Insights on the pathogenesis of type 2 diabetes as revealed by signature genomic classifiers in an African American population in the Washington, DC area

Mondal, Tanmoy; Loffredo, Christopher A.; Simhadri, Jyothirmai J.; Nunlee-Bland, Gail; Korba, Brent; Johnson, Jheannelle; Cotin, Sharleine; Moses, Gemeyel; Quartey, Ruth; Howell, Charles D.; Noreen, Zarish; Arif, Muhammad; Ghosh, Somiranjan

doi:10.1002/dmrr.3589

Cited by 3 publications

(4 citation statements)

References 58 publications

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“…As there are survival differences between commercial pigs and local pigs, we have identified genes that may be related to adaptability, such as APBA1 . Previous research has linked APBA1 to cognitive function, and its absence has been associated with the onset of neurobehavioral disorders [ 39 , 40 ]. This could indicate that Chinese indigenous pigs are more intelligent and better suited to adapting to their environment.…”

Section: Discussionmentioning

confidence: 99%

Evaluation of the Genetic Diversity, Population Structure and Selection Signatures of Three Native Chinese Pig Populations

Zhong

Wang

Xie

et al. 2023

Animals

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Indigenous pig populations in Hainan Province live in tropical climate conditions and a relatively closed geographical environment, which has contributed to the formation of some excellent characteristics, such as heat tolerance, strong disease resistance and excellent meat quality. Over the past few decades, the number of these pig populations has decreased sharply, largely due to a decrease in growth rate and poor lean meat percentage. For effective conservation of these genetic resources (such as heat tolerance, meat quality and disease resistance), the whole-genome sequencing data of 78 individuals from 3 native Chinese pig populations, including Wuzhishan (WZS), Tunchang (TC) and Dingan (DA), were obtained using a 150 bp paired-end platform, and 25 individuals from two foreign breeds, including Landrace (LR) and Large White (LW), were downloaded from a public database. A total of 28,384,282 SNPs were identified, of which 27,134,233 SNPs were identified in native Chinese pig populations. Both genetic diversity statistics and linkage disequilibrium (LD) analysis indicated that indigenous pig populations displayed high genetic diversity. The result of population structure implied the uniqueness of each native Chinese pig population. The selection signatures were detected between indigenous pig populations and foreign breeds by using the population differentiation index (FST) method. A total of 359 candidate genes were identified, and some genes may affect characteristics such as immunity (IL-2, IL-21 and ZFYVE16), adaptability (APBA1), reproduction (FGF2, RNF17, ADAD1 and HIPK4), meat quality (ABCA1, ADIG, TLE4 and IRX5), and heat tolerance (VPS13A, HSPA4). Overall, the findings of this study will provide some valuable insights for the future breeding, conservation and utilization of these three Chinese indigenous pig populations.

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Section: Discussionmentioning

confidence: 99%

Evaluation of the Genetic Diversity, Population Structure and Selection Signatures of Three Native Chinese Pig Populations

Zhong

Wang

Xie

et al. 2023

Animals

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“…With the development of microarray technology, the transcriptome of peripheral whole blood can be readily profiled accurately and reproducibly. Due to the richness of gene expression information, the whole blood transcriptome is an attractive field of biomarker studies for various diseases, such as infectious diseases, neurodegenerative diseases, diabetes, and cancers [15][16][17][23][24][25][26][27]. The primary objective of our study was to use a less invasive way to conduct sample collection ('liquid biopsy') to investigate the biological processes, signaling pathways, and key differentially expressed genes associated with MASLD in an understudied AA population in the US.…”

Section: Discussionmentioning

confidence: 99%

Transcriptomics of MASLD Pathobiology in African American Patients in the Washington DC Area †

