Perturbations in lipid metabolism and gut microbiota composition precede cardiac dysfunction in a mouse model of thalassemia

Cardiomyopathy is a major complication of thalassemia, yet the precise underlying molecular mechanisms remain unclear. We examined whether altered lipid metabolism is an early driving factor in the development of cardiomyopathy using the Th3/+ mouse model of thalassemia. At age 20 weeks, male and female Th3/+ mice manifested anemia and iron overload; however, only males displayed metabolic defects and altered cardiac function. Untargeted lipidomics indicated that the circulating levels of 35 lipid species were significantly altered in Th3/+ mice compared to wild-type controls: triglycerides (TGs) with saturated fatty acids (FAs; TG42:0 and TG44:0) were elevated, while TGs with unsaturated FAs (TG(18:2_20:5_18:2 and TG54:8)) were reduced. Similarly, phosphatidylcholines (PCs) with long chain FAs (palmitic (16:0) or oleic (18:1)) were increased, while PCs with polyunsaturated FAs decreased. Circulating PC(16:0_14:0), GlcCer(d18:1/24:0) correlated significantly with iron overload and cardiac hypertrophy. 16S rRNA gene profiling revealed alterations in the intestinal microbiota of Th3/+ mice. Differentially abundant bacterial genera correlated with PC(39:6), PC(18:1_22:6), GlcCer(d18:1/24:1) and CE(14:0). These results provide new knowledge on perturbations in lipid metabolism and the gut microbiota of Th3/+ mice and identify specific factors which may represent early biomarkers or therapeutic targets to prevent development of cardiomyopathy in β-thalassemia.

Remodeling of lipid landscape in high fat fed very-long chain acyl-CoA dehydrogenase null mice favors pro-arrhythmic polyunsaturated fatty acids and their downstream metabolites

Very-long chain acyl-CoA dehydrogenase (VLCAD) catalyzes the initial step of mitochondrial long chain (LC) fatty acid β-oxidation (FAO). Inherited VLCAD deficiency (VLCADD) predisposes to neonatal arrhythmias whose pathophysiology is still not understood. We hypothesized that VLCADD results in global disruption of cardiac complex lipid homeostasis, which may set conditions predisposing to arrhythmia. To test this, we assessed the cardiac lipidome and related molecular markers in seven-month-old VLCAD-/- mice, which mimic to some extent the human cardiac phenotype. Mice were sacrificed in the fed or fasted state after receiving for two weeks a chow or a high-fat diet (HFD), the latter condition being known to worsen symptoms in human VLCADD. Compared to their littermate counterparts, HFD/fasted VLCAD-/- mouse hearts displayed the following lipid alterations: (1) Lower LC, but higher VLC-acylcarnitines accumulation, (2) higher levels of arachidonic acid (AA) and lower docosahexaenoic acid (DHA) contents in glycerophospholipids (GPLs), as well as (3) corresponding changes in pro-arrhythmogenic AA-derived isoprostanes and thromboxane B2 (higher), and anti-arrythmogenic DHA-derived neuroprostanes (lower). These changes were associated with remodeling in the expression of gene or protein markers of (1) GPLs remodeling: higher calcium-dependent phospholipase A2 and lysophosphatidylcholine-acyltransferase 2, (2) calcium handling perturbations, and (3) endoplasmic reticulum stress. Altogether, these results highlight global lipid dyshomeostasis beyond FAO in VLCAD-/- mouse hearts, which may set conditions predisposing the hearts to calcium mishandling and endoplasmic reticulum stress and thereby may contribute to the pathogenesis of arrhythmias in VLCADD in mice as well as in humans.

Serum Lipidomic Screen Identifies Key Metabolites, Pathways, and Disease Classifiers in Crohn's Disease

BACKGROUND

There is an unmet medical need for biomarkers that capture host and environmental contributions in inflammatory bowel diseases (IBDs). This study aimed at testing the potential of circulating lipids as disease classifiers given their major roles in inflammation.

METHODS

We applied a previously validated comprehensive high-resolution liquid chromatography-mass spectrometry-based untargeted lipidomic workflow covering 25 lipid subclasses to serum samples from 100 Crohn's disease (CD) patients and 100 matched control subjects. Findings were replicated and expanded in another 200 CD patients and 200 control subjects. Key metabolites were tested for associations with disease behavior and location, and classification models were built and validated. Their association with disease activity was tested using an independent cohort of 42 CD patients.

