Biology subjects

Lindberg, J.

Publications and source records attributed to Lindberg, J..

4 recordsLinked to original sources

bioRxiv2024

Profiling the intestinal microbiota, plasma bile acids and inflammation markers reveals novel associations in Crohn's disease and Ulcerative colitis.

Background and aimsOur study explores signatures for Crohns disease (CD) and Ulcerative Colitis (UC) reflecting the interplay between the intestinal microbiota, systemic inflammation, and plasma bile acid homeostasis. Methods1,257 individuals scheduled for colonoscopy were included and completed a comprehensive questionnaire. Individuals with IBD ( CD n=64 and UC n= 55), were age- and gender-matched to controls without findings during colonoscopy. Taxonomic profiles of the fecal microbiota and plasma profiles of inflammatory proteins and bile acids were used to build disease classifiers. Omics integration identified associations across datasets. ResultsB. hydrogenotrophica was associated with CD and C. eutactus, C. sp. CAG 167, B. cellulosilyticus, C. mitsuokai with controls. Ten inflammation markers were increased in CD, and eleven bile acids and derivatives were decreased in CD, while 7a-Hydroxy-3-oxo-4-cholestenoate (7-HOCA) and chenodeoxycholic acid (CDCA) were increased compared to controls. In UC, commensals such as F. prausnitzii and A. muciniphila were depleted. CCL11, IL-17A, and TNF were increased in UC and associated to gut microbial changes. Correlations between taxa and bile acids were all positive. ConclusionsFor both CD and UC, taxonomic differences were primarily characterized by a reduction in commensal gut microbes which exhibited positive correlations with secondary bile acids and negative correlations with inflammation markers, potentially reflecting protective mechanisms of these commensal microbes.

bioinformatics↗

bioRxiv2021

Discovering fragment length signatures of circulating tumor DNA using Non-negative Matrix Factorization

Sequencing of cell-free DNA (cfDNA) is currently being used to detect cancer by searching both for mutational and non-mutational alterations. Recent work has shown that the length distribution of cfDNA fragments from a cancer patient can inform tumor load and type. Here, we propose non-negative matrix factorization (NMF) of fragment length distributions as a novel method to study fragment lengths in cfDNA samples. Using shallow whole-genome sequencing (sWGS) of cfDNA from a cohort of patients with metastatic castration-resistant prostate cancer (mCRPC), we demonstrate how NMF accurately infers the true tumor fragment length distribution as an NMF component - and that the sample weights of this component correlate with ctDNA levels (r=0.75). We further demonstrate how using several NMF components enables accurate cancer detection on data from various early stage cancers (AUC=0.96). Finally, we show that NMF, when applied across genomic regions, can be used to discover fragment length signatures associated with open chromatin.

bioinformatics↗

bioRxiv2018

Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

BackgroundThere are multiple existing and emerging therapeutic avenues for metastatic prostate cancer, with a common denominator, which is the need for predictive biomarkers. Circulating tumor DNA (ctDNA) has the potential to cost-efficiently accelerate precision medicine trials to improve clinical efficacy and diminish costs and toxicity. However, comprehensive ctDNA profiling in metastatic prostate cancer to date has been limited.\n\nMethodsA combination of targeted- and low-pass whole genome sequencing was performed on plasma cell-free DNA and matched white blood cell germline DNA in 364 blood samples from 217 metastatic prostate cancer patients.\n\nResultsctDNA was detected in 85.9% of baseline samples, correlated to line of therapy and was mirrored by circulating tumor cell enumeration of synchronous blood samples. Comprehensive profiling of the androgen receptor (AR) revealed a continuous increase in the fraction of patients with intra-AR structural variation, from 15.4% during first line mCRPC therapy to 45.2% in fourth line, indicating a continuous evolution of AR during the course of the disease. Patients displayed frequent alterations in DNA repair deficiency genes (18.0%). Additionally, the microsatellite instability phenotype was identified in 3.81% of eligible samples ([≥]0.1 ctDNA fraction). Sequencing of non-repetitive intronic- and exonic regions of PTEN, RB1 and TP53 detected biallelic inactivation in 47.5%, 20.3% and 44.1% of samples with [≥]0.2 ctDNA fraction, respectively. Only one patient carried a clonal high-impact variant without a detectable second hit. Intronic high-impact structural variation was twice as common as exonic mutations in PTEN and RB1. Finally, 14.6% of patients presented false positive variants due to clonal hematopoiesis, commonly ignored in commercially available assays.\n\nConclusionsctDNA profiles appear to mirror the genomic landscape of metastatic prostate cancer tissue and may cost-efficiently provide somatic information in clinical trials designed to identify predictive biomarkers. However, intronic sequencing of the interrogated tumor suppressors challenge the ubiquitous focus on coding regions and is vital, together with profiling of synchronous white blood cells, to minimize erroneous assignments which in turn may confound results and impede true associations in clinical trials.

genomics↗

bioRxiv2017

Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomes

Over 95% of human multi-exon genes undergo alternative splicing, a process important in normal development and often dysregulated in disease. We sought to analyze the global splicing regulatory network of CELF2 in human T cells, a well-studied splicing regulator critical to T cell development and function. By integrating high-throughput sequencing data for binding and splicing quantification with sequence features and probabilistic splicing code models, we find evidence of splicing antagonism between CELF2 and the RBFOX family of splicing factors. We validate this functional antagonism through knockdown and overexpression experiments in human cells and find CELF2 represses RBFOX2 mRNA and protein levels. Because both families of proteins have been implicated in the development and maintenance of neuronal, muscle, and heart tissues, we analyzed publicly available data in these systems. Our analysis suggests global, antagonistic co-regulation of splicing by the CELF and RBFOX proteins in mouse muscle and heart in several physiologically relevant targets including proteins involved in calcium signaling and members of the MEF2 family of transcription factors. Importantly, a number of these co-regulated events are aberrantly spliced in mouse models and human patients with diseases that affect these tissues including heart failure, diabetes, or myotonic dystrophy. Finally, analysis of exons regulated by ancient CELF family homologs in chicken, and Drosophila suggests this antagonism is conserved through evolution.

genomics↗