SREBP1c-PAX4 Axis Mediates Pancreatic β-Cell Compensatory Responses Upon Metabolic Stress

Nuclear regulatory disturbances precede and predict the development of Type-2 diabetes in Asian populations

To identify biomarkers and pathways to Type-2 diabetes (T2D), a major global disease, we completed array-based epigenome-wide association in whole blood in 5,709 Asian people. We found 323 Sentinel CpGs (from 314 genetic loci) that predict future T2D. The CpGs reveal coherent, nuclear regulatory disturbances in canonical immune activation pathways, as well as metabolic networks involved in insulin signalling, fatty acid metabolism and lipid transport, which are causally linked to development of T2D. The CpGs have potential clinical utility as biomarkers. An array-based composite Methylation Risk Score (MRS) is predictive for future T2D (RR: 5.2 in Q4 vs Q1; P=7×10-25), and is additive to genetic risk. Targeted methylation sequencing revealed multiple additional CpGs predicting T2D, and synthesis of a sequencing-based MRS that is strongly predictive for T2D (RR: 8.3 in Q4 vs Q1; P=1.0×10-11). Importantly, MRS varies between Asian ethnic groups, in a way that explains a large fraction of the difference in T2D risk between populations. We thus provide new insights into the nuclear regulatory disturbances that precede development of T2D, and reveal the potential for sequence-based DNA methylation markers to inform risk stratification in diabetes prevention.

Integrating Mendelian randomization and single-cell RNA sequencing to identify therapeutic targets of baicalin for type 2 diabetes mellitus

Background

Alternative and complementary therapies play an imperative role in the clinical management of Type 2 diabetes mellitus (T2DM), and exploring and utilizing natural products from a genetic perspective may yield novel insights into the mechanisms and interventions of the disorder.

Methods

To identify the therapeutic target of baicalin for T2DM, we conducted a Mendelian randomization study. Druggable targets of baicalin were obtained by integrating multiple databases, and target-associated cis-expression quantitative trait loci (cis-eQTL) originated from the eQTLGen consortium. Summary statistics for T2DM were derived from two independent genome-wide association studies available through the DIAGRAM Consortium (74,124 cases vs. 824,006 controls) and the FinnGen R9 repository (9,978 cases vs. 12,348 controls). Network construction and enrichment analysis were applied to the therapeutic targets of baicalin. Colocalization analysis was utilized to assess the potential for the therapeutic targets and T2DM to share causative genetic variations. Molecular docking was performed to validate the potency of baicalin. Single-cell RNA sequencing was employed to seek evidence of therapeutic targets' involvement in islet function.

Results

Eight baicalin-related targets proved to be significant in the discovery and validation cohorts. Genetic evidence indicated the expression of ANPEP, BECN1, HNF1A, and ST6GAL1 increased the risk of T2DM, and the expression of PGF, RXRA, SREBF1, and USP7 decreased the risk of T2DM. In particular, SREBF1 has significant interaction properties with other therapeutic targets and is supported by strong colocalization. Baicalin had favorable combination activity with eight therapeutic targets. The expression patterns of the therapeutic targets were characterized in cellular clusters of pancreatic tissues that exhibited a pseudo-temporal dependence on islet cell formation and development.

Conclusion

This study identified eight potential targets of baicalin for treating T2DM from a genetic perspective, contributing an innovative analytical framework for the development of natural products. We have offered fresh insights into the connections between therapeutic targets and islet cells. Further, fundamental experiments and clinical research are warranted to delve deeper into the molecular mechanisms of T2DM.

PAX4 gene delivery improves β-cell function in human islets of Type II diabetes

Aim: Type II diabetes (T2D) stems from insulin resistance, with β-cell dysfunction as a hallmark in its progression. Studies reveal that β cells undergo apoptosis or dedifferentiation during T2D development. The transcription factor PAX4 is vital for β differentiation and survival, thus may be a potential enhancer of β-cell function in T2D islets. Materials & methods: Human PAX4 cDNA was delivered into T2D human islets with an adenoviral vector, and its effects on β cells were examined. Results: PAX4 gene delivery significantly improved β-cell survival, and increased β-cell composition in the T2D human islets. Basal insulin and glucose-stimulated insulin secretion in PAX4-expressing islets were substantially higher than untreated or control-treated T2D human islets. Conclusion: Introduced PAX4 expression in T2D human islets improves β-cell function, thus could provide therapeutic benefits for T2D treatment.