RESULTS

We identified >70 metabolites with strong association (P < 1 × 10-4, q < 5 × 10-4) to CD. Highly performing classification models (area under the curve > 0.84-0.97) could be built with as few as 5 to 9 different metabolites, representing 6 major correlated lipid clusters. These classifiers included a phosphatidylethanolamine ether (O-16:0/20:4), a sphingomyelin (d18:1/21:0) and a cholesterol ester (14:1), a very long-chain dicarboxylic acid [28:1(OH)] and sitosterol sulfate. These classifiers and correlated lipids indicate a dysregulated metabolism in host cells, notably in peroxisomes, as well as dysbiosis, oxidative stress, compromised inflammation resolution, or intestinal membrane integrity. A subset of these were associated with disease behavior or location.

CONCLUSIONS

Untargeted lipidomic analyses uncovered perturbations in the circulating human CD lipidome, likely resulting from multiple pathogenic mechanisms. Models using as few as 5 biomarkers had strong disease classifier characteristics, supporting their potential use in diagnosis or prognosis.

Lipidomics unveils lipid dyshomeostasis and low circulating plasmalogens as biomarkers in a monogenic mitochondrial disorder

Mitochondrial dysfunction characterizes many rare and common age-associated diseases. The biochemical consequences, underlying clinical manifestations, and potential therapeutic targets, remain to be better understood. We tested the hypothesis that lipid dyshomeostasis in mitochondrial disorders goes beyond mitochondrial fatty acid β-oxidation, particularly in liver. This was achieved using comprehensive untargeted and targeted lipidomics in a case-control cohort of patients with Leigh syndrome French-Canadian variant (LSFC), a mitochondrial disease caused by mutations in LRPPRC, and in mice harboring liver-specific inactivation of Lrpprc (H-Lrpprc-/-). We discovered a plasma lipid signature discriminating LSFC patients from controls encompassing lower levels of plasmalogens and conjugated bile acids, which suggest perturbations in peroxisomal lipid metabolism. This premise was reinforced in H-Lrpprc-/- mice, which compared with littermates recapitulated a similar, albeit stronger peroxisomal metabolic signature in plasma and liver including elevated levels of very-long-chain acylcarnitines. These mice also presented higher transcript levels for hepatic markers of peroxisome proliferation in addition to lipid remodeling reminiscent of nonalcoholic fatty liver diseases. Our study underscores the value of lipidomics to unveil unexpected mechanisms underlying lipid dyshomeostasis ensuing from mitochondrial dysfunction herein implying peroxisomes and liver, which likely contribute to the pathophysiology of LSFC, but also other rare and common mitochondrial diseases.

Comprehensive and Reproducible Untargeted Lipidomic Workflow Using LC-QTOF Validated for Human Plasma Analysis

The goal of this work was to develop a label-free, comprehensive, and reproducible high-resolution liquid chromatography-mass spectrometry (LC-MS)-based untargeted lipidomic workflow using a single instrument, which could be applied to biomarker discovery in both basic and clinical studies. For this, we have (i) optimized lipid extraction and elution to enhance coverage of polar and nonpolar lipids as well as resolution of their isomers, (ii) ensured MS signal reproducibility and linearity, and (iii) developed a bioinformatic pipeline to correct remaining biases. Workflow validation is reported for 48 replicates of a single human plasma sample: 1124 reproducible LC-MS signals were extracted (median signal intensity RSD = 10%), 50% of which are redundant due to adducts, dimers, in-source fragmentation, contaminations, or positive and negative ion duplicates. From the resulting 578 unique compounds, 428 lipids were identified by MS/MS, including acyl chain composition, of which 394 had RSD < 30% inside their linear intensity range, thereby enabling robust semiquantitation. MS signal intensity spanned 4 orders of magnitude, covering 16 lipid subclasses. Finally, the power of our workflow is illustrated by a proof-of-concept study in which 100 samples from healthy human subjects were analyzed and the data set was investigated using three different statistical testing strategies in order to compare their capacity in identifying the impact of sex and age on circulating lipids.

