laser-induced magnetic dipole spectroscopy (LaserIMD) with a spin pair consisting of GdIII(PymiMTA) and a photoexcited porphyrin as an alternative technique. We show that the excited state of the porphyrin is not disturbed by the presence of the GdIII complex and that herewith modulation depths of almost 40% are possible. This is significantly higher than the value of 7.2% that was achieved with GdIII-GdIII DEER.


Assuntos
Porfirinas , Espectroscopia de Ressonância de Spin Eletrônica , Marcadores de Spin , Fenômenos Magnéticos , Lasers
20.
Sci Rep ; 12(1): 13503, 2022 08 05.
Artigo em Inglês | MEDLINE | ID: mdl-35931808

RESUMO

Clear cell renal cell carcinoma (ccRCC) is the most common renal cancer. Identification of ccRCC likely to progress, despite an apparent low risk at the time of surgery, represents a key clinical issue. From a cohort of adult ccRCC patients (n = 443), we selected low-risk tumors progressing within a 5-years average follow-up (progressors: P, n = 8) and non-progressing (NP) tumors (n = 16). Transcriptome sequencing, miRNA sequencing and proteomics were performed on tissues obtained at surgery. We identified 151 proteins, 1167 mRNAs and 63 miRNAs differentially expressed in P compared to NP low-risk tumors. Pathway analysis demonstrated overrepresentation of proteins related to "LXR/RXR and FXR/RXR Activation", "Acute Phase Response Signaling" in NP compared to P samples. Integrating mRNA, miRNA and proteomic data, we developed a 10-component classifier including two proteins, three genes and five miRNAs, effectively differentiating P and NP ccRCC and capturing underlying biological differences, potentially useful to identify "low-risk" patients requiring closer surveillance and treatment adjustments. Key results were validated by immunohistochemistry, qPCR and data from publicly available databases. Our work suggests that LXR, FXR and macrophage activation pathways could be critically involved in the inhibition of the progression of low-risk ccRCC. Furthermore, a 10-component classifier could support an early identification of apparently low-risk ccRCC patients.


Assuntos
Carcinoma de Células Renais , Neoplasias Renais , MicroRNAs , Adulto , Biomarcadores Tumorais/genética , Carcinoma de Células Renais/patologia , Progressão da Doença , Perfilação da Expressão Gênica/métodos , Regulação Neoplásica da Expressão Gênica , Humanos , Neoplasias Renais/patologia , MicroRNAs/genética , MicroRNAs/metabolismo , Proteômica , RNA Mensageiro/genética , RNA Mensageiro/metabolismo
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