Mondal,

Smith,

Loffredo

et al. 2023

IJMS

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Metabolic-dysfunction-associated steatotic liver disease (MASLD) is becoming the most common chronic liver disease worldwide and is of concern among African Americans (AA) in the United States. This pilot study evaluated the differential gene expressions and identified the signature genes in the disease pathways of AA individuals with MASLD. Blood samples were obtained from MASLD patients (n = 23) and non-MASLD controls (n = 24) along with their sociodemographic and medical details. Whole-blood transcriptomic analysis was carried out using Affymetrix Clarion-S Assay. A validation study was performed utilizing TaqMan Arrays coupled with Ingenuity Pathway Analysis (IPA) to identify the major disease pathways. Out of 21,448 genes in total, 535 genes (2.5%) were significantly (p < 0.05) and differentially expressed when we compared the cases and controls. A significant overlap in the predominant differentially expressed genes and pathways identified in previous studies using hepatic tissue was observed. Of note, TGFB1 and E2F1 genes were upregulated, and HMBS was downregulated significantly. Hepatic fibrosis signaling is the top canonical pathway, and its corresponding biofunction contributes to the development of hepatocellular carcinoma. The findings address the knowledge gaps regarding how signature genes and functional pathways can be detected in blood samples (‘liquid biopsy’) in AA MASLD patients, demonstrating the potential of the blood samples as an alternative non-invasive source of material for future studies.

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“…In contrast, whole blood is an incredibly useful tissue sample that requires minimal risk during collection (minimally invasive) and can be accurately profiled due to its richness in gene expression information. [12,13]. In our previous study, we successfully identified signature genes associated with Type 2 diabetes and related comorbidities in an US African American (AA) population by analyzing peripheral blood samples [12][13][14][15][16].…”

Section: Introductionmentioning

confidence: 99%

“…[12,13]. In our previous study, we successfully identified signature genes associated with Type 2 diabetes and related comorbidities in an US African American (AA) population by analyzing peripheral blood samples [12][13][14][15][16]. The present study aims to investigate the expression levels of genes involved in Amyloid Processing using peripheral blood tissue samples from Pakistani patients with AD.…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic Analysis of Alzheimer’s Disease Pathways in a Pakistani Population

Mondal,

Noreen,

Loffredo

et al. 2024

Journal of Alzheimer's Disease Reports

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Background: Alzheimer’s disease (AD) is a multifactorial neurodegenerative disorder that is most prevalent in elderly individuals, especially in developed countries, and its prevalence is now increasing in developing countries like Pakistan. Objective: Our goal was to characterize key genes and their levels of expression and related molecular transcriptome networks associated with AD pathogenesis in a pilot case-control study in a Pakistani population. Methods: To obtain the spectrum of molecular networks associated with pathogenesis in AD patients in Pakistan (comparing cases and controls), we used high-throughput qRT-PCR (TaqMan Low-Density Array; n = 33 subjects) coupled with Affymetrix Arrays (n = 8) and Ingenuity Pathway Analysis (IPA) to identify signature genes associated with Amyloid processing and disease pathways. Results: We confirmed 16 differentially expressed AD-related genes, including maximum fold changes observed in CAPNS2 and CAPN1. The global gene expression study observed that 61% and 39% of genes were significantly (p-value 0.05) up- and downregulated, respectively, in AD patients compared to healthy controls. The key pathways include, e.g., Amyloid Processing, Neuroinflammation Signaling, and ErbB4 Signaling. The top-scoring networks in Diseases and Disorders Development were Neurological Disease, Organismal Injury and Abnormalities, and Psychological Disorders. Conclusions: Our pilot study offers a non-invasive and efficient way of investigating gene expression patterns by combining TLDA and global gene expression method in AD patients by utilizing whole blood. This provides valuable insights into the expression status of genes related to Amyloid Processing, which could play potential role in future studies to identify sensitive, early biomarkers of AD in general.

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Insights on the pathogenesis of type 2 diabetes as revealed by signature genomic classifiers in an African American population in the Washington, DC area

Cited by 3 publications

References 58 publications

Evaluation of the Genetic Diversity, Population Structure and Selection Signatures of Three Native Chinese Pig Populations

Evaluation of the Genetic Diversity, Population Structure and Selection Signatures of Three Native Chinese Pig Populations

Transcriptomics of MASLD Pathobiology in African American Patients in the Washington DC Area †

Transcriptomic Analysis of Alzheimer’s Disease Pathways in a Pakistani Population

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