Assignment of human pancreatic lipase gene (PNLIP) to chromosome 10q24-q26

Exploring the enigmatic association between PNLIP variants and risk of chronic pancreatitis in a large Chinese cohort

BACKGROUND & AIMS

Protease-sensitive PNLIP variants were recently associated with chronic pancreatitis (CP) in European populations. The pathological mechanism yet remains elusive. Herein, we performed a comprehensive genetic and functional analysis of PNLIP variants found in a large Chinese cohort, aiming to further unravel the enigmatic association of PNLIP variants with CP.

METHODS

All coding and flanking intronic regions of the PNLIP gene were analyzed for rare variants by targeted next-generation sequencing in 1082 Chinese CP patients and 1196 controls. All novel missense variants were subject to analysis of secretion, lipase activity, and proteolytic degradation. One variant was further analyzed for its potential to misfold and induce endoplasmic reticulum (ER) stress. p.F300L, the most common PNLIP variant associated with CP, was used as a control.

RESULTS

We identified 12 rare heterozygous PNLIP variants, with 10 being novel. The variant carrier frequency did not differ between the groups. Of them, only the variant p.A433T found in a single patient was considered pathologically relevant. p.A433T exhibited increased susceptibility to proteolytic degradation, which was much milder than p.F300L. Interestingly, both variants exhibited an increased tendency to misfold, leading to intracellular retention as insoluble aggregates, reduced secretion, and elevated ER stress.

CONCLUSIONS

Our genetic and functional analysis of PNLIP variants identified in a Chinese CP cohort suggests that the p.A433T variant and the previously identified p.F300L variant are not only protease-sensitive but also may be potentially proteotoxic. Mouse studies of the PNLIP p.F300L and p.A433T variants are needed to clarify their role in CP.

Diet evolution of carnivorous and herbivorous mammals in Laurasiatheria

Background

Laurasiatheria contains taxa with diverse diets, while the molecular basis and evolutionary history underlying their dietary diversification are less clear.

Results

In this study, we used the recently developed molecular phyloecological approach to examine the adaptive evolution of digestive system-related genes across both carnivorous and herbivorous mammals within Laurasiatheria. Our results show an intensified selection of fat and/or protein utilization across all examined carnivorous lineages, which is consistent with their high-protein and high-fat diets. Intriguingly, for herbivorous lineages (ungulates), which have a high-carbohydrate diet, they show a similar selection pattern as that of carnivorous lineages. Our results suggest that for the ungulates, which have a specialized digestive system, the selection intensity of their digestive system-related genes does not necessarily reflect loads of the nutrient components in their diets but appears to be positively related to the loads of the nutrient components that are capable of being directly utilized by the herbivores themselves. Based on these findings, we reconstructed the dietary evolution within Laurasiatheria, and our results reveal the dominant carnivory during the early diversification of Laurasiatheria. In particular, our results suggest that the ancestral bats and the common ancestor of ruminants and cetaceans may be carnivorous as well. We also found evidence of the convergent evolution of one fat utilization-related gene, APOB, across carnivorous taxa.

Conclusions

Our molecular phyloecological results suggest that digestive system-related genes can be used to determine the molecular basis of diet differentiations and to reconstruct ancestral diets.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02033-6.

Whole Exome Sequencing Study in a Family with Type 2 Diabetes Mellitus

Background

Type 2 diabetes mellitus (T2DM) is characterized by β cell decline in the pancreas and insulin resistance. This study aimed to investigate the possible pathogenic gene mutation sites of T2DM patients using whole exome sequencing.

Materials and Methods

We recruited a Chinese family with 3-generation history of diabetes. The whole blood genomic DNA of seven members of the family was extracted and sent for whole exome sequencing. Biological information was analyzed with in silico prediction methods, including significance analysis of single nucleotide polymorphism (SNP)/Indel site, and analysis of specific SNP/Indel proteins and their potential mechanisms.

