Multi-omics in Crohn's disease: New insights from inside

Mu, Chenlu; Zhao, Qi; Zhao, Qing; Yang, Ling; Pang, Xiaoqi; Li, Tianyu; Li, Yongming; Wang, Bangmao; Fung, Shan‐Yu; Cao, Hailong

doi:10.1016/j.csbj.2023.05.010

Cited by 7 publications

(4 citation statements)

References 205 publications

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“…Epigenome-wide association studies brought advantages such as (1) finding novel methylation sites associated with disease; (2) evaluating the environmental impact of genetic regulation; and (3) explaining part of the heritability missed out by genome-wide association analysis. On the other hand, there are still gaps such as (1) expansion of sample size and ethnic diversity; (2) existence of the heterogeneity of sample material; and (3) causal inference of the identified epigenetic is challenging[ 6 ].…”

Section: Advantages and Limitations Of Epigenome Studiesmentioning

confidence: 99%

“…In patients with IBD, the most studied modifications have been DNA-methylation and noncoding RNA that may be induced by smoking and diet[ 4 , 5 ]. Interestingly, this DNA-methylation is a process that is dependent on cofactors dietary such as substrates and nutrients (folate, vitamins B12, D, and others)[ 2 ] and is associated with inflammation, microbiota composition, and microRNAs (miRNAs) which can affect IBD by interfering with T cells differentiation[ 6 ]. Marangoni et al [ 1 ] provided an elegant review of the role of DNA methylation in IBD and its consequences to the inflammatory process.…”

Section: Introductionmentioning

confidence: 99%

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Interaction between diet and genetics in patients with inflammatory bowel disease

Magro,

Sassaki,

Chebli

2024

World J Gastroenterol

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In this editorial, we comment on the article by Marangoni et al , published in the recent issue of the World Journal of Gastroenterology 2023; 29: 5618-5629, about “Diet as an epigenetic factor in inflammatory bowel disease”. The authors emphasized the role of diet, especially the interaction with genetics, in promoting the inflammatory process in inflammatory bowel disease (IBD) patients, focusing on DNA methylation, histone modifications, and the influence of microRNAs. In this editorial, we explore the interaction between genetics, gut microbiota, and diet, in an only way. Furthermore, we provided dietary recommendations for patients with IBD. The Western diet, characterized by a low fiber content and deficiency the micronutrients, impacts short-chain fatty acids production and may be related to the pathogenesis of IBD. On the other hand, the consumption of the Mediterranean diet and dietary fibers are associated with reduced risk of IBD flares, particularly in Crohn’s disease (CD) patients. According to the dietary guidance from the International Organization for the Study of Inflammatory Bowel Diseases (IOIBD), the regular consumption of fruits and vegetables while reducing the consumption of saturated, trans, dairy fat, additives, processed foods rich in maltodextrins, and artificial sweeteners containing sucralose or saccharine is recommended to CD patients. For patients with ulcerative colitis, the IOIBD recommends the increased intake of natural sources of omega-3 fatty acids and follows the same restrictive recommendations aimed at CD patients, with the possible inclusion of red meats. In conclusion, IBD is a complex and heterogeneous disease, and future studies are needed to elucidate the influence of epigenetics on diet and microbiota in IBD patients.

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Section: Advantages and Limitations Of Epigenome Studiesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Interaction between diet and genetics in patients with inflammatory bowel disease

Magro,

Sassaki,

Chebli

2024

World J Gastroenterol

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“…Inflammatory bowel diseases such as Crohn's disease (CD) are characterized by chronic transmural inflammation of the gut. While CD is a heterogeneous disorder with multifactorial etiology, in which genetics and environment interact, genome-wide association studies have linked polymorphisms in the autophagy gene ATG16L1 to Crohn's disease susceptibility [100][101][102]. Compromised intestinal epithelial barrier functions in ATG16L1 mutant (ATG16L1 T300A ) mice and patients with CD homozygous for the ATG16L1T 300A mutation have been associated with a reduced viability of Paneth cells, a subtype of intestinal epithelial cells which are important producers of antimicrobial peptides [103].…”

Section: Paneth Cell Protective Action Of Api5 As a Putative Therapeu...mentioning

confidence: 99%

Apoptosis Inhibitor 5: A Multifaceted Regulator of Cell Fate

Abbas,

Derkaoui,

Jeammet

et al. 2024

Biomolecules

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Apoptosis, or programmed cell death, is a fundamental process that maintains tissue homeostasis, eliminates damaged or infected cells, and plays a crucial role in various biological phenomena. The deregulation of apoptosis is involved in many human diseases, including cancer. One of the emerging players in the intricate regulatory network of apoptosis is apoptosis inhibitor 5 (API5), also called AAC-11 (anti-apoptosis clone 11) or FIF (fibroblast growth factor-2 interacting factor). While it may not have yet the same level of notoriety as some other cancer-associated proteins, API5 has garnered increasing attention in the cancer field in recent years, as elevated API5 levels are often associated with aggressive tumor behavior, resistance to therapy, and poor patient prognosis. This review aims to shed light on the multifaceted functions and regulatory mechanisms of API5 in cell fate decisions as well as its interest as therapeutic target in cancer.

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“…However, the disadvantage of single-omics studies is their narrow focus, and they often fail to provide insights into the interactions and integration of the overall biological system. Life science often involves multi-level and complex interactions, so relying solely on data from a single research field may not fully understand the integrity and comprehensiveness of biological systems (301)(302)(303). Furthermore, each omics approach has its own limitations, including technical constraints, experimental setups, and data analysis.…”

Section: Necessity Of Multi-omics Integration In Personalized Medicinementioning

confidence: 99%

From multi-omics approaches to personalized medicine in myocardial infarction

Zhan,

Tang,

et al. 2023

Front. Cardiovasc. Med.

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Myocardial infarction (MI) is a prevalent cardiovascular disease characterized by myocardial necrosis resulting from coronary artery ischemia and hypoxia, which can lead to severe complications such as arrhythmia, cardiac rupture, heart failure, and sudden death. Despite being a research hotspot, the etiological mechanism of MI remains unclear. The emergence and widespread use of omics technologies, including genomics, transcriptomics, proteomics, metabolomics, and other omics, have provided new opportunities for exploring the molecular mechanism of MI and identifying a large number of disease biomarkers. However, a single-omics approach has limitations in understanding the complex biological pathways of diseases. The multi-omics approach can reveal the interaction network among molecules at various levels and overcome the limitations of the single-omics approaches. This review focuses on the omics studies of MI, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, and other omics. The exploration extended into the domain of multi-omics integrative analysis, accompanied by a compilation of diverse online resources, databases, and tools conducive to these investigations. Additionally, we discussed the role and prospects of multi-omics approaches in personalized medicine, highlighting the potential for improving diagnosis, treatment, and prognosis of MI.

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Multi-omics in Crohn's disease: New insights from inside

Cited by 7 publications

References 205 publications

Interaction between diet and genetics in patients with inflammatory bowel disease

Interaction between diet and genetics in patients with inflammatory bowel disease

Apoptosis Inhibitor 5: A Multifaceted Regulator of Cell Fate

From multi-omics approaches to personalized medicine in myocardial infarction

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