Loss of hepatic LRPPRC alters mitochondrial bioenergetics, regulation of permeability transition and trans-membrane ROS diffusion

The French-Canadian variant of Leigh Syndrome (LSFC) is an autosomal recessive oxidative phosphorylation (OXPHOS) disorder caused by a mutation in LRPPRC, coding for a protein involved in the stability of mitochondrially-encoded mRNAs. Low levels of LRPPRC are present in all patient tissues, but result in a disproportionately severe OXPHOS defect in the brain and liver, leading to unpredictable subacute metabolic crises. To investigate the impact of the OXPHOS defect in the liver, we analyzed the mitochondrial phenotype in mice harboring an hepatocyte-specific inactivation of Lrpprc. Loss of LRPPRC in the liver caused a generalized growth delay, and typical histological features of mitochondrial hepatopathy. At the molecular level, LRPPRC deficiency caused destabilization of polyadenylated mitochondrial mRNAs, altered mitochondrial ultrastructure, and a severe complex IV (CIV) and ATP synthase (CV) assembly defect. The impact of LRPPRC deficiency was not limited to OXPHOS, but also included impairment of long-chain fatty acid oxidation, a striking dysregulation of the mitochondrial permeability transition pore, and an unsuspected alteration of trans-membrane H2O2 diffusion, which was traced to the ATP synthase assembly defect, and to changes in the lipid composition of mitochondrial membranes. This study underscores the value of mitochondria phenotyping to uncover complex and unexpected mechanisms contributing to the pathophysiology of mitochondrial disorders.

SLC25A46 is required for mitochondrial lipid homeostasis and cristae maintenance and is responsible for Leigh syndrome

Mitochondria form a dynamic network that responds to physiological signals and metabolic stresses by altering the balance between fusion and fission. Mitochondrial fusion is orchestrated by conserved GTPases MFN1/2 and OPA1, a process coordinated in yeast by Ugo1, a mitochondrial metabolite carrier family protein. We uncovered a homozygous missense mutation in SLC25A46, the mammalian orthologue of Ugo1, in a subject with Leigh syndrome. SLC25A46 is an integral outer membrane protein that interacts with MFN2, OPA1, and the mitochondrial contact site and cristae organizing system (MICOS) complex. The subject mutation destabilizes the protein, leading to mitochondrial hyperfusion, alterations in endoplasmic reticulum (ER) morphology, impaired cellular respiration, and premature cellular senescence. The MICOS complex is disrupted in subject fibroblasts, resulting in strikingly abnormal mitochondrial architecture, with markedly shortened cristae. SLC25A46 also interacts with the ER membrane protein complex EMC, and phospholipid composition is altered in subject mitochondria. These results show that SLC25A46 plays a role in a mitochondrial/ER pathway that facilitates lipid transfer, and link altered mitochondrial dynamics to early‐onset neurodegenerative disease and cell fate decisions.

Epigenetic regulation of GATA2 and its impact on normal karyotype acute myeloid leukemia

The GATA2 gene encodes a zinc-finger transcription factor that acts as a master regulator of normal hematopoiesis. Mutations in GATA2 have been implicated in the development of myelodysplastic syndrome and acute myeloid leukemia (AML). Using RNA sequencing we now report that GATA2 is either mutated with a functional consequence, or expressed at low levels in the majority of normal karyotype AML (NK-AML). We also show that low-GATA2-expressing specimens (GATA2(low)) exhibit allele-specific expression (ASE) (skewing) in more than half of AML patients examined. We demonstrate that the hypermethylation of the silenced allele can be reversed by exposure to demethylating agents, which also restores biallelic expression of GATA2. We show that GATA2(low) AML lack the prototypical R882 mutation in DNMT3A frequently observed in NK-AML patients and that The Cancer Genome Atlas AML specimens with DNMT3A R882 mutations are characterized by CpG hypomethylation of GATA2. Finally, we validate that several known missense single-nucleotide polymorphisms in GATA2 are actually loss-of-function variants, which, when combined with ASE, represent the equivalent of homozygous GATA2 mutations. From a broader perspective, this work suggests for the first time that determinants of ASE likely have a key role in human leukemia.

Proteomics-based confirmation of protein expression and correction of annotation errors in the Brucella abortus genome

Background

Brucellosis is a major bacterial zoonosis affecting domestic livestock and wild mammals, as well as humans around the globe. While conducting proteomics studies to better understand Brucella abortus virulence, we consolidated the proteomic data collected and compared it to publically available genomic data.

Results

The proteomic data was compiled from several independent comparative studies of Brucella abortus that used either outer membrane blebs, cytosols, or whole bacteria grown in media, as well as intracellular bacteria recovered at different times following macrophage infection. We identified a total of 621 bacterial proteins that were differentially expressed in a condition-specific manner. For 305 of these proteins we provide the first experimental evidence of their expression. Using a custom-built protein sequence database, we uncovered 7 annotation errors. We provide experimental evidence of expression of 5 genes that were originally annotated as non-expressed pseudogenes, as well as start site annotation errors for 2 other genes.