Maturity-onset diabetes of the young type 9 or latent autoimmune diabetes in adults: A case report and review of literature

BACKGROUND

Maturity-onset diabetes of the young (MODY) is a monogenic genetic disease often clinically misdiagnosed as type 1 or type 2 diabetes. MODY type 9 (MODY9) is a rare subtype caused by mutations in the PAX4 gene. Currently, there are limited reports on PAX4-MODY, and its clinical characteristics and treatments are still unclear. In this report, we described a Chinese patient with high autoimmune antibodies, hyperglycemia and a site mutation in the PAX4 gene.

CASE SUMMARY

A 42-year-old obese woman suffered diabetes ketoacidosis after consuming substantial amounts of beverages. She had never had diabetes before, and no one in her family had it. However, her autoantibody tested positive, and she managed her blood glucose within the normal range for 6 mo through lifestyle inter-ventions. Later, her blood glucose gradually increased. Next-generation sequencing and Sanger sequencing were performed on her family. The results revealed that she and her mother had a heterozygous mutation in the PAX4 gene (c.314G>A, p.R105H), but her daughter did not. The patient is currently taking liraglutide (1.8 mg/d), and her blood glucose levels are under control. Previous cases were retrieved from PubMed to investigate the relationship between PAX4 gene mutations and diabetes.

CONCLUSION

We reported the first case of a PAX4 gene heterozygous mutation site (c.314G>A, p.R105H), which does not appear pathogenic to MODY9 but may facilitate the progression of latent autoimmune diabetes in adults.

The functions and roles of C2H2 zinc finger proteins in hepatocellular carcinoma

C2H2 zinc finger (C2H2-ZF) proteins are the majority group of human transcription factors and they have many different molecular functions through different combinations of zinc finger domains. Hepatocellular carcinoma (HCC) is one of the most prevalent malignant tumors and the main reason for cancer-related deaths worldwide. More and more findings support the abnormal expression of C2H2-ZF protein in the onset and progression of HCC. The C2H2-ZF proteins are involved in various biological functions in HCC, such as EMT, stemness maintenance, metabolic reprogramming, cell proliferation and growth, apoptosis, and genomic integrity. The study of anti-tumor drug resistance also highlights the pivotal roles of C2H2-ZF proteins at the intersection of biological functions (EMT, stemness maintenance, autophagy)and chemoresistance in HCC. The involvement of C2H2-ZF protein found recently in regulating different molecules, signal pathways and pathophysiological activities indicate these proteins as the possible therapeutic targets, and diagnostic or prognostic biomarkers for HCC.

Pax4 in Health and Diabetes

Paired box 4 (Pax4) is a key transcription factor involved in the embryonic development of the pancreatic islets of Langerhans. Consisting of a conserved paired box domain and a homeodomain, this transcription factor plays an essential role in early endocrine progenitor cells, where it is necessary for cell-fate commitment towards the insulin-secreting β cell lineage. Knockout of Pax4 in animal models leads to the absence of β cells, which is accompanied by a significant increase in glucagon-producing α cells, and typically results in lethality within days after birth. Mutations in Pax4 that cause an impaired Pax4 function are associated with diabetes pathogenesis in humans. In adulthood, Pax4 expression is limited to a distinct subset of β cells that possess the ability to proliferate in response to heightened metabolic needs. Upregulation of Pax4 expression is known to promote β cell survival and proliferation. Additionally, ectopic expression of Pax4 in pancreatic islet α cells or δ cells has been found to generate functional β-like cells that can improve blood glucose regulation in experimental diabetes models. Therefore, Pax4 represents a promising therapeutic target for the protection and regeneration of β cells in the treatment of diabetes. The purpose of this review is to provide a thorough and up-to-date overview of the role of Pax4 in pancreatic β cells and its potential as a therapeutic target for diabetes.

Physiological and pathological roles of lipogenesis

Lipids are essential metabolites, which function as energy sources, structural components and signalling mediators. Most cells are able to convert carbohydrates into fatty acids, which are often converted into neutral lipids for storage in the form of lipid droplets. Accumulating evidence suggests that lipogenesis plays a crucial role not only in metabolic tissues for systemic energy homoeostasis but also in immune and nervous systems for their proliferation, differentiation and even pathophysiological roles. Thus, excessive or insufficient lipogenesis is closely associated with aberrations in lipid homoeostasis, potentially leading to pathological consequences, such as dyslipidaemia, diabetes, fatty liver, autoimmune diseases, neurodegenerative diseases and cancers. For systemic energy homoeostasis, multiple enzymes involved in lipogenesis are tightly controlled by transcriptional and post-translational modifications. In this Review, we discuss recent findings regarding the regulatory mechanisms, physiological roles and pathological importance of lipogenesis in multiple tissues such as adipose tissue and the liver, as well as the immune and nervous systems. Furthermore, we briefly introduce the therapeutic implications of lipogenesis modulation.