Results

Six out of seven members of the family were diagnosed with diabetes. All DNA samples (23 kb) met quality requirements of library construction. Clean reads of each sample demonstrated high Q20 and Q30 (>80%), indicating good sequencing quality of sequencing data. A total of 130,693 SNPs and 15,928 Indels were found in DNA samples. A total of 22 significant SNPs and Indel mutation sites located on 19 genes were obtained, including ZCCHC3, SYN2, RPL14, SRRD, AMD1, CAMKK2, ZNF787, RNF157, NPIPB15, ALG3, KIAA0040, MAST2, ESRRA, C8orf58, PNLIPRP1, DACH1, MACC1, CAPN9 and DMKN. An rs2305205 mutation of PNLIPRP1 gene and an rs778701848 mutation of CAMKK2 gene may be associated with the pathogenesis of T2DM in this family.

Conclusion

Exons of these diabetic patients demonstrated an rs2305205 mutation in PNLIPRP1 gene and an rs778701848 mutation in CAMKK2 gene. These two mutations might promote T2DM occurrence through reducing sensitivity of peripheral tissue to insulin and reducing insulin secretion.

Design, synthesis, evaluation, and molecular modeling studies of indolyl oxoacetamides as potential pancreatic lipase inhibitors

A series of indolyl oxoacetamide analogs was synthesized, characterized, and evaluated for their pancreatic lipase inhibitory activity using porcine pancreatic lipase (type II) and 4-nitrophenyl butyrate. Compound 8d exhibited a potent inhibition, with an IC₅₀ value of 4.53 µM, followed by 8c (IC₅₀  = 5.12 µM), compared with the standard drug, orlistat (IC₅₀  = 0.99 µM). Furthermore, analogs 8c and 8d exhibited a reversible competitive inhibition, similar to orlistat. Molecular docking studies of the compounds 7a-f and 8a-f were in agreement with the in vitro results, wherein 8d exhibited a potential MolDock score of -163.052 kcal/mol. A 10-ns molecular dynamics simulation of 8d complexed with pancreatic lipase confirmed the role of π-π stacking and π-cation interactions with the lid domain and Arg 256, respectively, in stabilizing the ligand at the active site (maximum observed root mean square deviation ≈ 2 Å). The present study led to the identification of novel indolyl oxoacetamides (8a-d) as potential pancreatic lipase inhibitory leads that might further result in enhanced potency through lead optimization.

Reduced Function of the Glutathione S-Transferase S1 Suppresses Behavioral Hyperexcitability in Drosophila Expressing Mutant Voltage-Gated Sodium Channels

Voltage-gated sodium (Na_v) channels play a central role in the generation and propagation of action potentials in excitable cells such as neurons and muscles. To determine how the phenotypes of Na_v-channel mutants are affected by other genes, we performed a forward genetic screen for dominant modifiers of the seizure-prone, gain-of-function Drosophila melanogaster Na_v-channel mutant, para^Shu. Our analyses using chromosome deficiencies, gene-specific RNA interference, and single-gene mutants revealed that a null allele of glutathione S-transferase S1 (GstS1) dominantly suppresses para^Shu phenotypes. Reduced GstS1 function also suppressed phenotypes of other seizure-prone Na_v-channel mutants, para^GEFS+ and para^bss. Notably, para^Shu mutants expressed 50% less GstS1 than wild-type flies, further supporting the notion that para^Shu and GstS1 interact functionally. Introduction of a loss-of-function GstS1 mutation into a para^Shu background led to up- and down-regulation of various genes, with those encoding cytochrome P450 (CYP) enzymes most significantly over-represented in this group. Because GstS1 is a fly ortholog of mammalian hematopoietic prostaglandin D synthase, and in mammals CYPs are involved in the oxygenation of polyunsaturated fatty acids including prostaglandins, our results raise the intriguing possibility that bioactive lipids play a role in GstS1-mediated suppression of para^Shu phenotypes.

Patterns of genetic structure and adaptive positive selection in the Lithuanian population from high-density SNP data

The analysis of geographically specific regions and the characterization of fine-scale patterns of genetic diversity may facilitate a much better understanding of the microevolutionary processes affecting local human populations. Here we generated genome-wide high-density SNP genotype data in 425 individuals from six geographical regions in Lithuania and combined our dataset with available ancient and modern data to explore genetic population structure, ancestry components and signatures of natural positive selection in the Lithuanian population. Our results show that Lithuanians are a homogenous population, genetically differentiated from neighbouring populations but within the general expected European context. Moreover, we not only confirm that Lithuanians preserve one of the highest proportions of western, Scandinavian and eastern hunter-gather ancestry components found in European populations but also that of an steppe Early to Middle Bronze Age pastoralists, which together configure the genetic distinctiveness of the Lithuanian population. Finally, among the top signatures of positive selection detected in Lithuanians, we identified several candidate genes related with diet (PNLIP, PPARD), pigmentation (SLC24A5, TYRP1 and PPARD) and the immune response (BRD2, HLA-DOA, IL26 and IL22).

