J Obes Metab Syndr 2023; 32(1): 98-102
Published online March 30, 2023 https://doi.org/10.7570/jomes22065
Copyright © Korean Society for the Study of Obesity.
1Faculty of Bioinformatics and Data Science, College of Health Professions and Natural Sciences, Wilmington University, New Castle, DE; 2National Coalition of Independent Scholars, Battleboro, VT; 3Faculty of Sciences, Mathematics and Biotechnology, University of California-Berkeley Extension, Berkeley, CA, USA
Faculty of Sciences, Mathematics and Biotechnology, University of California-Berkeley Extension, 1995 University Avenue Ste 130, Berkeley, CA 94704, USA
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Background: Bariatric surgery is the most effective intervention for weight loss possibly through modulating subcutaneous adipose tissue (SAT) molecular programs. The post-operative molecular and biological impacts, including gene expression, deserve in-depth investigation especially given the small sample sizes in the literature.
Methods: Five existing datasets (n=237 SATs) were re-processed and corrected for batch-to-batch variation. Unsupervised approaches and robust linear mixed effect model were used to compare gene expression post- (n=126) to pre-operation (n=111).
Results: Post-operative SATs showed distinct global gene expression. Forty-four and 395 genes were over- and under-expressed post-operation (all Bonferroni P<0.05). The under-expressed genes significantly enriched for 21 biological processes/pathways (all Bonferroni P<0.05), 17 (76.2%) and two (9.5%) directly involved in immunity and amino/proteo-glycan metabolism, respectively.
Conclusion: Post-operative SATs might adopt distinct transcriptomic landscapes and undergo a reduction in immune-related processes and amino/proteo-glycan metabolism.
Keywords: Bariatric surgery, Gene expression profiling, Subcutaneous fat, Adipose tissue, white
Obesity is a rising threat to public health with comorbidities including type 2 diabetes and hypertension.1 To date, bariatric surgery is the most effective procedure to treat obesity and achieve weight loss.1,2 The benefits of bariatric surgery, including improved outcomes from multiple comorbidities and reduced all-cause mortality, far outweigh the low short-term risks and rare complications.1
The molecular and cellular mechanisms behind the effectiveness of bariatric surgery remain elusive.3 One hypothesis is that the bariatric procedure reprograms metabolic networks in adipose tissue. Subcutaneous adipose tissue (SAT) is a major subtype of human adipose with an important role in fat storage and has been implicated in obesity.4,5 Proteome-wide profiling, validated by targeted experiments, showed substantially reduced fat stored in SAT after bariatric surgery.2
Transcriptome-wide studies also attempted to address the biological changes after bariatric surgery.3-6 However, existing studies in SAT profiling suffer from small sample sizes with as few as eight subjects measured in multiple batches.4 The present study leverages publicly available transcriptomic datasets and conducts pooled profiling with rigorous statistics to investigate the effect of bariatric surgery on SAT gene expression.
Summarized in Fig. 1A, Supplementary Table 1, five datasets (GSE29411, GSE42715, GSE65540, GSE66921, and GSE199063) were publicly accessed from Gene Expression Omnibus (www.ncbi. nlm.nih.gov/geo).3-7 The study is Institutional Review Board exempt because all clinical information was de-identified, previously published, and publicly available. Further processing of gene expression data was performed in two phases. First, genes coded outside of chromosomes 1-22 and X, measured by control probes, without the Hugo/RefSeq annotation, or having flat-zero expression were excluded. Expression values of genes with duplicate names were mean-aggregated, standard-normalized, and subjected to a 0.5% least-variant filter. Second, all datasets were inner-joined followed by batch-effect correction (sva-ComBat3.38.08), constrained within ±5.0, and standard-scaled. Non-SATs and one SAT with distinct global expression were excluded, leaving n=237 from 118 unique subjects. Pre-operative (PreOP) SATs were defined as being collected before or at the time of bariatric surgery, while post-operative (PostOP) SATs were collected 3 to 60 months after surgery.
The first two principal components (PCs) were computed on all 5,000 genes with R function ‘prcomp.’ PC regions were identified based on whether a sample is above or below the negative identity line. Unsupervised hierarchical clustering with Manhattan distance and Ward-D linkage was performed on 1,188 (23.8%) genes with inter-sample standard deviation exceeding 0.99 (‘pheatmap1.0.12’).