CTRP9 overexpression attenuates palmitic acid‑induced inflammation, apoptosis and impaired migration in HTR8/SVneo cells through AMPK/SREBP1c signaling

Obesity in pregnant mothers often leads to a range of obstetric complications, including miscarriage, pre-eclampsia, gestational hypertension and diabetes. C1q/TNF-related protein 9 (CTRP9) is an adipokine with an anti-inflammatory effect. The aim of the present study was to identify the role of CTRP9 in the pathogenesis of maternal obesity during pregnancy. Following treatment with palmitic acid (PA), HTR8/SVneo cell viability and CTRP9 expression were analyzed using Cell Counting Kit-8 (CCK-8), reverse transcription-quantitative PCR (RT-qPCR) and western blot analyses. The effects of CTRP9 overexpression on cell viability, apoptosis, pro-inflammatory cytokine levels and migration were assessed using CCK-8, TUNEL, RT-qPCR and Transwell assays, respectively. Subsequently, sterol-regulatory element binding protein 1c (SREBP1c) overexpression efficiency was verified using RT-qPCR, and its effects on cell viability, apoptosis, pro-inflammatory cytokines and migration damage were then examined in HTR8/SVneo cells. The results showed that CTRP9 overexpression attenuated the inhibition of cell viability and apoptosis caused by PA in HTR8/SVneo cells, reduced pro-inflammatory cytokine release, improved cell migration and regulated the protein expression level of AMP-activated protein kinase (AMPK)/SREBP1c signaling. In addition, CTRP9 inhibited SREBP1c expression through AMPK signaling, thereby attenuating the inflammation, apoptosis and inhibited migration caused by PA in HTR8/SVneo cells. In brief, CTRP9 protected against inflammation, apoptosis and migration defects in HTR8/SVneo cells exposed to PA treatment through AMPK/SREBP1c signaling, which suggested the potential role of CTRP9 in alleviating the toxicity of PA.

SREBP1c-PARP1 axis tunes anti-senescence activity of adipocytes and ameliorates metabolic imbalance in obesity

Emerging evidence indicates that the accretion of senescent cells is linked to metabolic disorders. However, the underlying mechanisms and metabolic consequences of cellular senescence in obesity remain obscure. In this study, we found that obese adipocytes are senescence-susceptible cells accompanied with genome instability. Additionally, we discovered that SREBP1c may play a key role in genome stability and senescence in adipocytes by modulating DNA-damage responses. Unexpectedly, SREBP1c interacted with PARP1 and potentiated PARP1 activity during DNA repair, independent of its canonical lipogenic function. The genetic depletion of SREBP1c accelerated adipocyte senescence, leading to immune cell recruitment into obese adipose tissue. These deleterious effects provoked unhealthy adipose tissue remodeling and insulin resistance in obesity. In contrast, the elimination of senescent adipocytes alleviated adipose tissue inflammation and improved insulin resistance. These findings revealed distinctive roles of SREBP1c-PARP1 axis in the regulation of adipocyte senescence and will help decipher the metabolic significance of senescence in obesity.

It's What and When You Eat: An Overview of Transcriptional and Epigenetic Responses to Dietary Perturbations in Pancreatic Islets

Our ever-changing modern environment is a significant contributor to the increased prevalence of many chronic diseases, and particularly, type 2 diabetes mellitus (T2DM). Although the modern era has ushered in numerous changes to our daily living conditions, changes in "what" and "when" we eat appear to disproportionately fuel the rise of T2DM. The pancreatic islet is a key biological controller of an organism's glucose homeostasis and thus plays an outsized role to coordinate the response to environmental factors to preserve euglycemia through a delicate balance of endocrine outputs. Both successful and failed adaptation to dynamic environmental stimuli has been postulated to occur due to changes in the transcriptional and epigenetic regulation of pathways associated with islet secretory function and survival. Therefore, in this review we examined and evaluated the current evidence elucidating the key epigenetic mechanisms and transcriptional programs underlying the islet's coordinated response to the interaction between the timing and the composition of dietary nutrients common to modern lifestyles. With the explosion of next generation sequencing, along with the development of novel informatic and -omic approaches, future work will continue to unravel the environmental-epigenetic relationship in islet biology with the goal of identifying transcriptional and epigenetic targets associated with islet perturbations in T2DM.

