Extracting biological meaning from lipidomics data through biostatistics, machine learning and pathway analysis

In recent years, due to significant advancements in mass spectrometry, lipidomics has emerged as a fast growing scientific field that provides deep insights into complex changes in lipidome of human cells and tissues. Human blood is a self-regenerating lipid-rich biological fluid, a tissue that is easily collected in hospitals. Blood/plasma is rich in lipids and related metabolites, and its lipid composition (LIPIDOME) reflects diverse aspects of lipid metabolism and may give us insight into general human physiology in health and disease. Plasma lipidome is a tightly regulated and precisely defined constellation of lipid molecules and disturbances in the plasma lipidome occur in many diseases such as cardiovascular diseases and cancer, but also in conditions that are not directly linked to lipid metabolism. Hence, plasma lipidomics is an emerging tool in an array of clinical diagnostics. The most sought-after goals in the lipidomics community are to identify disease biomarkers, monitor a clinical treatment or confirm a biological hypothesis on a causality between a disease onset/progression and lipid profile. A recommended plasma lipidomics workflow consists of: preanalytics, analytics and post analytics, including study design, research hypotheses, sample collection, demographics data collection, lipid extraction, quality control, liquid chromatography and mass spectrometry, raw data processing, lipid annotation/identification, normalization, lipid quantitation, databases, data sharing and data analysis. The topic of this presentation is data analysis so I will put an accent to it. Lipidomics community nowadays uses dozens of biostatistical tools, artificial intelligence (AI), machine learning (ML) algorithms and chemometrics for data analysis, depending on size of datasets, data structure and the expertise of data scientists involved. Smart analysis of lipidomic data (provided these are of good quality) is of paramount importance for identifying potential biomarkers and understanding disease mechanisms. To accomplish this, they use, besides classical statistics-between groups comparisons, principal component analysis (PCA), orthogonal projections to latent structures discriminant analysis (OPLS-DA), partial least square analysis (PLS) and correlation analysis, all accompanied by various data pattern recognition and data visualization tools. Less often used are ML algorithms such as random forests (RF) and support vector machines (SVM), with only few applying deep learning and neural networks. Finally, to extract biological knowledge, i.e. metabolic pathways affected by a disease or applied treatment, data are subjected to different enrichment analyses, network analyses and pathway analysis. Life scientists working outside clinical setting, such as those investigating neurodegenerative changes in brain will also benefit from applying lipidomics to their model systems.International workshop “Modern information technologies in biology and medicine”, November 22-24, 2023, Onlin

Plasma Profile of Inflamatory Mediators in NHL Patients

Both cancer and inflammation are almost invariably accompanied by lipidome dysregulation. Hence, various lipid species have been reported as candidate markers for many solid tumours 1-3 .However, neitherthe globallipidome norsub-lipidome ofinflammatory pathways in Non-Hodgkin lymphoma (NHL) has been studied. In order to fill this gap and shed light on the inflammatory pathways accompanying NHL, we designed a targeted liquid chromatography – Multiple Reaction Monitoring of bioactive lipids/lipid mediators in plasma of female patients with Diffuse Large B-cell Lymphoma (DLBCL), the most often type of NHL. We chose to quantify lipids known or hypothesized to be involved in inflammation and cancer progression along with theirmembrane precursors. In a pilot study encompassing plasma samples from 17 DLBCL patients and 21 BMI-matched controls, we analysed levels of pro-inlammatory arachidonic acid (AA)-derived oxylipins, focusing on lipoxygenase (LOX) and cytochrome P450 monooxygenase products: hydroxyeicosatetraenoic acids (HETEs) and dihydroxyeicosatrienoic acids; several AA-containing phospholipids (PLs); specificlysophospholipid subclasses; sphingomyelins (SMs), sphingosine 1-phosphate (S1P) and polyunsaturated fatty acids. Data were subjected to classical statistics and multivariate unsupervised and supervised machine learning (ML) algorithms. The DLBCL status was profoundly associated with altered S1P, SM 34:1, SM 36:1 and phosphatidylinositol PI 34:1 abundance. On the other hand, eicosanoids 12(S)-HETE, 15(S)-HETE and thromboxane B2 were major lipid species discriminating between DLBCL and healthy status, as well as lysophosphatidylinositol LPI 20:4. The correlations between lipid species varied considerably between the cancer and controls, reflecting significant changes in lipid metabolic and/or signalling pathways, particularly those within LOX pathway and cell membrane PL remodelling. We suggest S1P, SM 36:1, SM 34:1 and PI 34:1 may beviewed as lipid signatures of DLBCL. Furthermore, these four lipid species could serve asa basis for the prospective validation in larger DLBCL/NHL clinical studies. As far as we know, this is the first plasma lipid profiling in DLBCL/NHL and, as such, brings new knowledge on the metabolic basis of inflammation in this cancer. The added value of our plasma lipid profiling in DLBCL is a deeper understanding of particulate lipid dysregulations in this tumourSePA : 6th Symposium of a Serbian proteomic society: „Discussion and Application of New Methods of Proteomics“; June 2, Rektorat Univerziteta u Kragujevc