Design, synthesis, biological evaluation and molecular modelling studies of indole glyoxylamides as a new class of potential pancreatic lipase inhibitors

A series of eighteen indole glyoxylamide analogues were synthesized, characterized and evaluated for their pancreatic lipase inhibitory activity. Porcine pancreatic lipase (Type II) was used with 4-nitrophenyl butyrate (as substrate) for the in vitro assay. Compound 8f exhibited competitive inhibition against pancreatic lipase with IC₅₀ value of 4.92 µM, comparable to that of the standard drug, orlistat (IC₅₀ = 0.99 µM). Compounds 7a-i and 8a-i were subjected to molecular docking into the active site of human PL (PDB ID: 1LPB) wherein compound 8f possessed a potential MolDock score of -153.037 kcal/mol. Molecular dynamics simulation of 8f complexed with pancreatic lipase, confirmed the role of aromatic substitution in stabilizing the ligand through hydrophobic interactions (maximum observed RMSD = 3.5 Å).

'Obesity' is healthy for cetaceans? Evidence from pervasive positive selection in genes related to triacylglycerol metabolism

Cetaceans are a group of secondarily adapted marine mammals with an enigmatic history of transition from terrestrial to fully aquatic habitat and subsequent adaptive radiation in waters around the world. Numerous physiological and morphological cetacean characteristics have been acquired in response to this drastic habitat transition; for example, the thickened blubber is one of the most striking changes that increases their buoyancy, supports locomotion, and provides thermal insulation. However, the genetic basis underlying the blubber thickening in cetaceans remains poorly explored. Here, 88 candidate genes associated with triacylglycerol metabolism were investigated in representative cetaceans and other mammals to test whether the thickened blubber matched adaptive evolution of triacylglycerol metabolism-related genes. Positive selection was detected in 41 of the 88 candidate genes, and functional characterization of these genes indicated that these are involved mainly in triacylglycerol synthesis and lipolysis processes. In addition, some essential regulatory genes underwent significant positive selection in cetacean-specific lineages, whereas no selection signal was detected in the counterpart terrestrial mammals. The extensive occurrence of positive selection in triacylglycerol metabolism-related genes is suggestive of their essential role in secondary adaptation to an aquatic life, and further implying that 'obesity' might be an indicator of good health for cetaceans.

Changes of the expressions of multiple metabolism genes in rat pancreatic islets after ventromedial hypothalamic lesioning

It was recently reported that ventromedial hypothalamic lesions change the expression of cell proliferation-related genes and morphology-related genes in rat pancreatic islets. This study has examined how gene families involved in metabolism are regulated in rat pancreatic islets after VMH lesions formation. Total pancreatic islets RNA was extracted, and differences in the gene expression profiles between rats at day 3 after VMH lesioning and sham-VMH-lesioned rats were investigated using DNA microarray and real-time polymerase chain reaction. The VMH lesions regulated the genes that are involved in functions related to metabolism in the pancreas islets. Real-time polymerase chain reaction also confirmed that gene expressions of arachidonate 15-lipoxygenase (Alox15) was up-regulated and pancreatic lipase (Pnlip) was downregulated at day 3 after the VMH lesions. Ventromedial hypothalamic lesions may change the expression of multiple metabolism genes in rat pancreatic islets.

Identification of a novel mutation in the PNLIP gene in two brothers with congenital pancreatic lipase deficiency

Congenital pancreatic lipase (PNLIP) deficiency is a rare monoenzymatic form of exocrine pancreatic failure characterized by decreased absorption of dietary fat and greasy voluminous stools, but apparent normal development and an overall good state of health. While considered to be an autosomal recessive state affecting a few dozens of individuals world-wide and involving the PNLIP gene, no causative mutations for this phenotype were so far reported. Here, we report the identification of the homozygote missense mutation, Thr221Met [c.662C>T], in two brothers from a consanguineous family of Arab ancestry. The observed genotypes among the family members were concordant with an autosomal recessive mode of inheritance but moreover a clear segregation between the genotype state and the serum PNLIP activity was evident. Based on biophysical computational tools, we suggest the mutation disrupts the protein's stability and impairs its normal function. Although the role of PNLIP is well established, our observations provide genetic evidence that PNLIP mutations are causative for this phenotype.