Srebf1c preserves hematopoietic stem cell function and survival as a switch of mitochondrial metabolism

Mitochondria are fundamental but complex determinants for hematopoietic stem cell (HSC) maintenance. However, the factors involved in the regulation of mitochondrial metabolism in HSCs and the underlying mechanisms have not been fully elucidated. Here, we identify sterol regulatory element binding factor-1c (Srebf1c) as a key factor in maintaining HSC biology under both steady-state and stress conditions. Srebf1c knockout (Srebf1c^-/-) mice display increased phenotypic HSCs and less HSC quiescence. In addition, Srebf1c deletion compromises the function and survival of HSCs in competitive transplantation or following chemotherapy and irradiation. Mechanistically, SREBF1c restrains the excessive activation of mammalian target of rapamycin (mTOR) signaling and mitochondrial metabolism in HSCs by regulating the expression of tuberous sclerosis complex 1 (Tsc1). Our study demonstrates that Srebf1c plays an important role in regulating HSC fate via the TSC1-mTOR-mitochondria axis.

Effect of high-fat diet for rats at different stages on glucose and lipid metabolism in offspring and related mechanisms

OBJECTIVES

To study the effect of high-fat diet for maternal Sprague-Dawley rats at different stages on glucose and lipid metabolism in offspring and related mechanisms.

METHODS

According to the diet before pregnancy and during pregnancy and lactation, maternal rats were randomly divided into four groups (n=9 each): CC (control diet before pregnancy and during pregnancy and lactation), HC (high-fat diet before pregnancy and control diet during pregnancy and lactation), CH (control diet before pregnancy and high-fat diet during pregnancy and lactation), and HH (high-fat diet before pregnancy and during pregnancy and lactation), and all offspring rats were given control diet after weaning. The body weight of maternal rats was recorded before and during pregnancy. Male offspring rats were selected from each group at the juvenile stage (3-week old) and the adult stage (12-week old) to measure the levels of fasting blood glucose (FBG) and fasting insulin (FINS) and the levels of triglyceride (TG) and total cholesterol (TC) in the liver. Homeostasis Model Assessment of Insulin Resistance (HOMA-IR) index was calculated, and the area under the curve (AUC) was calculated for glucose tolerance test (GTT) and insulin tolerance test (ITT). Lipid deposition in the liver was observed, and the mRNA and protein expression levels of the key genes in glucose and lipid metabolism (IR, IRS, and AKT), FASN, SREBP1c, and PPARα in the liver were also measured.

RESULTS

Compared with the control diet groups (CC and CH groups), the groups with high-fat diet before pregnancy (HC and HH groups) had a significant increase in body weight (P<0.001). Compared with the CC group, the HC, CH, and HH groups had a significantly greater increase in body weight (P<0.001). Compared with the CC group, the HC, CH, and HH groups had significant increases in body weight, the levels of TG and TC in the liver, and the mRNA and protein expression levels of FASN, SREBP1c, and PPARα in the offspring rats at week 3 after birth (P<0.05), as well as a significant increase in lipid deposition in the liver, with the most significant increase of the parameters in the HH group. Compared with the CC group, the HH group had significant increases in the levels of FBG and FINS, HOMA-IR index, GTT-AUC, ITT-AUC, and the protein expression level of p-IRS in the liver and significant reductions in the mRNA and protein expression levels of IR and IRS in the liver in the offspring rats at week 3 after birth (P<0.05). Compared with the CC group, the HC, CH, and HH groups had significant increases in body weight, the levels of FBG and FINS, HOMA-IR index, GTT-AUC, ITT-AUC, the levels of TG and TC in the liver, protein expression level of p-IRS in the liver, and the mRNA and protein expression levels of FASN, SREBP1c, and PPARα in the offspring rats at week 12 after birth (P<0.05), as well as a significant increase in lipid deposition in the liver, with the most increase of the parameters in the HH group. Compared with the CC group, the HC, CH, and HH groups had significant reductions in the mRNA expression levels of IR, IRS, and AKT and the protein expression levels of IR, IRS, and p-AKT in the offspring rats at week 12 after birth (P<0.05). There were no significant differences in the levels of glucose and lipid metabolism between the HC and CH groups at various stages (P>0.05).