Conclusions

An essential element for ensuring correct functional studies is the correspondence between reported genome sequences and subsequent proteomics studies. In this study, we have used proteomics evidence to confirm expression of multiple proteins previously considered to be putative, as well as correct annotation errors in the genome of Brucella abortus strain 2308.

Intracellular adaptation of Brucella abortus

Macrophages were infected with virulent Brucella abortus strain 2308 or attenuated strain 19. Intracellular bacteria were recovered at different times after infection and their proteomes compared. The virulent strain initially reduced most biosynthesis and altered its respiration; adaptations reversed later in infection. The attenuated strain was unable to match the magnitude of the virulent strain's adjustments. The results provide insight into mechanisms utilized by Brucella to establish intracellular infections.

[Transfusion in elderly patients]

The frequency of anemia is responsible of a frequent use of transfusion in elderly patients. However, transfusion in elderly patients requires several warnings. First, semiology of elderly patients is characterized with atypical clinical signs, and anemia tolerance is often difficult to appreciate. Second, numerous comorbidities make of elderly patients an heterogeneous population, in which guidelines are poorly applicable. Last, elderly patients are particularly sensitive to iatrogenic events, and the haemodynamic overload related to transfusion has to be carefully managed. All these difficulties raise the need of prospective studies on transfusion in elderly patients to validate clinical practice.

[Retinal detachments caused by giant tear]

52 eyes in 50 patients have been treated for a retinal detachment with a giant tear extending over at least 70 degrees. 27 eyes had an inverted posterior retinal flap covering the posterior pole. Conventional extraocular surgery was performed on 20 eyes. There was no success in 6 folded cases and a 42,85% success rate in 14 non-folded retinas. Endocular surgery by vitrectomy plus internal tamponade using air or silicone oil was done on 32 eyes with an 87,50% success rate at the end of surgery. Post-operative retinal retraction reduced the success rates to 45,45% for non-folded cases and 52,38% with folded retinas. There is no question in our mind about the value of endocular surgery for folded retinas. We think that endocular surgery is also the best choice for non folded retinas because of the excellent initial results. Secondary retraction phenomena are caused by endocular cellular proliferation and membrane formation and contraction. We presently try to minimize these by avoiding excess cryopexy, performing a vitrectomy as complete as possible and treating the reattached retina as soon as possible by argon laser photocoagulation. An efficient and safe antiproliferative drug is definitely needed.

[Undergoing retinal detachment and primitive ocular hypertension (author's transl)]

In a survey of 907 patients undergoing retinal detachment surgery, primitive ocular hypertension was found in 3,85%. This ocular hypertension was most often bilateral (85,7%) with open angle (88%) and was found at the time of retinal surgery or on the follow up (54,3%). Retinal detachments in these patients offered no particular character. This percentage of 3,85% is not greater than the percentage of primitive ocular hypertensions in a normal population over 40 years old. However the analysis of our data leads us to think that the presence of ocular hypertension increases the risk of retinal detachment when the patient is aphakic.

[Indentation of large retinal tears (author's transl)]

According to us large retinal tears are between 20 degrees and 70 degrees in their largest dimension, which excludes true giant tears. Study of the data collected on 42 patients has shown us the following facts:--these retinal tears occur in phakic and often highly myopic eyes;--our global success rate is 73,8%;--tears smaller than 2 to 3 papillary diameters radially are on the whole easy to indent and failures are quite often related to a surgical fault;--tears wider than 3 papillary diameters radially are on the whole difficult to indent and failures are not always related to an obvious surgical fault, fishmouth phenomenon plays an important role;--in every case presence of blood in the vitreous seems to be unfavourable to the prognosis;--use of episcleral pockets solves must of times surgical problems related to fishmouth or tear dimension;--post operative intern limiting membrane retraction is frequent (10% vs 5,7% for all the retinal tears and detachments cured in the same period of time).

[Silicone sponges rejection (author's transl)]

Out of 633 retinal tears or detachments treated by cryocoagulation and Lincoff sponges without scleral dissection, our rate of sponge rejection is 8 per cent (51 out of 633). Out of these 51 rejections we have 4 spontaneous expulsions and 45 surgical removals. In 2 cases we could preserve the buckle by medical treatment. The most pre-eminent causes are in decreasing frequency: --the peroperative sponge infection, mostly by staphylococcus epidermidis, --the existence of an anterior positioned sponge, more than a quadrant long, factor of bad mechanical tolerance, --several operations. The rate of anatomical success is of 86% in this group of 51 patients (80% if we only number successes at six months). We have had 8 recurrences after sponge removals (15%). Recurrences are due to sponge infection; they are mainly due to the reopening of the primitive lesions (6 times out of 8). Only 5 recurrences have been cured (62,5%). This result seems, however, better than the one reached by authors using scleral dissection techniques; according to us this is due to the relatively rare severe vitreous reactions when episcleral sponges' infection occurs.

