Compound heterozygous mutations affect protein folding and function in patients with congenital sucrase-isomaltase deficiency

Exploring congenital sucrase-isomaltase deficiency in autism spectrum disorder patients with irritable bowel syndrome symptoms: A prospective SI gene sequencing study

Congenital sucrase-isomaltase deficiency (CSID) is an inherited metabolic disorder causing chronic gastrointestinal symptoms and malnutrition when untreated. Most CSID patients are likely to remain under- or misdiagnosed. This study aimed to investigate prevalence of CSID among patients with autism spectrum disorder (ASD) presenting with irritable bowel syndrome (IBS) symptoms via prospective SI gene sequencing. A prospective cross-sectional study was conducted on 98 ASD patients exhibiting gastrointestinal symptoms consistent with IBS. Participants were assessed according to Rome IV criteria and underwent SI gene sequencing. Demographic, clinical, and dietary data were collected and analyzed. Sucrose content in various fruits and vegetables was evaluated using three-day food record, and gastrointestinal symptoms were rated on Likert scale. Seven patients (7%) were diagnosed with CSID based on SI gene analysis, revealing six different variants, including four novel mutations. One patient was homozygous for one variant, and six patients were heterozygous. Clinical presentations predominantly included diarrhea, abdominal pain, and bloating, with two patients showing growth retardation. One patient was diagnosed in adulthood. Food allergy and lactose intolerance were the misdiagnoses prior to CSID diagnosis in two patients. Real prevalence of CSID is likely underestimated. Clinical heterogeneity and non-specific symptoms contribute to diagnostic challenges. Gastrointestinal symptoms consistent with IBS in ASD patients should include CSID in differential diagnosis. Early genetic screening for SI variants in ASD patients with IBS symptoms can facilitate timely diagnosis and management, improving outcomes. Heterozygous variants of the SI gene should also be considered, as heterozygous patients can exhibit typical CSID symptoms.

Exploring genetic variants in congenital monosaccharide-disaccharide metabolism: Carrier ratios and phenotypic insights

OBJECTIVES

Adverse food reactions, often underestimated, encompass congenital monosaccharide-disaccharide metabolism disorders, yielding diverse outcomes such as abdominal pain, diarrhea, bleeding disorders, and even death. This study retrospectively scrutinized genetic variants linked to these disorders in a cohort subjected to whole-exome sequence analysis (WES), determining carrier frequencies and genotype-phenotype correlations.

METHODS

Data from 484 patients, were retrospectively analyzed using a gene panel (ALDOB, FBP1, GALE, GALK1, GALM, GALT, LCT, SLC2A2, SLC5A1, SI) for congenital monosaccharide-disaccharide metabolism disorders. WES was performed on patients using the xGen Exome Research Panel v2 kit, utilizing Next Generation Sequence Analysis (NGS). The study encompassed pathogenic, likely pathogenic, and variant of uncertain significance (VUS) variants.

RESULTS

Among 484 patients (244 female, 240 male), 17.35% carried 99 variants (67 distinct) in the analyzed genes. Pathogenic/likely pathogenic allele frequency stood at 0.013, while VUS allele frequency was 0.088. Notably, 44% (37/84) of patients harboring mutations manifested at least one relevant phenotype. Carriage frequencies ranged from 1:25 (SI gene) to 1:968 (GALE gene), with the estimated disease frequency spanning from 1:2500 to 1:3748000.

CONCLUSIONS

Our study underscores clinical manifestations in heterozygous carriers of recessive genetic disorders, addressing gaps in carrier frequencies and phenotypic effects for congenital monosaccharide-disaccharide metabolism disorders. This knowledge can improve these conditions' diagnosis and management, potentially preventing adverse food reactions and their associated complications.

Congenital sucrase-isomaltase deficiency in Türkiye; a single center experience

BACKGROUND

Congenital sucrase-isomaltase deficiency (CSID) is a rare inherited carbohydrate malabsorption disorder caused by sucrase-isomaltase (SI) gene variants. In CSID, an autosomal recessively inherited disease, symptoms can also be seen in individuals with heterozygous mutations.

METHODS

The variant spectrum was evaluated retrospectively in individuals who presented with chronic diarrhea between 2014 and 2022 and had undergone genetic testing of the SI gene considering CSID due to diet-related complaints.

RESULTS

Ten patients with chronic diarrhea were genetically evaluated with SI gene sequencing. In patients diagnosed with CSID and whose symptoms improved with enzyme replacement therapy, the genetic mutation zygosity was found to be heterozygous at a rate of 90%. In 10% of the patients, the mutation was homozygous. Limiting consuming sucrose and isomaltose foods reduced the patients' complaints, but the symptoms did not disappear completely. With the initiation of sacrosidase enzyme replacement therapy, the patient's complaints completely disappeared.

CONCLUSION

In CSID, defined as an autosomal recessive disease, clinical symptoms can also be seen in heterozygous cases previously described as carriers, and these patients also benefit from sacrosidase enzyme replacement therapy. In light of these findings, the autosomal recessive definition of CSID does not fully characterize the disease.What is Known:CSID is a rare inherited carbohydrate malabsorption disorder caused by sucrase-isomaltase gene variants.In congenital sucrase-isomaltase deficiency, an autosomal recessively inherited disorder, symptoms can also be seen in individuals with heterozygous mutations.What is new:Severe disease symptoms can also be seen in heterozygous cases, which were thought to be carriers because the disease was previously described as autosomal recessive.Sacrosidase enzyme replacement therapy also eliminates the disease symptoms in patients with heterozygous CSID mutations.This is the second study on sucrase-isomaltase enzyme deficiency pediatric groups in Türkiye and Europe.

Impaired digestive function of sucrase-isomaltase in a complex with the Greenlandic sucrase-isomaltase variant

Sucrase isomaltase (SI) is the most prominent disaccharidase in the small intestine. Congenital sucrase-isomaltase deficiency (CSID) is an autosomal recessive disorder caused by variants in the SI gene. A homozygous frameshift mutation, c.273_274delAG (p.Gly92Leufs*8), has been identified in CSID in the Greenlandic population. This variant eliminates the luminal domain of SI and results in loss of its digestive function. Surprisingly, the truncated mutant is transport-competent and localized at the cell surface; it interacts avidly with wild type SI and negatively impacts its enzymatic function. The data propose that heterozygote carriers of p.Gly92Leufs*8 may also present with CSID symptoms.

Accurate prediction of protein tertiary structural changes induced by single-site mutations with equivariant graph neural networks

Predicting the change of protein tertiary structure caused by singlesite mutations is important for studying protein structure, function, and interaction. Even though computational protein structure prediction methods such as AlphaFold can predict the overall tertiary structures of most proteins rather accurately, they are not sensitive enough to accurately predict the structural changes induced by single-site amino acid mutations on proteins. Specialized mutation prediction methods mostly focus on predicting the overall stability or function changes caused by mutations without attempting to predict the exact mutation-induced structural changes, limiting their use in protein mutation study. In this work, we develop the first deep learning method based on equivariant graph neural networks (EGNN) to directly predict the tertiary structural changes caused by single-site mutations and the tertiary structure of any protein mutant from the structure of its wild-type counterpart. The results show that it performs substantially better in predicting the tertiary structures of protein mutants than the widely used protein structure prediction method AlphaFold.

