A PHP Error was encountered

Severity: Warning

Message: fopen(/var/lib/php/sessions/ci_sessionsqj9r2hrkkv3bpp2s5ergbo4olagp9m3): Failed to open stream: No space left on device

Filename: drivers/Session_files_driver.php

Line Number: 177

Backtrace:

File: /var/www/html/index.php
Line: 316
Function: require_once

A PHP Error was encountered

Severity: Warning

Message: session_start(): Failed to read session data: user (path: /var/lib/php/sessions)

Filename: Session/Session.php

Line Number: 137

Backtrace:

File: /var/www/html/index.php
Line: 316
Function: require_once

Department of Pathology and Clinical Bi... Publications | LitMetric

77 results match your criteria: "Department of Pathology and Clinical Bioinformatics[Affiliation]"

Editorial: Molecular informatics in precision medicine.

Front Med (Lausanne)

December 2024

Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.

View Article and Find Full Text PDF

Label-free single-cell RNA multiplexing leveraging genetic variability.

Nat Commun

December 2024

Department of Medicine 2 (Nephrology, Rheumatology, Clinical Immunology and Hypertension), Medical Faculty, RWTH Aachen University, Aachen, Germany.

Single cell RNA sequencing has provided unprecedented insights into the molecular cues and cellular heterogeneity underlying human disease. However, the high costs and complexity of single cell methods remain a major obstacle for generating large-scale human cohorts. Here, we compare current state-of-the-art single cell multiplexing technologies, and provide a widely applicable demultiplexing method, SoupLadle, that enables simple, yet robust high-throughput multiplexing leveraging genetic variability of patients.

View Article and Find Full Text PDF

OTP, CD44, and Ki-67: A prognostic marker panel for relapse free survival in patients with surgically resected pulmonary carcinoid.

Mod Pathol

December 2024

Department of Pathology, GROW School for Oncology and Reproduction, Maastricht University Medical Centre, Maastricht, The Netherlands; Department of Pathology and Clinical Bioinformatics, Erasmus MC, Rotterdam, the Netherlands. Electronic address:

Although most patients with pulmonary carcinoid (PC) can be cured by surgery, relapse may occur until 15 years after resection in up to 10% of patients. This is unpredictable at the outset, necessitating extensive follow-up (FU). We sought to determine whether an immunohistochemical marker panel (OTP, CD44, Ki-67) could provide better indication for relapse-free survival (RFS) and increase uniformity among pathologists regarding carcinoid classification.

View Article and Find Full Text PDF

Identification of Defined Molecular Subgroups on the Basis of Immunohistochemical Analyses and Potential Therapeutic Vulnerabilities of Pulmonary Carcinoids.

J Thorac Oncol

November 2024

GROW Research Institute for Oncology and Reproduction, Maastricht University Medical Centre, Maastricht, The Netherlands; Department of Pulmonary Medicine, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands. Electronic address:

Introduction: Multi-omic studies have identified three molecular separated pulmonary carcinoid (PC) subgroups (A1, A2, B) with distinctive mRNA expression profiles (e.g., orthopedia homeobox protein [OTP], achaete-scute homolog [ASCL1], and hepatocyte nuclear factor 1 homeobox A [HNF1A]).

View Article and Find Full Text PDF

Copy Number Variations (CNVs) are crucial in various diseases, especially cancer, but detecting them accurately from SNP genotyping arrays remains challenging. Therefore, this study benchmarked five CNV detection tools-PennCNV, QuantiSNP, iPattern, EnsembleCNV, and R-GADA-using SNP array and WGS data from 2002 individuals of the DRAGEN re-analysis of the 1000 Genomes project. Results showed significant variability in tool performance.

View Article and Find Full Text PDF
Article Synopsis
  • - Cholangiocarcinoma (CCA) is a type of aggressive bile duct cancer with limited prognostic markers and targets; however, the gene ITIH5, known for its tumor-suppressing functions, has been found to be upregulated in CCA, making it a promising marker for detection and prognosis.
  • - A study involving 175 CCA patients showed that high ITIH5 protein expression was linked to better survival rates, lower cancer stages, and reduced perineural invasion, indicating its potential as a useful biomarker.
  • - The findings suggest that ITIH5 could serve both as a marker for early detection through blood tests and a prognostic indicator in tissue samples, especially in cases of intrahepatic C
View Article and Find Full Text PDF

The XVI-th Banff Meeting for Allograft Pathology was held in Banff, Alberta, Canada, from 19th-23rd September 2022, as a joint meeting with the Canadian Society of Transplantation. To mark the 30 anniversary of the first Banff Classification, pre-meeting discussions were held on the past, present, and future of the Banff Classification. This report is a summary of the meeting highlights that were most important in terms of their effect on the Classification, including discussions around microvascular inflammation and biopsy-based transcript analysis for diagnosis.