Evidence for a quantitative trait locus affecting low levels of apolipoprotein B and low density lipoprotein on chromosome 10 in Caucasian families

High plasma apolipoprotein B (apoB) and LDL cholesterol levels increase cardiovascular disease risk. These highly correlated measures may be partially controlled by common genetic polymorphisms. To identify chromosomal regions that contain genes causing low plasma levels of one or both parameters in Caucasian families ascertained for familial hypobetalipoproteinemia (FHBL), we conducted a whole-genome scan using 443 microsatellite markers typed in nine multigenerational families with at least two members with FHBL. Both variance components and regression-based linkage methods were used to identify regions of interest. Common linkage regions were identified for both measures on chromosomes 10q25.1-10q26.11 [maximum log of the odds (LOD) = 4.2 for LDL and 3.5 for apoB] and 6q24.3 (maximum LOD = 1.46 for LDL and 1.84 for apoB). There was also evidence for linkage to apoB on chromosome 13q13.2 (LOD = 1.97) and to LDL on chromosome 3p14.1 at 94 centimorgan (LOD = 1.52). Bivariate linkage analysis provided further evidence for loci contributing to both traits (6q24.3, LOD = 1.43; 10q25.1, LOD = 1.74). We evaluated single nucleotide polymorphisms (SNPs) in genes within our linkage regions to identify variants associated with apoB or LDL levels. The most significant finding was for rs2277205 in the 5' untranslated region of acyl-coenzyme A dehydrogenase short/branched chain and LDL (P = 10(-7)). Three additional SNPs were associated with apoB and/or LDL (P < 0.01). Although only the linkage signal on chromosome 10 reached genome-wide statistical significance, there are likely multiple chromosomal regions with variants that contribute to low levels of apoB and LDL and that may protect against coronary heart disease.

Constitutive expression of human pancreatic lipase-related protein 1 in Pichia pastoris

High-level constitutive expression of the human pancreatic lipase-related protein 1 (HPLRP1) was achieved using the methylotrophic yeast Pichia pastoris. The HPLRP1 cDNA, including its original leader sequence, was subcloned into the pGAPZB vector and further integrated into the genome of P. pastoris X-33 under the control of the glyceraldehyde 3-phosphate dehydrogenase (GAP) constitutive promoter. A major protein with a molecular mass of 50 kDa was found to be secreted into the culture medium and was identified using anti-HPLRP1 polyclonal antibodies as HPLRP1 recombinant protein. The level of expression reached 100-120 mg of HPLRP1 per liter of culture medium after 40 h, as attested by specific and quantitative enzyme-linked immunosorbent assay. A single cation-exchange chromatography sufficed to obtain a highly purified recombinant HPLRP1 after direct batch adsorption onto S-Sepharose of the HPLRP1 present in the culture medium, at pH 5.5. N-terminal sequencing and mass spectrometry analysis were carried out to monitor the production of the mature protein and to confirm that its signal peptide was properly processed.

Lipoatrophic panniculitis and chromosome 10 abnormality

We report a 3-year-old girl with a 12-month history of an acquired lipoatrophy that was rapidly progressive. Her karyotype revealed additional material on chromosome 10 at the 10q26 location. The human pancreatic lipase gene maps to chromosome 10q24-26, and we postulate an association. Lipoatrophic panniculitis describes the panniculitides in which atrophy is a feature. The classification of these diseases is confusing in the literature and the precise diagnosis still relies on a combination of clinical and laboratory assessment. Our finding of a chromosomal abnormality on chromosome 10q26 has not been described previously.