Genetic Variants in Carbohydrate Digestive Enzyme and Transport Genes Associated with Risk of Irritable Bowel Syndrome

Irritable Bowel Syndrome (IBS) is characterized by abdominal pain and alterations in bowel pattern, such as constipation (IBS-C), diarrhea (IBS-D), or mixed (IBS-M). Since malabsorption of ingested carbohydrates (CHO) can cause abdominal symptoms that closely mimic those of IBS, identifying genetic mutations in CHO digestive enzymes associated with IBS symptoms is critical to ascertain IBS pathophysiology. Through candidate gene association studies, we identify several common variants in TREH, SI, SLC5A1 and SLC2A5 that are associated with IBS symptoms. By investigating rare recessive Mendelian or oligogenic inheritance patterns, we identify case-exclusive rare deleterious variation in known disease genes (SI, LCT, ALDOB, and SLC5A1) as well as candidate disease genes (MGAM and SLC5A2), providing potential evidence of monogenic or oligogenic inheritance in a subset of IBS cases. Finally, our data highlight that moderate to severe IBS-associated gastrointestinal symptoms are often observed in IBS cases carrying one or more of deleterious rare variants.

A mutation-induced drug resistance database (MdrDB)

Mutation-induced drug resistance is a significant challenge to the clinical treatment of many diseases, as structural changes in proteins can diminish drug efficacy. Understanding how mutations affect protein-ligand binding affinities is crucial for developing new drugs and therapies. However, the lack of a large-scale and high-quality database has hindered the research progresses in this area. To address this issue, we have developed MdrDB, a database that integrates data from seven publicly available datasets, which is the largest database of its kind. By integrating information on drug sensitivity and cell line mutations from Genomics of Drug Sensitivity in Cancer and DepMap, MdrDB has substantially expanded the existing drug resistance data. MdrDB is comprised of 100,537 samples of 240 proteins (which encompass 5119 total PDB structures), 2503 mutations, and 440 drugs. Each sample brings together 3D structures of wild type and mutant protein-ligand complexes, binding affinity changes upon mutation (ΔΔG), and biochemical features. Experimental results with MdrDB demonstrate its effectiveness in significantly enhancing the performance of commonly used machine learning models when predicting ΔΔG in three standard benchmarking scenarios. In conclusion, MdrDB is a comprehensive database that can advance the understanding of mutation-induced drug resistance, and accelerate the discovery of novel chemicals.

Intestinal Disaccharidase Deficiency in Adults: Evaluation and Treatment

PURPOSE OF REVIEW

Disaccharidase deficiency in adults causes carbohydrate malabsorption, resulting in symptoms which significantly overlap with irritable bowel syndrome (IBS). This article discusses the diagnosis and treatment of disaccharidase deficiency within the context of recent literature.

RECENT FINDINGS

Disaccharidase deficiency in adults is more common than previously thought, which includes lactase, sucrase, maltase and isomaltase enzymes. Deficiency in disaccharidases, which are produced by the intestinal brush border, will interfere with the breakdown and absorption of carbohydrates and may result in abdominal pain, gas, bloating and diarrhea. Patients deficient in all 4 disaccharidases are known as having "pan-disaccharidase" deficiency, which has a distinct phenotype with more reported weight loss than patients deficient in one enzyme. IBS patients who do not respond to low FODMAP dietary restriction may have undiagnosed disaccharidase deficiency and may benefit from testing. Diagnostic testing methods are limited to duodenal biopsies, which is the gold standard, and breath testing. Dietary restriction and enzyme replacement therapy have been shown to be effective treatments in these patients. Disaccharidase deficiency is an underdiagnosed condition in adults with chronic GI symptoms. Patients who do not respond to traditional treatment strategies for DBGI may benefit from testing for disaccharidase deficiency. Further studies delineating the distinctions between disaccharidase deficient patients and those with other motility disorders are needed.

Interaction between the α-glucosidases, sucrase-isomaltase and maltase-glucoamylase, in human intestinal brush border membranes and its potential impact on disaccharide digestion

The two major intestinal α-glycosidases, sucrase-isomaltase (SI) and maltase-glucoamylase (MGAM), are active towards α-1,4 glycosidic linkages that prevail in starch. These enzymes share striking structural similarities and follow similar biosynthetic pathways. It has been hypothesized that starch digestion can be modulated via “toggling” of activities of these mucosal α-glycosidases, suggesting a possible interaction between these two enzyme complexes in the intestinal brush border membrane (BBM). Here, the potential interaction between SI and MGAM was investigated in solubilized BBMs utilizing reciprocal pull down assays, i.e., immunoprecipitation with anti-SI antibody followed by Western blotting with anti-MGAM antibody and vice versa. Our results demonstrate that SI interacts avidly with MGAM concomitant with a hetero-complex assembly in the BBMs. This interaction is resistant to detergents, such as Triton X-100 or Triton X-100 in combination with sodium deoxycholate. By contrast, inclusion of sodium deoxycholate into the solubilization buffer reduces the enzymatic activities towards sucrose and maltose substantially, most likely due to alterations in the quaternary structure of either enzyme. In view of their interaction, SI and MGAM regulate the final steps in starch digestion in the intestine, whereby SI assumes the major role by virtue of its predominant expression in the intestinal BBMs, while MGAM acts in auxiliary supportive fashion. These findings will help understand the pathophysiology of carbohydrate malabsorption in functional gastrointestinal disorders, particularly in irritable bowel syndrome, in which gene variants of SI are implicated.

Genetic Loss of Sucrase-Isomaltase Function: Mechanisms, Implications, and Future Perspectives

Genetic variants causing loss of sucrase-isomaltase (SI) function result in malabsorption of sucrose and starch components and the condition congenital sucrase-isomaltase deficiency (CSID). The identified genetic variants causing CSID are very rare in all surveyed populations around the globe, except the Arctic-specific c.273_274delAG loss-of-function (LoF) variant, which is common in the Greenlandic Inuit and other Arctic populations. In these populations, it is, therefore, possible to study people with loss of SI function in an unbiased way to elucidate the physiological function of SI, and investigate both short-term and long-term health effects of reduced small intestinal digestion of sucrose and starch. Importantly, a recent study of the LoF variant in Greenlanders reported that adult homozygous carriers have a markedly healthier metabolic profile. These findings indicate that SI inhibition could potentially improve metabolic health also in individuals not carrying the LoF variant, which is of great interest considering the massive number of individuals with obesity and type 2 diabetes worldwide. Therefore, the objectives of this review, are 1) to describe the biological role of SI, 2) to describe the metabolic impact of the Arctic SI LoF variant, 3) to reflect on potential mechanisms linking reduced SI function to metabolic health, and 4) to discuss what knowledge is necessary to properly evaluate whether SI inhibition is a potential therapeutic target for improving cardiometabolic health.

