Molecular characteristics of a pancreatic adenocarcinoma associated with Shwachman‐Diamond syndrome

Dhanraj, Santhosh; Manji, Arif; Pinto, Dalila; Scherer, Stephen W.; Favre, H.; Loh, Mignon L.; Chetty, Runjan; Wei, Alice C.; Dror, Yigal

doi:10.1002/pbc.24453

Cited by 23 publications

(23 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…7): (1) ASIC2 acid sensing ion channel 2, (2) GABRE—gamma-aminobutyric acid A receptor, epsilon, (3) LINC00525—long intergenic non-protein coding RNA 525, (4) CTNNA3—catenin alpha 3. The CTNNA3 gene has been shown to be linked to the Shwachman-Diamond syndrome which is characterized by a high risk of leukaemia [31]. In terms of relation to the bone marrow processes the GABRE gene which is a gammaaminobutyric acid receptor has proved to play a role during bone marrow stromal cell transplantation in the injured spinal cord in mice [32].…”

Section: Resultsmentioning

confidence: 99%

Comprehensive Analysis of MILE Gene Expression Data Set Advances Discovery of Leukaemia Type and Subtype Biomarkers

Łabaj

Papież

Polański

et al. 2017

Interdiscip Sci Comput Life Sci

View full text Add to dashboard Cite

Large collections of data in studies on cancer such as leukaemia provoke the necessity of applying tailored analysis algorithms to ensure supreme information extraction. In this work, a custom-fit pipeline is demonstrated for thorough investigation of the voluminous MILE gene expression data set. Three analyses are accomplished, each for gaining a deeper understanding of the processes underlying leukaemia types and subtypes. First, the main disease groups are tested for differential expression against the healthy control as in a standard case-control study. Here, the basic knowledge on molecular mechanisms is confirmed quantitatively and by literature references. Second, pairwise comparison testing is performed for juxtaposing the main leukaemia types among each other. In this case by means of the Dice coefficient similarity measure the general relations are pointed out. Moreover, lists of candidate main leukaemia group biomarkers are proposed. Finally, with this approach being successful, the third analysis provides insight into all of the studied subtypes, followed by the emergence of four leukaemia subtype biomarkers. In addition, the class enhanced DEG signature obtained on the basis of novel pipeline processing leads to significantly better classification power of multi-class data classifiers. The developed methodology consisting of batch effect adjustment, adaptive noise and feature filtration coupled with adequate statistical testing and biomarker definition proves to be an effective approach towards knowledge discovery in high-throughput molecular biology experiments.Electronic supplementary materialThe online version of this article (doi:10.1007/s12539-017-0216-9) contains supplementary material, which is available to authorized users.

show abstract

Section: Resultsmentioning

confidence: 99%

Comprehensive Analysis of MILE Gene Expression Data Set Advances Discovery of Leukaemia Type and Subtype Biomarkers

Łabaj

Papież

Polański

et al. 2017

Interdiscip Sci Comput Life Sci

View full text Add to dashboard Cite

show abstract

“…DNA quantitative real-time PCR (DNA-qPCR) was performed using Power SYBR Green (Applied Biosystems, Warrington, UK) as described,30 with primers designed within the PARN deletion regions, and FOXP2 as a reference gene (see online supplementary table S2).…”

Section: Methodsmentioning

confidence: 99%

Bone marrow failure and developmental delay caused by mutations in poly(A)-specific ribonuclease (PARN)

et al. 2015

Self Cite

View full text Add to dashboard Cite

show abstract

“…An increase in Fas‐mediated apoptosis is also seen, presumably leading to bone marrow failure . A recent study demonstrated the possibility that pancreatic tumors may be associated with SDS, thereby broadening the clinical phenotype of the disease . In vivo SDS models based on mammals, insects, and fish replicate the genetic and/or developmental aspects of ribosomopathies, and have led to the identification of pathways and candidate molecules that are important in the pathogenesis of the diseases.…”

Section: Ribosomal Proteins and The Pathogenesis Of Human Diseasesmentioning

confidence: 99%

Ribosomal Proteins and Human Diseases: Pathogenesis, Molecular Mechanisms, and Therapeutic Implications

Wang

Nag

Zhang

et al. 2014

Medicinal Research Reviews

184

154

View full text Add to dashboard Cite

Ribosomes are essential components of the protein synthesis machinery. The process of ribosome biogenesis is well organized and tightly regulated. Recent studies have shown that ribosomal proteins (RPs) have extraribosomal functions that are involved in cell proliferation, differentiation, apoptosis, DNA repair, and other cellular processes. The dysfunction of RPs has been linked to the development and progression of hematological, metabolic, and cardiovascular diseases and cancer. Perturbation of ribosome biogenesis results in ribosomal stress, which triggers activation of the p53 signaling pathway through RPs-MDM2 interactions, resulting in p53-dependent cell cycle arrest and apoptosis. RPs also regulate cellular functions through p53-independent mechanisms. We herein review the recent advances in several forefronts of RP research, including the understanding of their biological features and roles in regulating cellular functions, maintaining cell homeostasis, and their involvement in the pathogenesis of human diseases. We also highlight the translational potential of this research for the identification of molecular biomarkers, and in the discovery and development of novel treatments for human diseases.

show abstract

Molecular characteristics of a pancreatic adenocarcinoma associated with Shwachman‐Diamond syndrome

Cited by 23 publications

References 40 publications

Comprehensive Analysis of MILE Gene Expression Data Set Advances Discovery of Leukaemia Type and Subtype Biomarkers

Comprehensive Analysis of MILE Gene Expression Data Set Advances Discovery of Leukaemia Type and Subtype Biomarkers

Bone marrow failure and developmental delay caused by mutations in poly(A)-specific ribonuclease (PARN)

Ribosomal Proteins and Human Diseases: Pathogenesis, Molecular Mechanisms, and Therapeutic Implications

Contact Info

Product

Resources

About