Plasma Profile of Inflamatory Mediators in NHL Patients

Both cancer and inflammation are almost invariably accompanied by lipidome dysregulation. Hence, various lipid species have been reported as candidate markers for many solid tumours1-3. However, neither the global lipidome nor sub-lipidome of inflammatory pathways in Non-Hodgkin lymphoma (NHL) has been studied. In order to fill this gap and shed light on the inflammatory pathways accompanying NHL, we designed a targeted liquid chromatography – Multiple Reaction Monitoring of bioactive lipids/lipid mediators in plasma of female patients with Diffuse Large B-cell Lymphoma (DLBCL), the most often type of NHL. We chose to quantify lipids known or hypothesized to be involved in inflammation and cancer progression along with their membrane precursors. In a pilot study encompassing plasma samples from 17 DLBCL patients and 21 BMI-matched controls, we analysed levels of pro-inlammatory arachidonic acid (AA)-derived oxylipins, focusing on lipoxygenase (LOX) and cytochrome P450 monooxygenase products: hydroxyeicosatetraenoic acids (HETEs) and dihydroxyeicosatrienoic acids; several AA-containing phospholipids (PLs); specificlysophospholipid subclasses; sphingomyelins (SMs), sphingosine 1-phosphate (S1P) and polyunsaturated fatty acids. Data were subjected to classical statistics and multivariate unsupervised and supervised machine learning (ML) algorithms. The DLBCL status was profoundly associated with altered S1P, SM 34:1, SM 36:1 and phosphatidylinositol PI 34:1 abundance. On the other hand, eicosanoids 12(S)-HETE, 15(S)-HETE and thromboxane B2 were major lipid species dis criminating between DLBCL and healthy status, as well as lysophosphatidylinositol LPI 20:4. The correlations between lipid species varied considerably between the cancer and controls, reflecting significant changes in lipid metabolic and/or signalling pathways, particularly those within LOX pathway and cell membrane PL remodelling. We suggest S1P, SM 36:1, SM 34:1 and PI 34:1 may beviewed as lipid signatures of DLBCL. Furthermore, these four lipid species could serve as a basis for the prospective validation in larger DLBCL/NHL clinical studies. As far as we know, this is the first plasma lipid profiling in DLBCL/NHL and, as such, brings new knowledge on the metabolic basis of inflammation in this cancer. The added value of our plasma lipid profiling in DLBCL is a deeper understanding of particulate lipid dysregulations in this tumour.SePA : 6th Symposium of a Serbian proteomic society: „Discussion and Application of New Methods of Proteomics“; June 2, Kragujevac

Highly water-soluble ruthenium(II) terpyridine coordination compounds form stable adducts with blood-borne metal transporting proteins