Genetics of irritable bowel syndrome: shifting gear via biobank-scale studies

The pathophysiology of irritable bowel syndrome (IBS) is multifactorial and probably involves genetic predisposition and the effect of environmental factors. Unlike other gastrointestinal diseases with a heritable component, genetic research in IBS has been scarce and mostly characterized by small underpowered studies, leading to inconclusive results. The availability of genomic and health-related data from large international cohorts and population-based biobanks offers unprecedented opportunities for long-awaited, well-powered genetic studies in IBS. This Review focuses on the latest advances that provide compelling evidence for the importance of genes involved in the digestion of carbohydrates, ion channel function, neurotransmitters and their receptors, neuronal pathways and the control of gut motility. These discoveries have generated novel information that might be further refined for the identification of predisposed individuals and selection of management strategies for patients. This Review presents a conceptual framework, the advantages and potential limitations of modern genetic research in IBS, and a summary of available evidence.

Severe pathogenic variants of intestinal sucrase-isomaltase interact avidly with the wild type enzyme and negatively impact its function and trafficking

Sucrase-isomaltase (SI) is the major disaccharidase of the small intestine, exhibiting a broad α-glucosidase activity profile. The importance of SI in gut health is typified by the development of sucrose and starch maldigestion in individuals carrying mutations in the SI gene, like in congenital sucrase-isomaltase deficiency (CSID). Common and rare defective SI gene variants (SIGVs) have also been shown to increase the risk of irritable bowel syndrome (IBS) with symptoms and clinical features similar to CSID and also in symptomatic heterozygote carriers. Here, we investigate the impact of the most abundant and highly pathogenic SIGVs that occur in heterozygotes on wild type SI (SI^WT) by adapting an in vitro system that recapitulates SI gene heterozygosity. Our results demonstrate that pathogenic SI mutants interact avidly with SI^WT, negatively impact its enzymatic function, alter the biosynthetic pattern and impair the trafficking behavior of the heterodimer. The in vitro recapitulation of a heterozygous state demonstrates potential for SIGVs to act in a semi-dominant fashion, by further reducing disaccharidase activity via sequestration of the SI^WT copy into an inactive form of the enzymatic heterodimer. This study provides novel insights into the potential role of heterozygosity in the pathophysiology of CSID and IBS.

E2UbcH5B-derived peptide ligands target HECT E3-E2 binding site and block the Ub-dependent SARS-CoV-2 egression: A computational study

Homologous to E6AP carboxyl-terminus (HECT)-type E3 ligase performs ubiquitin (Ub)-proteasomal protein degradation via forming a complex with E2∼Ub. Enveloped viruses including SARS-CoV-2 escape from the infected cells by harnessing the E-class vacuolar protein-sorting (ESCRT) machinery and mimic the cellular system through PPAY motif-based linking to HECT Ub ligase activity. In the present study, we have characterized the binding pattern of E2^UbcH5B to HECT domains of NEDD4L, WWP1, WWP2, HECW1, and HECW2 through in silico analysis to isolate the E2^UbcH5B-specific peptide inhibitors that may target SARS-CoV-2 viral egression. Molecular dynamics analysis revealed more opening of E2^UbcH5B-binding pocket upon binding to HECT^NEDD4L, HECT^WWP1, HECT^WWP2, HECT^HECW1, and HECT^HECW2. We observed similar binding pattern for E2^UbcH5B and mentioned HECT domains as previously reported for HECT^NEDD4L where Trp762, Trp709, and Trp657 residues of HECT^NEDD4L, HECT^WWP1, and HECT^WWP2 are involved in making contacts with Ser94 residue of E2^UbcH5B. Similarly, corresponding to HECT^NEDD4L Tyr756 residue, HECT^WWP1, HECT^WWP2, HECT^HECW1, and HECT^HECW2-specific Phe703, Phe651, Phe1387, and Phe1353 residues execute interaction with E2^UbcH5B. Our analysis suggests that corresponding to Cys942 of HECT^NEDD4L, Cys890, Cys838, Cys1574, and Cys1540 residues of HECT^WWP1, HECT^WWP2, HECT^HECW1, and HECT^HECW2, respectively are involved in E2-to-E3 Ub transfer. Furthermore, MM-PBSA free energy calculations revealed favorable energy values for E2^UbcH5B-HECT complexes along with the individual residue contributions. Subsequently, two E2^UbcH5B-derived peptides (His55-Phe69 and Asn81-Ala96) were tested for their binding abilities against HECT domains of NEDD4L, WWP1, WWP2, HECW1, and HECW2. Their binding was validated through substitution of Phe62, Pro65, Ile84, and Cys85 residues into Ala, which revealed an impaired binding, suggesting that the proposed peptide ligands may selectively target E2-HECT binding and Ub-transfer. Collectively, we propose that peptide-driven blocking of E2-to-HECT Ub loading may limit SARS-CoV-2 egression and spread in the host cells.

Multiaspect Examinations of Possible Alternative Mappings of Identified Variant Peptides: A Case Study on the HEK293 Cell Line

Adopting proteogenomics approach to validate single nucleotide variation events by identifying corresponding single amino acid variant peptides from mass spectrometry (MS)-based proteomics data facilitates translational and clinical research. Although variant peptides are usually identified from MS data with a stringent false discovery rate (FDR), FDR control could fail to eliminate dubious results caused by several issues; thus, postexamination to eliminate dubious results is required. However, comprehensive postexaminations of identification results are still lacking. Therefore, we propose a framework of three bottom-up levels, peptide-spectrum match, peptide, and variant event levels, that consists of rigorous 11-aspect examinations from the MS perspective to further confirm the reliability of variant events. As a proof of concept and showing feasibility, we demonstrate 11 examinations on the identified variant peptides from an HEK293 cell line data set, where various database search strategies were applied to maximize the number of identified variant PSMs with an FDR <1% for postexaminations. The results showed that only FDR criterion is insufficient to validate identified variant peptides and the 11 postexaminations can reveal low-confidence variant events detected by shotgun proteomics experiments. Therefore, we suggest that postexaminations of identified variant events based on the proposed framework are necessary for proteogenomics studies.

Effects of Supplemental Leucine on Growth, Nutrient Use, and Muscle and Visceral Tissue Mass in Holstein Bull Calves Fed Milk Replacer

To determine the effects of leucine supplementation on body weight (BW), tissue mass, nutrient digestibility, the concentration of serum amino acids (AAs) and metabolites, and protein abundance of elongation initiation factor 4E (eIF4E) in skeletal muscle, 23 Holstein bull calves (43. 3 ± 1.16 kg; 11.3 ± 0.57 days of age) fed milk replacer at 2.5% of body weight (BW; dry matter basis) were used in a randomized complete block design. Leucine was supplemented at 0, 0.4, 0.6, or 0.8 g Leu/kg BW per day for 28 d. Data were analyzed using the MIXED procedure of SAS. Leucine supplementation did not affect calf BW (P = 0.73), and digestibility of nitrogen (P = 0.21), organic matter (P = 0.28), and dry matter (P = 0.28). Masses proportional to BW of the pancreas (P = 0.04), omasum (P &lt; 0.01), and spleen (P = 0.01) were quadratically affected by treatment where tissue mass decreased at 0.4 g Leu/kg BW and increased at 0.6 and 0.8 g Leu/kg BW. Semitendinosus mass proportional to BW tended (P = 0.07) to be quadratically affected, as tissue mass increased at 0.4 g Leu/kg BW, and decreased at 0.6 and 0.8 g Leu/kg BW. Serum Leu concentration increased linearly (P = 0.002; day × time × treatment) across days and after feedings with increased supplemental Leu. Increasing supplemental Leu linearly decreased serum Ala (P &lt; 0.01), Arg (P = 0.04), Ile (P = 0.02), Met (P &lt; 0.01), and Pro (P = 0.05) concentrations, and quadratically affected serum Glu (P = 0.04) and Lys (P = 0.03) concentrations where serum Glu and Lys concentrations were decreased at 0.4 g Leu/kg BW and increased at 0.6 and 0.8 g Leu/kg BW. There was no effect of treatment on protein abundance of eIF4E in semitendinosus or longissimus dorsi. These data indicate that supplemental Leu did not influence ADG and nitrogen retention in calves fed milk replacer. However, changes in serum AA concentrations and tissue masses proportional to BW suggest that supplementation of Leu at lower levels could increase the use of AA for non-visceral tissue growth.