View Article and Find Full Text PDF

Ultrarare Variants in DNA Damage Repair Genes in Pediatric Acute-Onset Neuropsychiatric Syndrome or Acute Behavioral Regression in Neurodevelopmental Disorders.

Dev Neurosci

October 2024

Department of Psychiatry and Behavioral Sciences, Department of Medicine, Department of Genetics, Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, New York, USA.

Introduction: Acute onset of severe psychiatric symptoms or regression may occur in children with premorbid neurodevelopmental disorders, although typically developing children can also be affected. Infections or other stressors are likely triggers. The underlying causes are unclear, but a current hypothesis suggests the convergence of genes that influence neuronal and immunological function.

View Article and Find Full Text PDF
Article Synopsis
  • Granulomatous disease can occur in up to 20% of patients with Common Variable Immunodeficiency (CVID), with granulomas forming in response to unknown antigenic triggers.
  • This study aimed to compare the cellular organization and protein expression of CVID granulomas with those in other granulomatous diseases like sarcoidosis and tuberculosis.
  • Findings showed that CVID granulomas are smaller and have distinct cellular characteristics, including a higher presence of certain immune cells, indicating a different underlying cause for their formation compared to other granulomatous diseases.
View Article and Find Full Text PDF

Immunological aetiology is supported for a subgroup with obsessive compulsive disorder (OCD) and conceptualized as autoimmune OCD. The longitudinal clinical course is detailed for three severely ill cases with OCD and indications of immunological involvement with off-label rituximab treatment every six months. All cases showed clear and sustained gains regarding symptom burden and function for over 2.

View Article and Find Full Text PDF

The tumor immune microenvironment in resected treatment-naive pancreatic cancer patients with long-term survival.

Pancreatology

November 2024

Erasmus MC Cancer Institute, Department of Surgery, University Medical Center Rotterdam, the Netherlands; Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.

Background: Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers worldwide. Presently, only a fraction of patients undergo successful surgical resection, the most effective treatment. Enhancing treatment strategies necessitates a deep comprehension of the factors underlying extended survival after surgical resection in patients.

View Article and Find Full Text PDF

Assessing the pathogenicity of genetic variants is a critical aspect of genomic medicine and precision healthcare. Over the last decades, the identification of genetic variants and their characterization has become simpler (advent of high-throughput sequencing technologies, analysis, and visualization support tools, etc.).

View Article and Find Full Text PDF

Human papillomavirus (HPV) infections are an increasing cause of oropharyngeal squamous cell carcinomas (OPSCC). Integration of the viral genome into the host genome is suggested to affect carcinogenesis, however, the correlation with OPSCC patient prognosis is still unclear. Research on HPV integration is hampered by current integration detection technologies and their unsuitability for formalin-fixed paraffin-embedded (FFPE) tissues.

View Article and Find Full Text PDF

A patient-based murine model recapitulates human STAT3 gain-of-function syndrome.

Clin Immunol

September 2024

Laboratory Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, the Netherlands. Electronic address:

Article Synopsis
  • STAT3 gain-of-function variants lead to a complex clinical condition with symptoms like early immunodeficiency, autoimmunity, and lymphoproliferation, though individual variant effects are not fully understood.
  • Researchers created a mouse model based on a specific STAT3 variant from a family with common and rare symptoms, revealing increased STAT3 activity and associated health issues like splenomegaly and lymphadenopathy.
  • The study highlights the importance of variant-specific effects in understanding STAT3-associated diseases and suggests that these mouse models could help in developing personalized treatments.
View Article and Find Full Text PDF

Aims: Uveal melanoma has a high propensity to metastasize. Prognosis is associated with specific driver mutations and copy number variations, and these can only be obtained after genetic testing. In this study we evaluated the efficacy of patient outcome prediction using deep learning on haematoxylin and eosin (HE)-stained primary uveal melanoma slides in comparison to molecular testing.

View Article and Find Full Text PDF

Unraveling Differences in Molecular Mechanisms and Immunological Contrasts between Squamous Cell Carcinoma and Adenocarcinoma of the Cervix.