Three coordination compounds of ruthenium(II), belonging to a recently synthesised series of water-soluble compounds of general formula mer- [Ru(L3)(N-N)Cl]Cl, where L3 = 4'-chloro-2, 2':6', 2″-terpyridine (Cl-tpy), N-N = ethylenediamine (en), 1, 2-diaminocyclohexane (dach) or 2, 2'-bipyridine (bpy), have shown strong binding to calf thymus DNA and moderate in vitro cytotoxicity towards cancer cell lines. Knowing that serum proteins play a crucial role in the transport and deactivation of ruthenium drugs, we have conducted a detailed study of their interactions with two major metal-transporting serum proteins, albumin and transferrin, and it is presented herein. Ruthenated protein adducts were formed with various concentrations of the three compounds and then separated from the unbound portions by ultrafiltration through 10 kDa cut- off centrifugal filter units. The stoichiometry of binding was determined using inductively coupled plasma optical emission spectrometry. One mol of albumin bound up to 7, 8.5 and 1.5 mol of compound 1 ([Ru(Cl-tpy)(en)Cl][Cl]), 2 ([Ru(Cl-tpy)(dach)Cl][Cl] and 3 ([Ru(Cl-tpy) (bpy)Cl][Cl]), respectively. One mol of transferrin bound up to 3, 3.5 and 0.4 mol of 1, 2 and 3, respectively. The affinity of albumin and transferrin for the three ruthenium compounds was evaluated using fluorescence quenching. The binding constants for 1 and 2 lay within the range 104–105 M−1, suggesting moderate-to-strong attachment to albumin. Both compounds showed much lower affinity for transferrin (102–103 M−1). Compound 3 bound weakly to each studied protein. High resolution ESI qTOF mass spectra of albumin before and after binding of 1 revealed the high stoichiometry of binding. Although the binding of the compounds 1–3 to albumin and transferrin did not affect proteins’ secondary structure much, their tertiary structures underwent some alterations, as deduced from the circular dichroism study. Changes in the stability of albumin, after binding to compounds 1–3 were examined by differential scanning calorimetry

Hormonalni status i regulacija glikemije kod novorođene teladi tokom prvih sati postnatalnog života