CONCLUSIONS

High-fat diet for rats at different stages before and after pregnancy has different effects on glucose and lipid metabolism of offspring rats, and high-fat diet before pregnancy and during pregnancy and lactation has the greatest effect. The effect of high-fat diet on glucose and lipid metabolism of offspring rats is considered associated with the changes in the expression of genes involved in glucose and lipid metabolism.

Pax4 Gene Delivery Improves Islet Transplantation Efficacy by Promoting β Cell Survival and α-to-β Cell Transdifferentiation

The transcription factor Pax4 plays an essential role in the development of insulin-producing β cells in pancreatic islets. Ectopic Pax4 expression not only promotes β cell survival but also induces α-to-β cell transdifferentiation. This dual functionality of Pax4 makes it an appealing therapeutic target for the treatment of insulin-deficient type 1 diabetes (T1D). In this study, we demonstrated that Pax4 gene delivery by an adenoviral vector, Ad5.Pax4, improved β cell function of mouse and human islets by promoting islet cell survival and α-to-β cell transdifferentiation, as assessed by multiple viability assays and lineage-tracing analysis. We then explored the therapeutic benefits of Pax4 gene delivery in the context of islet transplantation using T1D mouse models. Both mouse-to-mouse and human-to-mouse islet transplantation, via either kidney capsule or portal vein, were examined. In all settings, Ad5.Pax4-treated donor islets (mouse or human) showed substantially better therapeutic outcomes. These results suggest that Pax4 gene delivery into donor islets may be considered as an adjunct therapy for islet transplantation, which can either improve the therapeutic outcome of islet transplantation using the same amount of donor islets or allow the use of fewer donor islets to achieve normoglycemia.

JunD Regulates Pancreatic β-Cells Function by Altering Lipid Accumulation

The impairment of pancreatic β-cells function is partly caused by lipotoxicity, which aggravates the development of type 2 diabetes mellitus. Activator Protein 1 member JunD modulates apoptosis and oxidative stress. Recently, it has been found that JunD regulates lipid metabolism in hepatocytes and cardiomyocytes. Here, we studied the role of JunD in pancreatic β-cells. The lipotoxic effects of palmitic acid on INS-1 cells were measured, and JunD small-interfering RNA was used to assess the effect of JunD in regulating lipid metabolism and insulin secretion. The results showed that palmitic acid stimulation induced the overexpression of JunD, impaired glucose-stimulated insulin secretion, and increased intracellular lipid accumulation of β-cells. Moreover, the gene expression involved in lipid metabolism (Scd1, Fabp4, Fas, Cd36, Lpl, and Plin5) was upregulated, while gene expression involved in the pancreatic β-cells function (such as Pdx1, Nkx6.1, Glut2, and Irs-2) was decreased. Gene silencing of JunD reversed the lipotoxic effects induced by PA on β-cells. These results suggested that JunD regulated the function of pancreatic β-cells by altering lipid accumulation.

Exploring the protective effect of Modified Xiaochaihu Decoction against hepatic steatosis and inflammation by network pharmacology and validation in ageing rats

Background

Based on therapy with syndrome differentiation and clinical studies on Xiaochaihu decoction (XCHD), we hypothesize that Modified Xiaochaihu Decoction (MXD) has an ability to ameliorate non-alcoholic fatty liver disease (NAFLD). This study aims to elucidate the pharmacological efficacy of MXD and its mechanism in the treatment of NAFLD by network pharmacology and experimental validation.

Methods

The active ingredients in MXD and their potential targets were identified using network analysis followed by experimental validation. First, we used data on the ingredients and targets obtained from professional database and related literature to do PPI network analysis, GO functional analysis, and KEGG pathway enrichment analysis. Core targets identified by network pharmacology were then tested in natural ageing female rats model. Indexes of lipid and glucose homeostasis were determined enzymatically and/or histologically. Gene expression was analyzed by real-time PCR and/or Western blot (WB).