A robust linear mixed effect model (LIMMA3.46.0)9 was used to identify differentially expressed genes in PostOP SATs with explicit consideration of the 49.8% (118 of 237) samples from repeated measurements, as follows:
PostOPyes=FixedEffect (gene)+RandomEffect (subject, withinsubject correlation coefficient)
The significantly over- and under-expressed genes, identified at Bonferroni
Two-sided Welch’s t and Fisher’s exact tests were used to evaluate differences and associations, respectively. All analysis code was executed in R4.0.3 and available at https://github.com/ydavidchen/bariatric-sat-profiling.
SAT global gene expression showed clearcut differences before and after bariatric surgery. The first two PCs could be delineated by a simple, linear decision boundary, and the regions created were significantly associated with PreOP/PostOP status (odds ratio [OR], 7.18; 95% confidence interval [CI], 3.93 to 13.42; Fisher’s exact P=1.91E-12) (Fig. 1B). Both PCs were significantly lower in Post- OP (both Welch t-test
A robust linear mixed effect model adjusting for repeated measurements identified 44 (0.9%) over- and 395 (7.9%) under-expressed genes in PostOP SATs (all Bonferroni-adjusted
Obesity is a global health problem with many comorbidities. Bariatric surgery, the most effective obesity intervention to date, remains underexplored. Through a pooled re-analysis maximizing sample size and power, this study confirms the gene and pathwaylevel changes post-surgery despite the heterogeneity in measurement and study designs.
All unsupervised analyses support a distinct global transcriptomic landscape associated with bariatric surgery. Many genes, including those with a known role in obesity, showed differential expression.
Many downregulated genes, including receptor CD4, were immune- related and enriched for immune-related biological processes. Notably, “granulocyte activation” and “neutrophil-mediated immunity” showed the highest enrichment and significance (OR >3.6 and Bonferroni
This study has limitations. First, potential confounders including obesity severity, the type of bariatric surgery, and the presence of other illnesses were not addressed due to limited data availability. Second, the biological findings of this study, especially the downregulated immune-related pathways, need elucidation partly because acquiring SATs for expression analysis requires a biopsy. Since molecular changes such as wound healing can be detected after solidtissue biopsy,14 future studies should consider evaluating less invasive procedures (e.g., blood sampling) that can detect bariatric surgery- associated changes with minimal bias. It will also be interesting to identify the specific cell types that contribute to such molecular changes, possibly through novel cell-type deconvolution methods, single-cell approaches, and integration of other molecular data types.
Supplementary materials can be found online at https://doi.org/10.7570/jomes22065.jomes-32-1-98-supple.pdf
The author declares no conflict of interest.
The author would like to thank the peer reviewers and the editorial team for their input.
Biologically relevant processes associated with the 395 downregulated genes in SATs after bariatric surgery
|Term ID||Description||Direct role||Available no.||Observed no.||Expected no.||OR||Raw
|(A) Gene Ontology: biological processes|
|GO:0002764||Immune response-regulating signaling pathway||Immunity||148||36||12.8||2.80||4.76E-09||3.97E-06|
|GO:0019882||Antigen processing and presentation||Immunity||76||21||6.6||3.19||9.49E-07||7.92E-04|
|GO:0002694||Regulation of leukocyte activation||Immunity||162||33||14.1||2.35||1.87E-06||1.56E-03|
|GO:0042110||T cell activation||Immunity||151||31||13.1||2.37||3.29E-06||2.75E-03|
|GO:0050867||Positive regulation of cell activation||Signaling||109||25||9.5||2.64||3.86E-06||3.22E-03|
|GO:2000147||Positive regulation of cell motility||Signaling||189||35||16.4||2.13||8.91E-06||7.43E-03|
|GO:0007159||Leukocyte cell-cell adhesion||Immunity||115||25||10.0||2.51||1.07E-05||8.92E-03|
|GO:0051701||Interaction with host||Immunity||71||18||6.2||2.92||2.14E-05||0.0179|
|GO:0006022||Aminoglycan metabolic process||Metabolism||56||15||4.9||3.09||5.26E-05||0.0439|
|GO:0002683||Negative regulation of immune system process||Immunity||119||24||10.3||2.32||5.96E-05||0.0497|
|(B) KEGG pathways|
|hsa05205||Proteoglycans in cancer||Metabolism||77||22||7.6||2.88||2.03E-06||5.97E-04|
|hsa04062||Chemokine signaling pathway||Immunity||65||17||6.5||2.63||1.11E-04||0.033|
All processes reached Bonferroni-adjusted
SAT, subcutaneous adipose tissue; OR, odds ratio; KEGG, Kyoto Encyclopedia of Genes and Genomes.
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