[Retinal detachment and argon laser prophylactic treatment (author's transl)]

We have studied 6 retinal detachments which hapened after a preventive photocoagulation with argon laser in 6 patients who had already had a severe retinal detachment on the other eye (2 anatomical success on 5 operated cases). This preventive photocoagulation was done on eyes which at the term were free of any retinal dehiscence. In this group of 6 we notice 2 giant tears (greater than 70 degrees) or 33% and 3 large tears (between 20 degrees and 70 degrees) or 33%. These high amounts do not correspond to what has been noticed before: - on the non photocoagulated fellow eyes (neither giant nor large tear) - on the whole lot of operated retinal detachments during the same period of time in our unit (2% of giant and 5,7% of large tears). We think that the responsability of laser in the development of these large lesions in predisposed eyes must be thought about. Studies on a larger scale will be necessary to have a more definite idea on this subject.

[Partial decalcifying algodystrophy]

Partial decalcifying algodystrophy (PDA) appears in two forms: one, a radial form, affects, following a certain metameric topography, one or two radiuses of the hand or of the foot (two cases reported); the other, a zonal form, is more peculiar: only part of a condyle or of the femoral head, are demineralized for two to three months. The authors report 7 cases of this misleading zonal form, 2 of them after histological verification. The image leads to various diagnostic errors: osteitis or infectious osteo-arthritis, acute inflammation close to the bone, and especially malignant processes. However, zonal PDA has its own characteristics: demineralization, that becomes clear only during the second month, and quickly extends over a rather long sub chondral bone surface. Tomography is very useful: it demonstrates better the severe sub chondral osteoporosis and the retention of the bone sole, which becomes detached from the bone. Scintigraphy shows the massive localized or panregional hyperfixation and sometimes other infraradiological sites (hips, knee or ankle). Zonal osteoporosis remains partial and misleading for only 2 or 3 months, after which it becomes a classical panregional form. The rate of development is that of DA. Painful impotence quickly increases, with cure in 6 months.

[Surgical treatment of retinoschisis (author's transl)]

We have made a review of 20 retinoschisis without retinal detachment operated on 12 patients. There is no case of hereditary retinoschisis, the affection may occur at any age, and there is no preferential refractive error. Main surgical indications were macular involvement or impending involvement, and associated retinal tears. A good anatomical result has been obtained in 90% of our cases (18 out of 20) with 2/3 complete reattachments and 1/3 almost complete reattachments (with minimal and well sealed residual schisis). Association of cryocoagulation and indentation is more effective than cryocoagulation alone. On the functional point of view we have had 15% of improved visual acuities and 30% of worsened ones, thus surgical intervention implies macular risks that one must try to prevent by using procedures as atraumatic as possible.

[Drainage of subretinal fluid: technic and results]

The drainage of subretinal fluid (S.R.F.) after choroidal diathermy offers a distinct advantage: important reduction of massive haemorrhages from the drainage site (4% vs 48% in the non diathermy group in our series). According to us it is not a decisive factor for the anatomical prognosis because complications of drainage in themselves seem to be a quite infrequent cause of anatomical failure. On the other hand we think that visual outcome is better in the diathermy group because of a diminution of macular haemorrhages.

[Prognosis of the retinal detachment in children (author's transl)]

Following features seem to characterize retinal detachments in children. High rate of difficult anatomical problems: invisible retinal breaks, macular or paramacular breaks, giant breaks or desinsertions (37% of our cases). High rate of severe traumatic macular lesions. Important delay in treatment with prolonged macular impairment. These facts explain the prognosis. Difficulties in the treatment of retinal breaks explain anatomical results (75% cure rate vs 78,6% for all the retinal detachments treated). In the same way they explain the high rate of multiple operations. Macular impairment and multiple operations explain visual results: 1/3 of the non amblyopic eyes recover a visual acuity comparable to the initial. So, the macular in children does not seem to have a special functional recuperation ability. Two supplementary facts may be mentioned. Delay in treatment has no adverse effect in anatomic prognosis. Non giant "simple" desinsertions expose to a noticeable risk of massive vitreous retraction.