Int J Mol Sci

June 2024

Department of Pathology and Clinical Bioinformatics, The Tumor Immuno-Pathology Laboratory, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands.

This study aims to refine our understanding of the inherent heterogeneity in cervical cancer by exploring differential gene expression profiles, immune cell infiltration dynamics, and implicated signaling pathways in the two predominant histological types of cervix carcinoma, Squamous Cell Carcinoma (SCC) and Adenocarcinoma (ADC). Targeted gene expression data that were previously generated from samples of primary cervical cancer were re-analyzed. The samples were grouped based on their histopathology, comparing SCC to ADC.

View Article and Find Full Text PDF

Banff 2022 Kidney Commentary: Reflections and Future Directions.

Transplantation

June 2024

Imperial College Renal and Transplant Centre, Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, United Kingdom.

Article Synopsis
  • - The XVIth Banff meeting in September 2022 marked the 30th anniversary of the Banff classification and focused on improving the classification system for kidney transplantation, resulting in two new publications.
  • - A group of 16 experts reviewed the manuscripts, highlighting the addition of two new entities that enhance the classification and enable better understanding of kidney transplant biopsies and their clinical implications.
  • - Despite the improvements, the Banff classification's complexity may still limit its use, necessitating further evidence and clinical trials to support the incorporation of molecular diagnostics and to refine diagnostic approaches for various types of kidney rejection.
View Article and Find Full Text PDF

Research on solid organ transplantation has taken advantage of the substantial acquisition of medical data and the use of artificial intelligence (AI) and machine learning (ML) to answer diagnostic, prognostic, and therapeutic questions for many years. Nevertheless, despite the question of whether AI models add value to traditional modeling approaches, such as regression models, their "black box" nature is one of the factors that have hindered the translation from research to clinical practice. Several techniques that make such models understandable to humans were developed with the promise of increasing transparency in the support of medical decision-making.

View Article and Find Full Text PDF

GATA6 identifies an immune-enriched phenotype linked to favorable outcomes in patients with pancreatic cancer undergoing upfront surgery.

Cell Rep Med

May 2024

Department of Pathology and Clinical Bioinformatics, Erasmus University Medical Centre, Rotterdam, the Netherlands; The Tumor Immuno-Pathology Laboratory, Erasmus University Medical Centre, Rotterdam, the Netherlands. Electronic address:

This study underscores GATA6's role in distinguishing classical and basal-like pancreatic ductal adenocarcinoma (PDAC) phenotypes. Retrospective studies associate GATA6 immunohistochemistry (IHC) expression with survival outcomes, warranting prospective validation. In a prospective treatment-naive cohort of patients with resected PDAC, GATA6 IHC proves a prognostic discriminator, associating high GATA6 expression with extended survival and the classical PDAC phenotype.

View Article and Find Full Text PDF
Article Synopsis
  • The cerebellar cortex, while appearing uniform, has significant structural, genetic, and physiological diversity, particularly among Purkinje cells (PCs), which are the main output neurons.
  • Purkinje cells can be grouped into different populations based on their unique molecular markers and physiological characteristics, such as action potential rates and plasticity tendencies.
  • The article aims to explore the mechanisms that control PC activity and plasticity, and includes a pathway analysis to connect specific molecular traits of PC populations with their physiological behaviors.
View Article and Find Full Text PDF

Despite decades of research, the prognosis of high-grade pediatric brain tumors (PBTs) remains dismal; however, recent cases of favorable clinical responses were documented in clinical trials using oncolytic viruses (OVs). In the current study, we employed four different species of OVs: adenovirus Delta24-RGD, herpes simplex virus rQNestin34.5v1, reovirus R124, and the non-virulent Newcastle disease virus rNDV-F0-GFP against three entities of PBTs (high-grade gliomas, atypical teratoid/rhabdoid tumors, and ependymomas) to determine their efficacy.

View Article and Find Full Text PDF
Article Synopsis
  • A study was conducted to compare two strategies for diagnosing interstitial lung disease (ILD): a step-up approach using transbronchial cryobiopsy followed by surgical lung biopsy (SLB) if needed, versus starting with immediate SLB.
  • The COLD study included 55 patients across six hospitals in the Netherlands and measured outcomes like unexpected chest tube drainage, diagnostic yield, and adverse events over a 12-week follow-up.
  • Findings showed that 11% of patients in the step-up group required unexpected chest tube drainage, indicating varying risks and benefits between the two biopsy methods.
View Article and Find Full Text PDF