Genomic and epigenomic responses to aspirin in human colonic organoids.

Aspirin (ASA) is a proven chemoprotective agent for colorectal cancer, though mechanisms underlying these effects are incompletely understood. Human organoids are an ideal system to study genomic and epigenomic host-environment interactions. We use human colonic organoids to profile ASA responses on genome-wide gene expression and chromatin accessibility. Human colonic organoids from one individual were cultured and treated in triplicate with 3 mM ASA or vehicle control (DMSO) for 24 h. Gene expression and chromatin accessibility were measured using RNA- and ATAC-sequencing, respectively. Differentially expressed genes were analyzed using DESeq2. Top genes were validated by qPCR. Gene set enrichment was performed by SetRank. Differentially accessible peaks were analyzed using DiffBind and edgeR. Peak annotation and differential transcription factor motifs were determined by HOMER and diffTF. The results showed robust transcriptional responses to ASA with significant enrichment for fatty acid oxidation and peroxisome proliferator-activated receptor (PPAR) signaling that were validated in independent organoid lines. A large number of differentially accessible chromatin regions were found in response to ASA with significant enrichment for Fos, Jun, and Hnf transcription factor motifs. Integrated analysis of epigenomic and genomic treatment responses highlighted gene regions that could mediate ASA's specific effects in the colon including those involved in chemoprotection and/or toxicity. Assessment of chromatin accessibility and transcriptional responses to ASA yielded new observations about genome-wide effects in the colon facilitated by application of human colonic organoids. This framework can be applied to study colonic ASA responses between individuals and populations in future studies.

Revisiting the association between human leukocyte antigen and end-stage renal disease.

Multiple works have studied possible associations between human leukocyte antigen (HLA) alleles and end stage renal disease (ESRD) showing, however, contradictory and inconsistent results. Here, we revisit the association between ESRD and HLA antigens, comparing HLA polymorphism (at HLA-A, -B, -C, -DRB1, -DQB1 and DQA1 loci) in ESRD patients (n = 497) and controls (n = 672). Our data identified several HLA alleles that displayed a significant positive or negative association with ESRD. We also determined whether heterozygosity or homozygosity of the ESRD-associated HLA alleles at different loci could modify the prevalence of the disease. Few HLA allele combinations displayed significant associations with ESRD, among which A*3_26 combination showed the highest strength of association (OR = 4.488, P≤ 0.05) with ESRD. Interestingly, the age of ESRD onset was not affected by HLA allele combinations at different loci. We also performed an extensive literature analysis to determine whether the association of HLA to ESRD can be similar across different ethnic groups. Our analysis showed that at least certain HLA alleles, HLA-A*11, HLA-DRB1*11, and HLA-DRB1*4, display a significant association with ESRD in different ethnic groups. The findings of our study will help in determining possible protective or susceptible roles of various HLA alleles in ESRD.

Lipid-load in peripheral blood mononuclear cells: Impact of food-consumption, dietary-macronutrients, extracellular lipid availability and demographic factors.

Lipid-load in peripheral blood mononuclear cells (PBMCs) has recently gained attention of the researchers working on nutritional regulation of metabolic health. Previous works have indicated that the metabolic circuitries in the circulating PBMCs are influenced by dietary-intake and macronutrient composition of diet. In the present work, we analyzed the impact of diet and dietary macronutrients on PBMCs' lipid-load. The overall analyses revealed that dietary carbohydrates and fats combinatorially induce triglyceride accumulation in PBMCs. On the other hand, dietary fats were shown to induce significant decrease in PBMCs' cholesterol-load. The effects of various demographic factors -including age, gender and body-weight- on PBMCs' lipid-load were also examined. Body-weight and age were both shown to affect PBMC's lipid-load. Our study fails to provide any direct association between extracellular lipid availability and cholesterol-load in both, freshly isolated and cultured PBMCs. The presented work significantly contributes to the current understanding of the impact of food-consumption, dietary macronutrients, extracellular lipid availability and demographic factors on lipid-load in PBMCs.

Leukemia cells display lower levels of intracellular cholesterol irrespective of the exogenous cholesterol availability.