Staphylococcus aureus Infection Influences the Function of Intestinal Cells by Altering the Lipid Raft-Dependent Sorting of Sucrase-Isomaltase

Staphylococcus aureus is an important nosocomial and community-acquired facultative intracellular pathogen. Many studies have reported that S. aureus infections are associated with intestinal symptoms, but little is known about the molecular mechanisms implicated in S. aureus-induced alterations of intestinal functions. In this study, we investigated the implication of lipid rafts in the interaction of S. aureus with Caco-2 cells. To assess potential alterations in the lipid raft structure and effects on the hydrolytic function, we utilized sucrase–isomaltase (SI) as the major intestinal α-glucosidase that is associated with and sorted to the apical membrane via lipid rafts. Seven days post-confluent, Caco-2 cells were infected with S. aureus Newman and further incubated for an additional 2 days. After 48 h, the levels of SI expression as well as the enzymatic function of this protein were assessed in the infected versus non-infected cells. Analysis of the sorting behavior of SI to the apical membrane constituted another crucial aspect in studying the effects of S. aureus on Caco-2 cells. For this purpose, the apical membranes or brush border membranes (BBMs; referred to as P2 fraction) were separated in both infected and non-infected cells from the basolateral and intracellular membranes (referred to as P1 fraction) by employing a cationic-based procedure using CaCl₂. The data show that there is no significant change in the overall expression levels of SI in the infected versus non-infected cells as assessed by Western blotting analysis using monoclonal anti-SI antibodies. By contrast, a significant decrease in the localization as well as the specific hydrolytic activities of SI toward sucrose and isomaltose (Palatinose) was observed in the BBM (P2 fraction) in Caco-2 cells 48 h post-infection. Concomitantly, the specific SI activities increased in the basolateral membrane/intracellular fraction (P1). Noteworthy, the specific activity of SI in the BBM of infected cells was markedly reduced as compared with that of the non-infected counterparts. The data accumulated from this study strongly suggest that infections with S. aureus influence the final step in the lipid raft-associated trafficking of human SI and thereby may trigger secondary functional gastrointestinal disorders.

RUNX1 mutation and elevated FLT3 gene expression cooperates to induce inferior prognosis in cytogenetically normal acute myeloid leukemia patients

Background

Acute myeloid leukemia (AML) is a bone marrow malignancy having multiple molecular pathways driving its progress. In recent years, the main causes of AML considered all over the world are genetic variations in cancerous cells. The RUNX1 and FLT3 genes are necessary for the normal hematopoiesis and differentiation process of hematopoietic stem cells into mature blood cells, therefore they are the most common targets for point mutations resulting in AML.

Methods

We screened 32 CN-AML patients for FLT3-ITD (by Allele-specific PCR) and RUNX1 mutations (by Sanger sequencing). The FLT3 mRNA expression was assessed in all AML patients and its subgroups.

Results

Eight patients (25%) carried RUNX1 mutation (K83E) while three patients (9.37%) were found to have internal tandem duplications in FLT3 gene. The RUNX1 mutation data were correlated with clinical parameters and FLT3 gene expression profile. The RUNX1 mutations were observed to be significantly prevalent in older males. Moreover, RUNX1 and FLT3-mutated patients had lower complete remission rate, event-free survival rate, and lower overall survival rate than patients with wild-type RUNX1 and FLT3 gene. The RUNX1 and FLT3 mutant patients with up-regulated FLT3 gene expression showed even worse prognosis. Bradford Assay showed that protein concentration was down-regulated in RUNX1 and FLT3 mutants in comparison to RUNX1 and FLT3 wild-type groups.

Conclusion

This study constitutes the first report from Pakistan reporting significant molecular mutation analysis of RUNX1 and FLT3 genes including FLT3 expression evaluation with follow-up. This provides an insight that aforementioned mutations are markers of poor prognosis but the study with a large AML cohort will be useful to further investigate their role in disease biology of AML.

The glucose-regulated protein GRP94 interacts avidly in the endoplasmic reticulum with sucrase-isomaltase isoforms that are associated with congenital sucrase-isomaltase deficiency

The glucose-regulated protein GRP94 is a molecular chaperone that is located in the endoplasmic reticulum (ER). Here, we demonstrate in pull down experiments an interaction between GRP94 and sucrase-isomaltase (SI), the most prominent disaccharidase of the small intestine. GRP94 binds to SI exclusively via its mannose-rich form compatible with an interaction occurring in the ER. We have also examined the interaction GRP94 to a panel of SI mutants that are associated with congenital sucrase-isomaltase deficiency (CSID). These mutants exhibited more efficient binding to GRP94 than wild type SI underlining a specific role of this chaperone in the quality control in the ER. In view of the hypoxic milieu of the intestine, we probed the interaction of GRP94 to SI and its mutants in cell culture under hypoxic conditions and observed a substantial increase in the binding of GRP94 to the SI mutants. The interaction of GRP94 to the major carbohydrate digesting enzyme and regulating its folding as well as retaining SI mutants in the ER points to a potential role of GRP94 in maintenance of intestinal homeostasis by chaperoning and stabilizing SI.

Sucrase-Isomaltase Deficiency Causing Persistent Bloating and Diarrhea in an Adult Female

Congenital sucrase isomaltase deficiency (CSID) is an autosomal recessive disorder which leads to chronic intestinal malabsorption of nutrients from ingested starch and sucrose. Symptoms usually present after consumption of fruits, juices, grains, and starches, leading to failure to thrive and malnutrition. Diagnosis is suspected on detailed patient history and confirmed by a disaccharidase assay using small intestinal biopsies or sucrose hydrogen breath test. Treatment of CSID consists of limiting sucrose in diet and replacement therapy with sacrosidase. Due to its nonspecific symptoms, CSID may be undiagnosed in many patients for several years. We present a case of a 50-year-old woman with persistent symptoms of bloating in spite of extensive evaluation and treatment.