The aim of this study was to examine changes in some hormones concentrations in calves during the first 32 hours of neonatal life and to estimate their association with glycemia. Thyrty two Holstein breed calves were selected for the study. Blood samples were taken at 30, 60 and 90 minutes postnatal. Calves received pooled colostrum: primary colostum (1.5 L, 2 hours after birth), secondary colostrum (2 L, 14 hours after birth) and tertiary colostrum (2 L, 26 hours after birth). Blood samples were taken at hours 5, 20 and 32 of neonatal life. Concentrations of glucose, insulin, cortisol, thyroid hormones and IGF-I and abundance of IGFBP-1, IGFBP-2 and IGFBP-3 were determined in the blood serum. The T3/T4 ratio was also calculated. Calves were born hypoglycemic (glycemia was 2.56±1.05 mmol/L at birth). Thereafter, glycemia significantly increased (p lt 0.001) to 3.05±0.89 mmol/L at min 90. Glucose concentration showed a further increase after colostrum intake and was significantly higher than at the initial value in all examined periods (p lt 0.001). During the first 90 minutes of neonatal life insulinemia decreased significantly (p lt 0.001) compared to initial value (26.33±10.05 μIU/L) and it measured 18.66±5.56 μIU/L at min 90. Cortisolemia was highest at minute 30 (85.08±19.36 nmol/L) and than decreased until the end of the experiment (p lt 0.001) compared to initial values in samples obtained during the period of colostrum intake. A significantly high correlation was determined between glycemia and cortisolemia in all examined periods before the first colostrums intake (r2=0.854; p lt 0.01 at min 30; r2=0.742; p lt 0.01 at min 60 and r2=0.551; p lt 0.01 at min 90). T4 concentrations significantly increased during the first 2 hours, while T3 concentrations decreased, significantly from min 30 to min 90 postnatal (p lt 0.05). T3/T4 ratio significantly increased during the first 2 hours of neonatal life. After first colostrum intake, concentrations of both hormones rose significantly compared to the initial level, but T3/T4 ratio did not change and maintained the value determined at minute 90. IGF- 1 concentrations significantly decreased during the first 2 postnatal hours. A significant positive correlation was observed between IGF-1 concentration and insulinemia (r2=0.463; p lt 0.05 at min 30, r2=0.662; p lt 0.01 at min 60 and r2=0.583; p lt 0.01 at min 90). IGFBP-3 abundance significantly decreased, while IGFBP-1 significantly increased in this period. IGFBP-2 abundance was highest at birth. Results presented in this study indicate that the increase in glucose concentration during the first 2 hours of neonatal life, before the first colostrum intake is mainly the result of increased activity of the adrenal cortex in cortisol secretion and extrathyroidal tissue thus providing sufficient triiodothyronine. Immaturity of mechanisms responsible for insulin secretion provides the dominance of catabolic processes. Changes of the IGF system provide a rise of glucose concentration and establishment of energy balance.Cilj ovog rada je bio da se ispitaju promene koncentracije pojedinih hormona kod novorođene teladi u prvim satima neonatalnog života i utvrdi njihov uticaj na glikemiju. Odabrana su 32 novorođena teleta Holštajn rase kojima je 30, 60. i 90. minuta postnatalnog života uzeta krv. Telad su bila napajana pulovima kolostruma. Pul primarnog kolostruma davan je u količinama od po 1,5 litar 2 sata nakon rođenja, dok su pulovi sekundarnog i tercijarnog kolostruma davani 12, odnosno 24 sata kasnije, u količinama od po 2 litra. Tokom perioda kolostralnog napoja, teladi je uzorkovana krv 5, 20 i 32. sata nakon rođenja. U uzorcima krvi određ ivana je koncentracija glukoze, insulina, kortizola, tireoidnih hormona i IGF-I, kao i zastupljenost IGFBP-1, IGFBP-2 i IGFBP-3. Takođe je obračunat indeks konverzije T3 u T4. Telad su bila rođena u stanju hipoglikemije (koncentracija glukoze na rođenju je iznosila 2,56 ± 1,05 mmol/l). Nakon toga, glikemija je značajno porasla (p lt 0,001) do 3,05 ±0,89 mmol/l (90. minut). Porast koncentracije glukoze je nastavljen i nakon unosa kolostruma, tako da je glikemija u svim ispitivanim uzorcima bila značajno veća u odnosu na početnu vrednost (p lt 0,001). Tokom prvih 90 minuta neonatalnog života, koncentracija insulina se značajno smanjivala (p lt 0,001) u odnosu na početnu vrednost (26,33 ± 10,05 μIU/l) tako da je 90. minuta postnatalnog života bila 18,66 ± 5,56 μIU/l. Porast insulinemije nakon unosa kolostruma nije bio značajan u odnosu na vrednost određenu 90. minuta. Koncentracija kortizola je bila najviša 30 minuta nakon teljenja (85,08 ± 19,36 nmol/l) a zatim je opadala do kraja perioda ispitivanja i to značajno u odnosu na početnu vrednost (p lt 0,001) u uzorcima dobijenim nakon unosa kolostruma. Visoka pozitivna korelacija je utvrđena između glikemije i kortizolemije u svim ispitivanim terminima pre kolostralnog napoja (r2 = 0,854 u 30. minutu; r2 = 0,742 u 60. minutu i r2= 0,551 u 90. minutu). Koncentracija T4 je značajno rasla tokom prva dva sata neonatalnog života, dok se koncentracija T3 smanjila, značajno od 30. do 90. minuta neonatalnog života (p lt 0,05). Konverzija T3 u T4 je značajno porasla tokom prva dva sata života. Nakon unosa kolostruma, koncentracija oba tireoidna hormona se povećavala (značajno u odnosu na početnu vrednost) a indeks konverzije se nije menjao, već se zadržao na vrednosti ustanovljenoj 90. minuta života. Koncentracija IGF-1 se značajno smanjivala tokom prva 2 sata neonatalnog života. Koncentracija IGF-1 je bila u visokoj pozitivnoj korelaciji sa insulinemijom (r2= 0,463 za 30. minut, r2=0,662 za 60. minut i r2=0,583 za 90. minut). Zastupljenost IGFBP-3 se značajno smanjivala, dok se zastupljenost IGFBP-1 značajno povećavala u ovom periodu. Zastupljenost IGFBP-2 je bila najveća na rođenju. Rezultati prikazani u ovom radu ukazuju da je porast glikemije u prvim satima života, pre unosa kolostruma, prevashodno posledica pojačane aktivnosti kore nadbubrega u sekreciji kortizola i dejodinaza u ekstratireoidnim tkivima koje obezbeđuju povećanu sintezu T3. Sistemi odgovorni za sintezu insulina nisu potpuno funkcionalni u ovom periodu, omogućavajući prevagu kataboličkih u odnosu na anaboličke procese. Promene unutar IGF sistema omogućavaju porast glikemije i uspostavljanje energetske ravnoteže

Disturbed Plasma Lipidomic Profiles in Females with Diffuse Large B-Cell Lymphoma: A Pilot Study