BACKGROUND: Different types of cancer cells are previously shown to accumulate intracellular cholesterol. However, the data on intracellular cholesterol levels in leukemia cells provide contradictory evidence. Various previous works indicate either increase, decrease or no difference in total cholesterol levels between leukemia cells and healthy peripheral blood mononuclear cells (PBMCs). METHODS: We studied the intracellular cholesterol levels in acute myeloid leukemia (AML) and acute lymphocytic leukemia (ALL) cells and compared with that in PBMCs from the healthy subjects. RESULTS: We observed that the PBMCs from AML (n=7) and ALL (n=7) patients displayed significantly lower intracellular levels of total cholesterol in comparison to PBMCs from the healthy subjects (n=26). Consistent with the patient data the ALL (CCRF-CEM and MOLT-3) and AML (KG-1 and THP-1) cell lines also displayed significantly lower intracellular levels of total cholesterol. We confirmed this observation using multiple methodological approaches. Both ALL and AML cell lines also displayed significantly lower levels of free cholesterol and cholesteryl ester contents in comparison to normal hematopoietic cells. We observed that >90% of the total cholesterol in leukemia cells as well as in normal PBMCs was present in the form of cholesteryl esters. It was also observed that the lower levels of cholesterol in leukemia cells are not affected by exogenous cholesterol availability. CONCLUSIONS: Present study provides convincing evidence to prove that the cellular free cholesterol and cholesteryl ester content is significantly reduced in leukemia cells in comparison to normal hematopoietic cells in circulation. Moreover, it was shown that the lower levels of cholesterol in leukemia cells are not affected by exogenous cholesterol availability.

Atypical plasma lipid profiles in leukemia.

Numerous studies have reported alterations in the plasma lipid profiles of leukemia patients. However, there are several inconsistencies in these reports. The present review highlights and compiles findings from different research groups regarding association of plasma lipoprotein levels with the risk of developing leukemia. We have also discussed the clinical significance of plasma lipid profiles in management of leukemia. Furthermore, the potential role of plasma lipids in promoting leukemogenesis is also highlighted.

Revisiting the dyslipidemia associated with acute leukemia.

BACKGROUND: Previous studies appreciate the leukemia-associated alterations in plasma lipid profiles but fail to provide a consistent pattern of lipid anomalies in leukemia patients. These inconsistencies could be due to overlooking the effects of related confounding risk-factors and comorbidities. METHODS: The plasma lipid profiles of acute-leukemia and control groups were compared. RESULTS: We observed that acute lymphocytic leukemia (ALL) patients display significantly higher triglycerides and very low-density lipoproteins, whereas, acute myeloid leukemia (AML) patients display significantly lower high-density lipoproteins. To assess the confounding effects of related risk factors gender-, age- and BMI-based analyses were performed. We observed that the aforementioned significant differences in the lipid profiles of leukemia patients were restricted to female participants of the respective groups. Moreover, a significant decrease in total cholesterol and low-density lipoprotein levels was observed only in male participants of the AML population. Various age-specific trends in plasma lipid profile of the leukemia patients were also observed. BMI-based analysis did not display many significant differences from the overall analyses. In addition to comparing the absolute values of plasma lipids in leukemia and control groups we also compared and observed significant differences in prevalence of various isolated- and mixed-dyslipidemias in these groups. CONCLUSIONS: These findings may help in outlining the prevalence and types of dyslipidemia in leukemia patients that may emerge as diagnostic/prognostic factors for the management of acute leukemia.

Atypical plasma lipid profile in cancer patients: cause or consequence?

The aberrant blood lipoprotein levels in cancer patients are reported to be associated with cancer risk and mortality incidents however, there are several discrepancies in the previous reports. Hence the clinical usefulness of plasma/serum levels in risk stratification of a variety of cancers remains elusive. The present review highlights and compiles findings from different research groups regarding association of plasma lipoprotein levels with the risk of developing various types of cancer. We will discuss some prospective underlying mechanisms for this reported association. In addition to that the potential roles of plasma lipids in promoting carcinogenesis will be conferred.