Results

In total, 4009 NAFLD-related targets and 1953 chemical ingredients of MXD were obtained. In-depth network analysis of 140 common targets indicated that MXD played a critical role in anti-NAFLD via multiple targets and pathways. Based on the data of PPI analysis, GO functional enrichment analysis, KEGG pathway enrichment analysis, and literatures on the mechanism of NAFLD, we chose the core targets related to lipid metabolism (SREBP-1c, ChREBP, FASN, PPARα, and ACACA) and inflammation (IL-6 and NF-κB) to do further study. Significantly, in further animal verification experiment we using naturally ageing rats with NAFLD as a model, we found that MXD administration ameliorated age-related NAFLD and mechanistically down-regulated the mRNA/protein expression of core targets in lipid metabolism and inflammation related pathways such as FASN, ACACA, IL-6, and NF-κB. In addition, 12 of 24 potential ingredients acting on verified targets came from BC, and 11 of 24 potential ingredients acting on verified targets were derived from SM, implying that both BC and SM served as the key role in MXD against NAFLD.

Conclusion

The bioinformatics data and in vivo experimental results suggest that the MXD-induced amelioration of NAFLD may be predominantly related to modulation of lipid metabolism and inflammation. Both BC and SM serve as the key role in MXD against NAFLD. These results may provide novel evidence for clinical implication of MXD.

RNF20 Functions as a Transcriptional Coactivator for PPARγ by Promoting NCoR1 Degradation in Adipocytes

Adipose tissue is the key organ coordinating whole-body energy homeostasis. Although it has been reported that ring finger protein 20 (RNF20) regulates lipid metabolism in the liver and kidney, the roles of RNF20 in adipose tissue have not been explored. Here, we demonstrate that RNF20 promotes adipogenesis by potentiating the transcriptional activity of peroxisome proliferator-activated receptor-γ (PPARγ). Under normal chow diet feeding, Rnf20 defective (Rnf20 ^+/- ) mice exhibited reduced fat mass with smaller adipocytes compared with wild-type littermates. In addition, high-fat diet-fed Rnf20 ^+/- mice alleviated systemic insulin resistance accompanied by a reduced expansion of fat tissue. Quantitative proteomic analyses revealed significantly decreased levels of PPARγ target proteins in adipose tissue of Rnf20 ^+/- mice. Mechanistically, RNF20 promoted proteasomal degradation of nuclear corepressor 1 (NCoR1), which led to stimulation of the transcriptional activity of PPARγ. Collectively, these data suggest that RNF20-NCoR1 is a novel axis in adipocyte biology through fine-tuning the transcriptional activity of PPARγ.

During Adipocyte Remodeling, Lipid Droplet Configurations Regulate Insulin Sensitivity through F-Actin and G-Actin Reorganization

Adipocytes have unique morphological traits in insulin sensitivity control. However, how the appearance of adipocytes can determine insulin sensitivity has not been understood. Here, we demonstrate that actin cytoskeleton reorganization upon lipid droplet (LD) configurations in adipocytes plays important roles in insulin-dependent glucose uptake by regulating GLUT4 trafficking. Compared to white adipocytes, brown/beige adipocytes with multilocular LDs exhibited well-developed filamentous actin (F-actin) structure and potentiated GLUT4 translocation to the plasma membrane in the presence of insulin. In contrast, LD enlargement and unilocularization in adipocytes downregulated cortical F-actin formation, eventually leading to decreased F-actin-to-globular actin (G-actin) ratio and suppression of insulin-dependent GLUT4 trafficking. Pharmacological inhibition of actin polymerization accompanied with impaired F/G-actin dynamics reduced glucose uptake in adipose tissue and conferred systemic insulin resistance in mice. Thus, our study reveals that adipocyte remodeling with different LD configurations could be an important factor to determine insulin sensitivity by modulating F/G-actin dynamics.

Detection of InDel variations within seven candidate genes and their associations with phenotypic traits in three cattle breeds

The Xinjiang brown cattle, Red steppe cattle, and Yunling cattle are indigenous cultivated cattle breeds in Chinese frontier provinces, and they produce high-grade beef and milk products, however, their genetic diversity in many important genes related to excellent meat and milk production is still unknown. Our previous studies have found that several candidate genes (e.g., SREBP1c and PAX7) were associated with bovine economically important phenotypic traits, but none has been reported in the above-mentioned three cattle breeds. Since the InDel (insertion/deletion) marker becomes a useful tool applied in the animal molecular breeding, herein, we firstly found that the InDel variations of seven candidate genes in these cattle. Results showed that the genotypic and allelic distributions of these seven genes were remarkably different among these three cattle (p < 0.05 or p < 0.01). Furthermore, the InDel variations of SREBP1c and PAX7 genes were significantly associated with eight phenotypic traits in Xinjiang brown cattle (p < 0.05 or p < 0.01), respectively, suggesting that they can become the useful DNA markers.