In silico characterization of mutations circulating in SARS-CoV-2 structural proteins

SARS-CoV-2 has recently emerged as a pandemic that has caused more than 2.4 million deaths worldwide. Since the onset of infections, several full-length sequences of viral genome have been made available which have been used to gain insights into viral dynamics. We utilised a meta-data driven comparative analysis tool for sequences (Meta-CATS) algorithm to identify mutations in 829 SARS-CoV-2 genomes from around the world. The algorithm predicted sixty-one mutations among SARS-CoV-2 genomes. We observed that most of the mutations were concentrated around three protein coding genes viz nsp3 (non-structural protein 3), RdRp (RNA-directed RNA polymerase) and Nucleocapsid (N) proteins of SARS-CoV-2. We used various computational tools including normal mode analysis (NMA), C-α discrete molecular dynamics (DMD) and all-atom molecular dynamic simulations (MD) to study the effect of mutations on functionality, stability and flexibility of SARS-CoV-2 structural proteins including envelope (E), N and spike (S) proteins. PredictSNP predictor suggested that four mutations (L37H in E, R203K and P344S in N and D614G in S) out of seven were predicted to be neutral whilst the remaining ones (P13L, S197L and G204R in N) were predicted to be deleterious in nature thereby impacting protein functionality. NMA, C-α DMD and all-atom MD suggested some mutations to have stabilizing roles (P13L, S197L and R203K in N protein) where remaining ones were predicted to destabilize mutant protein. In summary, we identified significant mutations in SARS-CoV-2 genomes as well as used computational approaches to further characterize the possible effect of highly significant mutations on SARS-CoV-2 structural proteins.

Communicated by Ramaswamy H. Sarma

The patient journey to diagnosis and treatment of congenital sucrase-isomaltase deficiency

Purpose

Congenital sucrase-isomaltase deficiency (CSID) is a rare genetic disorder characterized by a deficiency of the sucrase-isomaltase (SI) enzyme complex within the brush border membrane of the small intestine. Mutations in the SI gene result in abnormal synthesis and/or incorrect transport of the SI enzyme. Patients with CSID generally have reduced sucrase activity, but levels of isomaltase activity range from absent to almost normal. This study sought to better understand the experience of patients with CSID prior to, during, and after their diagnosis and its subsequent treatment with sacrosidase.

Methods

This was a cross-sectional interview study conducted in conjunction with a longitudinal, observational study of US patients prescribed and taking sacrosidase for at least three consecutive months as treatment for CSID. The observational study included both children and adults.

Results

This qualitative interview study explored the experiences of 43 adult and pediatric patients (n = 8 adults and n = 35 children/adolescents) with CSID pre-, during, and post-diagnosis. Findings suggest that a CSID diagnosis is particularly problematic given the disparate range of more commonly understood gastrointestinal (GI) disorders. After diagnosis and treatment with sacrosidase, participants reported considerable improvement in symptoms and health-related quality of life (HRQL), yet symptoms persist that continue to affect daily life, indicating areas of potential unmet need.

Conclusion

Educating clinicians about CSID may help improve the overall diagnosis experience. As this research is the first of its kind in CSID, additional research, qualitative and quantitative, will be important to furthering the understanding of HRQL impact and unmet need experienced by this population and identifying ways to best meet those needs.

Sucrase-isomaltase Gene Variants in Patients With Abnormal Sucrase Activity and Functional Gastrointestinal Disorders

OBJECTIVES

The aim of the study was to determine prevalence and characterize sucrase-isomaltase (SI) gene variants of congenital sucrase-isomaltase deficiency in non-Hispanic white pediatric and young adult patients with functional gastrointestinal disorders (FGIDs), and abnormal sucrase activity on histologically normal duodenal biopsy.

METHODS

Clinical symptoms and disaccharidase activities data were collected for an abnormal (low) sucrase (≤25.8 U, n = 125) activity group, and 2 normal sucrase activity groups with moderate (≥25.8-≤55 U, n = 250) and high (>55 U, n = 250) sucrase activities. SI gene variants were detected by next-generation sequencing of DNA from formalin-fixed paraffin-embedded tissues of these patients. FGIDs symptoms based on Rome IV criteria and subsequent clinical management of abnormal sucrase activity cases with pathogenic SI gene variants were analyzed.

RESULTS

Thirteen SI gene variants were found to be significantly higher in abnormal sucrase cases with FGIDs symptoms (36/125, 29%; 71% did not have a pathogenic variant) compared to moderate normal (16/250, 6.4%, P < 0.001) or high normal (5/250, 2.0%, P < 0.001) sucrase groups. Clinical management data were available in 26 of abnormal sucrase cases, and only 10 (38%) were correctly diagnosed and managed by the clinicians. Concomitant lactase deficiency (24%; 23/97) and pan-disaccharidase deficiency (25%; 13/51) were found in the abnormal sucrase group.

CONCLUSIONS

Heterozygous and compound heterozygous mutations in the SI gene were more prevalent in cases with abnormal sucrase activity presenting with FGIDs, and normal histopathology. This suggests heterozygous pathogenic variants of congenital sucrase-isomaltase deficiency may present as FGIDs. Concomitant lactase or pan-disaccharidase deficiencies were common in abnormal sucrase cases with SI gene variants.

Differential Effects of Sucrase-Isomaltase Mutants on Its Trafficking and Function in Irritable Bowel Syndrome: Similarities to Congenital Sucrase-Isomaltase Deficiency

Congenital sucrase-isomaltase deficiency (CSID) is a rare metabolic intestinal disorder with reduced or absent activity levels of sucrase-isomaltase (SI). Interestingly, the main symptoms of CSID overlap with those in irritable bowel syndrome (IBS), a common functional gastrointestinal disorder with unknown etiology. Recent advances in genetic screening of IBS patients have revealed rare SI gene variants that are associated with IBS. Here, we investigated the biochemical, cellular and functional phenotypes of several of these variants. The data demonstrate that the SI mutants can be categorized into three groups including immature, mature but slowly transported, and finally mature and properly transported but with reduced enzymatic activity. We also identified SI mutant phenotypes that are deficient but generally not as severe as those characterized in CSID patients. The variable effects on the trafficking and function of the mutations analyzed in this study support the view that both CSID and IBS are heterogeneous disorders, the severity of which is likely related to the biochemical phenotypes of the SI mutants as well as the environment and diet of patients. Our study underlines the necessity to screen for SI mutations in IBS patients and to consider enzyme replacement therapy as an appropriate therapy as in CSID.

Functional impact of cancer patient-associated Bcl-xL mutations

Bcl-xL, an antiapoptotic protein, is frequently overexpressed in cancer to promote survival of tumor cells. However, we have previously shown that Bcl-xL promotes migration, invasion, and metastasis independent of its antiapoptotic function in mitochondria. The pro-metastatic function of Bcl-xL may require its translocation into the nucleus. Besides overexpression, patient-associated mutations of Bcl-xL have been identified in large-scale cancer genomics projects. Understanding the functions of these mutations will guide the development of precision medicine. Here, we selected four patient-associated Bcl-xL mutations, R132W, N136K, R165W, and A201T, to investigate their impacts on antiapoptosis, migration, and nuclear translocation. We found that all four mutation proteins could be detected in both the nucleus and cytosol. Although all four mutations disrupted the antiapoptosis function, one of these mutants, N136K, significantly improved the ability to promote cell migration. These data suggest the importance of developing novel Bcl-xL inhibitors to ablate both antiapoptotic and pro-metastatic functions of Bcl-xL in cancer.