Discoordinate expression of pancreatic lipase and two related proteins in the human fetal pancreas

The lipase gene family contains a large number of members. Among the most closely related are pancreatic triglyceride lipase (PTL) and two pancreatic lipase-related proteins (PLRP1 and PLRP2). Previous studies in rodents demonstrated divergent temporal expression of the genes encoding these proteins. PLRP1 and PLRP2 were expressed in fetal pancreas, whereas PTL was not expressed until pups were several weeks old. To determine whether the human pancreas has a similar expression pattern for these genes, we determined the levels of each mRNA in fetal pancreas at various ages. A reverse transcriptase-PCR method was developed and used to quantify the mRNA levels for the three species normalized to the mRNA encoding cyclophillin. The mRNA encoding PLRP1 and PLRP2 was present by 16 wk in the fetal pancreas. In contrast, the mRNA encoding PTL was not present in the fetal pancreas. This pattern of expression suggests that the genes encoding theses proteins have different regulatory elements controlling temporal expression and provides another example of nonparallel expression of genes encoding pancreatic exocrine proteins.

Amylase and lipase in the emergency department evaluation of acute pancreatitis

Serum amylase and lipase levels are commonly obtained in the emergency department for the diagnosis of acute pancreatitis. The role of these enzymes has frequently been the subject of confusion and controversy. This article comprehensively reviews the history, biochemistry, clinical, and laboratory literature on both enzymes as used in the evaluation of pancreatitis. Specific guidelines are presented to assist the Emergency Physician in the appropriate use and interpretation of these clinical laboratory tests.

Lipases and esterases: a review of their sequences, structure and evolution

This chapter aims to provide a brief review on the enzyme family of lipases and esterases. The sequences, 3D structures and pH dependent electrostatic signatures are presented and analyzed. Since the family comprises more than 100 sequences, we have tried to focus on the most interesting features from our perspective, which translates into finding similarities and differences between members of this family, in particular in and around the active sites, and to identify residues that are partially or totally conserved. Such residues we believe are either important for maintaining the structural scaf-fold of the protein or to maintain activity or specificity. The structure function relationship for these proteins is therefore of central interest. Can we uniquely identify a protein from this large family of sequences--and if so, what is the identifier? The protein family displays some highly complex features: many of the proteins are interfacially activated, i.e. they need to be in physical contact with the aggregated substrate. Access to the active site is blocked with either a loop fragment or an alpha-helical fragment in the absence of interfacial contact. Although the number of known, relevant protein 3D structures is growing steadily, we are nevertheless faced with a virtual explosion in the number of known or deduced amino acid sequences. It is therefore unrealistic to expect that all protein sequences within the foreseeable future will have their 3D structure determined by X-ray diffractional analysis or through other methods. When feasible the gene and/or the amino acid sequences will be analyzed from an evolutionary perspective. As the 3D folds are often remarkably similar, both among the triglyceride lipases as well as among the esterases, the functional diversities (e.g. specificity) must originate in differences in surface residue utilization, in particular of charged residues. The pH variations in the isopotential surfaces of some of the most interesting lipases are presented and a qualitative interpretation proposed. Finally we illustrate that NMR has potential for becoming an important tool in the study of lipases, esterases and their kinetics.

Pancreatic triglyceride lipase and colipase: insights into dietary fat digestion

Dietary fats have an impact on health and disease. A pancreatic exocrine protein, pancreatic triglyceride lipase, is essential for the efficient digestion of dietary fats. This enzyme requires another pancreatic exocrine protein, colipase, for full activity in the gut lumen. In addition to its importance in fat digestion, pancreatic triglyceride lipase has potential applications in medical therapy, medical diagnostics, and industry. This potential stimulated interest in lipases; radiograph during the last few years, studies applying the technologies of molecular biology and radiograph crystallography greatly increased our knowledge about pancreatic triglyceride lipase and colipase protein structure, enzyme mechanism, and gene structure. This review focuses on these recent advances and discusses models for the kinetic properties of pancreatic triglyceride lipase and for the interaction of pancreatic triglyceride lipase with colipase.

Purification of lipase and other lipolytic enzymes from the human pancreas

A pure lipase has been isolated from extracts of the human pancreas. The purification process includes centrifugation, two ion-exchange chromatography steps, and one gel filtration step. Compared with other reports, a high recovery, large amounts, and a high specific activity were obtained. Lipase is present at 1-2 mg/g in the pancreatic gland. In the absence of colipase and bile salts with tributyrine as substrate, the specific activity at room temperature and at pH 7.0 is 4000 mumol/min/mg. It increases to 8000-10,000 in the presence of colipase and bile salts at a temperature of 37 degrees C. The fate of the other human lipolytic proteins during the different purification steps is also indicated. Lipase purified by this method has been used for crystallization.