Lipidome dysregulation is a hallmark of cancer and inflammation. The global plasma lipidome and sub-lipidome of inflammatory pathways have not been reported in diffuse large B-cell lymphoma (DLBCL). In a pilot study of plasma lipid variation in female DLBCL patients and BMI-matched disease-free controls, we performed targeted lipidomics using LC-MRM to quantify lipid mediators of inflammation and immunity, and those known or hypothesised to be involved in cancer progression: sphingolipids, resolvin D1, arachidonic acid (AA)-derived oxylipins, such as hydroxyeicosatetraenoic acids (HETEs) and dihydroxyeicosatrienoic acids, along with their membrane structural precursors. We report on the role of the eicosanoids in the separation of DLBCL from controls, along with lysophosphatidylinositol LPI 20:4, implying notable changes in lipid metabolic and/or signalling pathways, particularly pertaining to AA lipoxygenase pathway and glycerophospholipid remodelling in the cell membrane. We suggest here the set of S1P, SM 36:1, SM 34:1 and PI 34:1 as DLBCL lipid signatures which could serve as a basis for the prospective validation in larger DLBCL cohorts. Additionally, untargeted lipidomics indicates a substantial change in the overall lipid metabolism in DLBCL. The plasma lipid profiling of DLBCL patients helps to better understand the specific lipid dysregulations and pathways in this cancer

Lectin-induced alterations of the interaction of insulin and insulin-like growth factor 1 receptors with their ligands

Tesis (Ingeniero Industrial y de Sistemas)--Universidad de Piura. Facultad de Ingeniería. Programa Académico de Ingeniería Industrial y de Sistemas, 2003.Los objetivos logrados con esta tesis son: medición de la percepción común de los trabajadores sobre la estructura, sistemas, participación, etc. y elaboración de un plan de acción para una mejor gestión de la institución. Inicialmente se visitó la institución para conocer su cultura y políticas de trabajo a través de entrevistas personales con uno o dos trabajadores de cada área. Esta información fue procesada y se elaboró un plan de acción que busca la mejora continua de la institución. Según resultados: eficacia, atractividad y unidad, en conjunto dentro de la institución, se encuentran en un buen nivel. El factor objeto ha destacado sobre los demás, es decir, los trabajadores tienen conocimiento de las funciones que deben desempeñar y perciben una buena labor de capacitación. A pesar de esto, es de vital importancia elaborar un plan de capacitación y desarrollo para cada trabajador

Lectin-induced alterations of the interaction of insulin and insulin-like growth factor 1 receptors with their ligands

In order to study whether the carbohydrate moieties of the human placental IGF-I receptor (IGF1R), IGF-II receptor (IGF2R) and insulin receptors (IRs) play a role in ligand binding, solubilised cell membrane preparations were incubated with 125I-labelled IGF-I, IGF-II and insulin in the presence of lectins with different sugar specificities. Three incubation procedures were tested: ligand-first, co-incubation and lectin-first incubation. Wheat germ agglutinin (WGA), concanavalin A (Con A) and phytohaemagglutinin (PHA) altered the binding of IGF-I and insulin to their high-affinity receptors in a lectin specific and dose-dependent manner, whereas these lectins did not affect the interaction of IGF-II with its receptor(s). Moreover, the same lectins either inhibited or enhanced IGF-I and insulin binding, depending on the incubation scheme. These results also suggest that IR-A and IR-B from human placenta might be differently glycosylated

Membrane-associated insulin-like growth factor (IGF) binding structures in placental cells

The biological activities of IGF-I and II are mediated mainly by the type 1 IGF receptor (IGF 1R) and controlled by their interaction with soluble proteins, the IGF binding proteins (IGFBPs). Although there is a growing body of evidence that some IGFBPs may be cell surface-bound, published data concerning cell association of IGFBP-1 are scarce and none of them concern placental cells. The cell membranes used in this study were isolated from term human placentae. Detergent-solubilized membranes were shown to contain two types of IGF binding structures that were separated by gel filtration on a Sephadex G-100 column. Proteins in the first peak were eluted at V0 (Mr > 100 kD) and they bound IGF-I with greater specificity and affinity than IGF-II and insulin. Most likely, they represented the IGF 1R. Small proteins (Mr ~ 45 kD) were eluted with the membrane proteins in the second maximum. They were able to bind IGF-I and IGF-II, but not insulin. The identity of these proteins was shown to be IGFBP-1 on the basis of their reaction with specific anti-IGFBP-1 antibodies. To the best of our knowledge, the existence of IGFBP-1 associated with human placental cell membranes has not been reported in the literature before. Colocalisation of IGFBP-1 with IGF 1R in cell membranes could provide efficient modulation of IGF 1R receptor-ligand interactions