A mutation map for human glycoside hydrolase genes

Glycoside hydrolases (GHs) are found in all domains of life, and at least 87 distinct genes encoding proteins related to GHs are found in the human genome. GHs serve diverse functions from digestion of dietary polysaccharides to breakdown of intracellular oligosaccharides, glycoproteins, proteoglycans and glycolipids. Congenital disorders of GHs (CDGHs) represent more than 30 rare diseases caused by mutations in one of the GH genes. We previously used whole-exome sequencing of a homogenous Danish population of almost 2000 individuals to probe the incidence of deleterious mutations in the human glycosyltransferases (GTs) and developed a mutation map of human GT genes (GlyMAP-I). While deleterious disease-causing mutations in the GT genes were very rare, and in many cases lethal, we predicted deleterious mutations in GH genes to be less rare and less severe given the higher incidence of CDGHs reported worldwide. To probe the incidence of GH mutations, we constructed a mutation map of human GH-related genes (GlyMAP-II) using the Danish WES data, and correlating this with reported disease-causing mutations confirmed the higher prevalence of disease-causing mutations in several GH genes compared to GT genes. We identified 76 novel nonsynonymous single-nucleotide variations (nsSNVs) in 32 GH genes that have not been associated with a CDGH phenotype, and we experimentally validated two novel potentially damaging nsSNVs in the congenital sucrase-isomaltase deficiency gene, SI. Our study provides a global view of human GH genes and disease-causing mutations and serves as a discovery tool for novel damaging nsSNVs in CDGHs.

MinProtMaxVP: Generating a minimized number of protein variant sequences containing all possible variant peptides for proteogenomic analysis

Identifying single-amino-acid variants (SAVs) from mass spectrometry-based experiments is critical for validating single-nucleotide variants (SNVs) at the protein level to facilitate biomedical research. Currently, two approaches are usually applied to convert SNV annotations into SAV-harboring protein sequences. One approach generates one sequence containing exactly one SAV, and the other all SAVs. However, they may neglect the possibility of SAV combinations, e.g., haplotypes, existing in bio-samples. Therefore, it is necessary to consider all SAV combinations of a protein when generating SAV-harboring protein sequences. In this paper, we propose MinProtMaxVP, a novel approach which selects a minimized number of SAV-harboring protein sequences generated from the exhaustive approach, while still accommodating all possible variant peptides, by solving a classic set covering problem. Our study on known haplotype variations of TAS2R38 justifies the necessity for MinProtMaxVP to consider all combinations of SAVs. The performance of MinProtMaxVP is demonstrated by an in silico study on OR2T27 with five SAVs and real experimental data of the HEK293 cell line. Furthermore, assuming simulated somatic and germline variants of OR2T27 in tumor and normal tissues demonstrates that when adopting the appropriate somatic and germline SAV integration strategy, MinProtMaxVP is adaptable to labeling and label-free mass spectrometry-based experiments. SIGNIFICANCE: We present MinProtMaxVP, a novel approach to generate SAV-harboring protein sequences for constructing a customized protein sequence database, which is used in database searching for variant peptide identification. This approach outperforms the existing approaches in generating all possible variant peptides to be included in protein sequences and possibly leading to identification of more variant peptides in proteogenomic analysis.

Hypomorphic SI genetic variants are associated with childhood chronic loose stools

OBJECTIVE

The SI gene encodes the sucrase-isomaltase enzyme, a disaccharidase expressed in the intestinal brush border. Hypomorphic SI variants cause recessive congenital sucrase-isomaltase deficiency (CSID) and related gastrointestinal (GI) symptoms. Among children presenting with chronic, idiopathic loose stools, we assessed the prevalence of CSID-associated SI variants relative to the general population and the relative GI symptom burden associated with SI genotype within the study population.

METHODS

A prospective study conducted at 18 centers enrolled 308 non-Hispanic white children ≤18 years old who were experiencing chronic, idiopathic, loose stools at least once per week for >4 weeks. Data on demographics, GI symptoms, and genotyping for 37 SI hypomorphic variants were collected. Race/ethnicity-matched SI data from the Exome Aggregation Consortium (ExAC) database was used as the general population reference.

RESULTS

Compared with the general population, the cumulative prevalence of hypomorphic SI variants was significantly higher in the study population (4.5% vs. 1.3%, P < .01; OR = 3.5 [95% CI: 6.1, 2.0]). Within the study population, children with a hypomorphic SI variant had a more severe GI symptom burden than those without, including: more frequent episodes of loose stools (P < .01), higher overall stool frequency (P < .01), looser stool form (P = .01) and increased flatulence (P = .02).

CONCLUSION

Non-Hispanic white children with chronic idiopathic loose stools have a higher prevalence of CSID-associated hypomorphic SI variants than the general population. The GI symptom burden was greater among the study subjects with a hypomorphic SI variant than those without hypomorphic SI variants.

Mutation effect estimation on protein-protein interactions using deep contextualized representation learning

The functional impact of protein mutations is reflected on the alteration of conformation and thermodynamics of protein–protein interactions (PPIs). Quantifying the changes of two interacting proteins upon mutations is commonly carried out by computational approaches. Hence, extensive research efforts have been put to the extraction of energetic or structural features on proteins, followed by statistical learning methods to estimate the effects of mutations on PPI properties. Nonetheless, such features require extensive human labors and expert knowledge to obtain, and have limited abilities to reflect point mutations. We present an end-to-end deep learning framework, MuPIPR (Mutation Effects in Protein–protein Interaction PRediction Using Contextualized Representations), to estimate the effects of mutations on PPIs. MuPIPR incorporates a contextualized representation mechanism of amino acids to propagate the effects of a point mutation to surrounding amino acid representations, therefore amplifying the subtle change in a long protein sequence. On top of that, MuPIPR leverages a Siamese residual recurrent convolutional neural encoder to encode a wild-type protein pair and its mutation pair. Multi-layer perceptron regressors are applied to the protein pair representations to predict the quantifiable changes of PPI properties upon mutations. Experimental evaluations show that, with only sequence information, MuPIPR outperforms various state-of-the-art systems on estimating the changes of binding affinity for SKEMPI v1, and offers comparable performance on SKEMPI v2. Meanwhile, MuPIPR also demonstrates state-of-the-art performance on estimating the changes of buried surface areas. The software implementation is available at https://github.com/guangyu-zhou/MuPIPR.

Heterozygotes Are a Potential New Entity among Homozygotes and Compound Heterozygotes in Congenital Sucrase-Isomaltase Deficiency

Congenital sucrase-isomaltase deficiency (CSID) is an autosomal recessive disorder of carbohydrate maldigestion and malabsorption caused by mutations in the sucrase-isomaltase (SI) gene. SI, together with maltase-glucoamylase (MGAM), belongs to the enzyme family of disaccharidases required for breakdown of α-glycosidic linkages in the small intestine. The effects of homozygote and compound heterozygote inheritance trait of SI mutations in CSID patients have been well described in former studies. Here we propose the inclusion of heterozygote mutation carriers as a new entity in CSID, possibly presenting with milder symptoms. The hypothesis is supported by recent observations of heterozygote mutation carriers among patients suffering from CSID or patients diagnosed with functional gastrointestinal disorders. Recent studies implicate significant phenotypic heterogeneity depending on the character of the mutation and call for more research regarding the correlation of genetics, function at the cellular and molecular level and clinical presentation. The increased importance of SI gene variants in irritable bowel syndrome (IBS) or other functional gastrointestinal disorders FGIDs and their available symptom relief diets like fermentable oligo-, di-, mono-saccharides and polyols FODMAPs suggest that the heterozygote mutants may affect the disease development and treatment.

Phylogenetic analysis reveals key residues in substrate hydrolysis in the isomaltase domain of sucrase-isomaltase and its role in starch digestion

BACKGROUND

Starch constitutes one of the main sources of nutrition in the human diet and is broken down through a number of stages of digestion. Small intestinal breakdown of starch-derived substrates occurs through the mechanisms of small intestinal brush border enzymes, maltase-glucoamylase and sucrase-isomaltase. These enzymes each contain two functional enzymatic domains, and though they share sequence and structural similarities due to their evolutionary conservation, they demonstrate distinct substrate preferences and catalytic efficiency. The N-terminal isomaltase domain of sucrase-isomaltase has a unique ability to actively hydrolyze isomaltose substrates in contrast to the sucrase, maltase and glucoamylase enzymes.

METHODS

Through phylogenetic analysis, structural comparisons and mutagenesis, we were able to identify specific residues that play a role in the distinct substrate preference. Mutational analysis and comparison with wild-type activity provide evidence that this role is mediated in part by affecting interactions between the sucrase and isomaltase domains in the intact molecule.

RESULTS

The sequence analysis revealed three residues proposed to play key roles in isomaltase specificity. Mutational analysis provided evidence that these residues in isomaltase can also affect activity in the partner sucrase domain, suggesting a close interaction between the domains.

MAJOR CONCLUSIONS

The sucrase and isomaltase domains are closely interacting in the mature protein. The activity of each is affected by the presence of the other.

GENERAL SIGNIFICANCE

There has been little experimental evidence previously of the effects on activity of interactions between the sucrase-isomaltase enzyme domains. By extension, similar interactions might be expected in the other intestinal α-glucosidase, maltase-glucoamylase.

Structural Studies of the Intestinal α-Glucosidases, Maltase-glucoamylase and Sucrase-isomaltase

OBJECTIVES

Maltase-glucoamylase and sucrase-isomaltase are enzymes in the brush-border membrane of the small intestinal lumen responsible for the breakdown of postamylase starch polysaccharides to release monomeric glucose. As such, they are critical players in healthy nutrition and their malfunction can lead to severe disorders.

METHODS

This review covers investigations of the structures and functions of these enzymes.

RESULTS

Each consists of 2 enzyme domains of the glycoside hydrolase family GH31 classification, yet with somewhat differing enzymatic properties.

CONCLUSIONS

Crystallographic structures of 3 of the domains have been published. Insights into substrate binding and specificity will be discussed, along with future lines of inquiry related to the enzymes' roles in disease and potential avenues for therapeutics.

Identification of Mx gene nucleotide dimorphism (G/A) as genetic marker for antiviral activity in Egyptian chickens

Egyptian chickens, representing 2 breeds and 7 strains, were genotyped using the PCR-RFLP and sequencing techniques for detection of a non-synonymous dimorphism (G/A) in exon 14 of chicken Myxovirus resistance (Mx) gene. This dimorphic position is responsible for altering Mx protein's antiviral activity. Polymerase Chain reactions were performed using Egyptian chickens DNA and specific primer set to amplify Mx DNA fragments of 299 or 301 bp, containing the dimorphic position. Amplicons were cut with restriction enzyme Hpy81. Genotype and allele frequencies for the resistant allele A and sensitive allele G were calculated in all the tested chickens. Results of PCR-RFLP were confirmed by sequencing. The three genotypes AA, AG, GG at the target nucleotide position in Mx gene were represented in all the studied Egyptian chicken breeds and strains except Baladi strain which showed only one genotype AA. The average allele frequency of the resistant A allele in the tested birds (0.67) was higher than the sensitive G allele average frequency in the same birds (0.33). Appling PCR-RFLP technique in the breeding program can be used to select chickens carrying the A allele with high frequencies. This will help in improving poultry breeding in Egypt by producing infectious disease-resistant chickens.

Posttranslational Processing and Function of Mucosal Maltases

The final step of carbohydrate digestion in the intestine is performed by 2 major α-glucosidases of the intestinal mucosa, sucrase-isomaltase (SI) and maltase-glucoamylase. Both of these enzymes are type II membrane glycoproteins, which share a significant level of homology in gene and protein structures and yet have differences in the posttranslational processing, substrate specificity and functional capacity. Insufficient activity of these disaccharidases particularly SI as a result of genetic mutations or secondary intestinal pathologies is associated with carbohydrate maldigestion and gastrointestinal intolerances. This review will discuss the maturation profiles of SI and maltase-glucoamylase relative to their functional capacities and deficiencies.

Functional variants in the sucrase-isomaltase gene associate with increased risk of irritable bowel syndrome

OBJECTIVE

IBS is a common gut disorder of uncertain pathogenesis. Among other factors, genetics and certain foods are proposed to contribute. Congenital sucrase-isomaltase deficiency (CSID) is a rare genetic form of disaccharide malabsorption characterised by diarrhoea, abdominal pain and bloating, which are features common to IBS. We tested sucrase-isomaltase (SI) gene variants for their potential relevance in IBS.

DESIGN

We sequenced SI exons in seven familial cases, and screened four CSID mutations (p.Val557Gly, p.Gly1073Asp, p.Arg1124Ter and p.Phe1745Cys) and a common SI coding polymorphism (p.Val15Phe) in a multicentre cohort of 1887 cases and controls. We studied the effect of the 15Val to 15Phe substitution on SI function in vitro. We analysed p.Val15Phe genotype in relation to IBS status, stool frequency and faecal microbiota composition in 250 individuals from the general population.

RESULTS

CSID mutations were more common in patients than asymptomatic controls (p=0.074; OR=1.84) and Exome Aggregation Consortium reference sequenced individuals (p=0.020; OR=1.57). 15Phe was detected in 6/7 sequenced familial cases, and increased IBS risk in case-control and population-based cohorts, with best evidence for diarrhoea phenotypes (combined p=0.00012; OR=1.36). In the population-based sample, 15Phe allele dosage correlated with stool frequency (p=0.026) and Parabacteroides faecal microbiota abundance (p=0.0024). The SI protein with 15Phe exhibited 35% reduced enzymatic activity in vitro compared with 15Val (p<0.05).

CONCLUSIONS

SI gene variants coding for disaccharidases with defective or reduced enzymatic activity predispose to IBS. This may help the identification of individuals at risk, and contribute to personalising treatment options in a subset of patients.

Congenital Sucrase-isomaltase Deficiency: A Novel Compound Heterozygous Mutation Causing Aberrant Protein Localization

OBJECTIVES

Congenital diarrheal disorders is a group of inherited enteropathies presenting in early life and requiring parenteral nutrition. In most cases, genetics may be the key for precise diagnosis. We present an infant girl with chronic congenital diarrhea that resolved after introduction of fructose-based formula but had no identified mutation in the SLC5A1 gene. Using whole exome sequencing (WES) we identified other mutations that better dictated dietary adjustments.

METHODS

WES of the patient and her parents was performed. The analysis focused on recessive model including compound heterozygous mutations. Sanger sequencing was used to validate identified mutations and to screen the patient's newborn sister and grandparents. Expression and localization analysis were performed in the patient's duodenal biopsies using immunohistochemistry.

RESULTS

Using WES we identified a new compound heterozygote mutation in sucrase-isomaltase (SI) gene; a maternal inherited known V577G mutation, and a novel paternal inherited C1531W mutation. Importantly, the newborn offspring carried similar compound heterozygous mutations. Computational predictions suggest that both mutations highly destabilize the protein. SI expression and localization studies determined that the mutated SI protein was not expressed on the brush border membrane in the patient's duodenal biopsies, verifying the diagnosis of congenital sucrase-isomaltase deficiency (CSID).

CONCLUSIONS

The novel compound heterozygote V577G/C1531W SI mutations lead to lack of SI expression in the duodenal brush border, confirming the diagnosis of CSID. These cases of CSID extend the molecular spectrum of this condition, further directing a more adequate dietary intervention for the patient and newborn sibling.

Molecular pathogenicity of novel sucrase-isomaltase mutations found in congenital sucrase-isomaltase deficiency patients

BACKGROUND & AIMS

Congenital sucrase-isomaltase deficiency (CSID) is a genetic disorder associated with mutations in the sucrase-isomaltase (SI) gene. The diagnosis of congenital diarrheal disorders like CSID is difficult due to unspecific symptoms and usually requires invasive biopsy sampling of the intestine. Sequencing of the SI gene and molecular analysis of the resulting potentially pathogenic SI protein variants may facilitate a diagnosis in the future. This study aimed to categorize SI mutations based on their functional consequences.

METHODS

cDNAs encoding 13 SI mutants were expressed in COS-1 cells. The molecular pathogenicity of the resulting SI mutants was defined by analyzing their biosynthesis, cellular localization, structure and enzymatic functions.

RESULTS

Three biosynthetic phenotypes for the novel SI mutations were identified. The first biosynthetic phenotype was defined by mutants that are intracellularly transported in a fashion similar to wild type SI and with normal, but varying, levels of enzymatic activity. The second biosynthetic phenotype was defined by mutants with delayed maturation and trafficking kinetics and reduced activity. The third group of mutants is entirely transport incompetent and functionally inactive.

CONCLUSIONS

The current study unraveled CSID as a multifaceted malabsorption disorder that comprises three major classes of functional and trafficking mutants of SI and established a gradient of mild to severe functional deficits in the enzymatic functions of the enzyme.

GENERAL SIGNIFICANCE

This novel concept and the existence of mild consequences in a number of SI mutants strongly propose that CSID is an underdiagnosed and a more common intestinal disease than currently known.

Diagnosing and Treating Intolerance to Carbohydrates in Children

Intolerance to carbohydrates is relatively common in childhood, but still poorly recognized and managed. Over recent years it has come to the forefront because of progresses in our knowledge on the mechanisms and treatment of these conditions. Children with intolerance to carbohydrates often present with unexplained signs and symptoms. Here, we examine the most up-to-date research on these intolerances, discuss controversies relating to the diagnostic approach, including the role of molecular analysis, and provide new insights into modern management in the pediatric age, including the most recent evidence for correct dietary treatment.

The clinical consequences of sucrase-isomaltase deficiency

Primary sucrase-isomaltase deficiency, originally thought to be a homozygous recessive disorder, has been found to have numerous genetic variants that alone or in combination (compound heterozygosity) express varying degrees of clinical illness, most commonly causing chronic diarrhea, abdominal pain, and bloating. These symptoms are also present with secondary sucrase-isomaltase deficiency. Recent investigations are providing evidence that sucrase-isomaltase deficiency is more prevalent and of greater clinical significance than previously suspected. Further research is required to correlate the specific genotypes and phenotypes with their clinical expressions and to determine the most appropriate treatment algorithm for these patients.

Natural Selection at the Brush-Border: Adaptations to Carbohydrate Diets in Humans and Other Mammals

Dietary shifts can drive molecular evolution in mammals and a major transition in human history, the agricultural revolution, favored carbohydrate consumption. We investigated the evolutionary history of nine genes encoding brush-border proteins involved in carbohydrate digestion/absorption. Results indicated widespread adaptive evolution in mammals, with several branches experiencing episodic selection, particularly strong in bats. Many positively selected sites map to functional protein regions (e.g., within glucosidase catalytic crevices), with parallel evolution at SI (sucrase-isomaltase) and MGAM (maltase-glucoamylase). In human populations, five genes were targeted by positive selection acting on noncoding variants within regulatory elements. Analysis of ancient DNA samples indicated that most derived alleles were already present in the Paleolithic. Positively selected variants at SLC2A5 (fructose transporter) were an exception and possibly spread following the domestication of specific fruit crops. We conclude that agriculture determined no major selective event at carbohydrate metabolism genes in humans, with implications for susceptibility to metabolic disorders.

Long term differential consequences of miglustat therapy on intestinal disaccharidases

Miglustat is an oral medication for treatment of lysosomal storage diseases such as Gaucher disease type I and Niemann Pick disease type C. In many cases application of Miglustat is associated with symptoms similar to those observed in intestinal carbohydrate malabsorption. Previously, we have demonstrated that intestinal disaccharidases are inhibited immediately by Miglustat in the intestinal lumen. Nevertheless, the multiple functions of Miglustat hypothesize long term effects of Miglustat on intracellular mechanisms, including glycosylation, maturation and trafficking of the intestinal disaccharidases. Our data show that a major long term effect of Miglustat is its interference with N-glycosylation of the proteins in the ER leading to a delay in the trafficking of sucrase-isomaltase. Also association with lipid rafts and plausibly apical targeting of this protein is partly affected in the presence of Miglustat. More drastic is the effect of Miglustat on lactase-phlorizin hydrolase which is partially blocked intracellularly. The de novo synthesized SI and LPH in the presence of Miglustat show reduced functional efficiencies according to altered posttranslational processing of these proteins. However, at physiological concentrations of Miglustat (≤50 μM) a major part of the activity of these disaccharidases is found to be still preserved, which puts the charge of the observed carbohydrate maldigestion mostly on the direct inhibition of disaccharidases in the intestinal lumen by Miglustat as the immediate side effect.

Recent advances in small bowel diseases: Part II

As is the case in all areas of gastroenterology and hepatology, in 2009 and 2010 there were many advances in our knowledge and understanding of small intestinal diseases. Over 1000 publications were reviewed, and the important advances in basic science as well as clinical applications were considered. In Part II we review six topics: absorption, short bowel syndrome, smooth muscle function and intestinal motility, tumors, diagnostic imaging, and cystic fibrosis.