Mevalonate pathway regulates cell size homeostasis and proteostasis through autophagy

SummaryBalance between cell growth and proliferation determines cell size homeostasis, but little is known about how metabolic pathways are involved in the maintenance of this balance. Here, we perform a screen with a library of clinically used drug molecules for their effects on cell size. We find that statins, inhibitors of the mevalonate pathway, reduce cell proliferation and increase cell size and cellular protein density in various cell types, including primary human cells. Mevalonate pathway effects on cell size and protein density are mediated through geranylgeranylation of the small GTPase RAB11, which is required for basal autophagic flux. Our results identify the mevalonate pathway as a metabolic regulator of autophagy and expose a paradox in the regulation of cell size and proteostasis, where inhibition of an anabolic pathway can cause an increase in cell size and cellular protein density

Pain phenotypes, sleep problems and other comorbidities in patients with persistent pain

The validity of pain intensity as the primary measure in chronic pain treatment has been questioned. It may be important to look at other pain-related factors as well, such as how widespread the pain is or how it interferes with different life activities. These pain-related factors may combine into different pain phenotypes. Understanding how these pain phenotypes associate with, for example, lifestyle and psychological factors may help in targeting treatment better. The aim of this dissertation was to examine pain phenotypes of patients entering tertiary pain care and the features or problems that are associated with them. More specifically, the aims were: · to investigate pain phenotypes with respect to different levels of pain interference and factors associated with them; · to use a data-driven approach to elucidate patient subgroups with different pain phenotypes and investigate factors associated with these, using machine learning methods from a multifactorial set of data; · to elucidate metabolomic markers associated with more severe pain phenotypes by investigating metabolomic markers and pathways with respect to the pain phenotypes found in the previous study, and to two common comorbidities of severe pain, obesity and recurring sleep problems; and · to examine how patients with recurring sleep problems differ from those who sleep normally in the areas of pain and pain-related anxiety, childhood adversities experienced, use of sleep and pain medications, self-reported diseases, and sleep disorders. This was a cross-sectional study. The study data were collected at six pain clinics (three multidisciplinary and three facial pain clinics) in Finland. The whole cohort comprised 473 patients from whom broad data were collected, including sociodemographic factors, previous treatments, comorbidities, lifestyle variables, psychological factors, and others. At multidisciplinary pain clinics with 320 participants, nurses also measured patients’ weight, height, waist circumference, and blood pressure; blood samples were taken for the analysis of metabolomics data. Pain phenotypes combined with levels of pain interference showed adverse changes in different sets of factors when pain interfered highly with either the “activity” or the “affective” dimension. High activity pain interference was associated with reduced exercising, higher body mass index, and higher avoidance of pain, than where both interference dimensions remained low. High affective pain interference was associated with more depression, greater cognitive anxiety, and lower activity engagement when pain was present. When both interference dimensions were high, the previous adverse changes accumulated, smoking was more prevalent, and pain-related anxiety was more pronounced, with fear of pain and physiological anxiety reactions higher than with other pain phenotypes. Data-driven subgrouping of patients resulted in three groups. The groups at the extremes showed pain phenotypes with low pain intensity and pain interference at one end, and combination of high pain intensity, high pain interference and the greatest number of pain sites at the other. In the machine learning analysis, the most informative variables among pain-related factors predicting group membership were affective pain interference and number of pain sites. Of the other factors, sleep problems was the most informative, followed by fear of pain, poorer self-rated health, and lower systolic blood pressure. When metabolomic factors were investigated in relation to pain phenotypes elucidated in the previous data-driven study (least severe pain phenotype in contrast to the two more severe phenotypes combined), obesity, and sleep problems, three metabolomic markers (NAD, AMP, and cysteine) emerged across analyses. Obesity showed association with alterations in amino acid metabolism. Sleep problems were associated with several markers relating to methionine metabolism, which results suggested was downregulated in recurring sleep problems. Patients with recurring sleep problems showed more pain-related anxiety than those sleeping normally, and results suggested physiological anxiety reactions as significant factors for greater difficulties with sleep. Multiple health conditions (for example, asthma and depression) were more prevalent among those with recurring sleep problems. Those with sleep problems reported significantly more restless legs symptoms than those sleeping normally. Having five or more childhood adversities was associated with recurring sleep problems. Finally, the reported use of pain and sleep medications was higher in those with recurring sleep problems than in those who slept normally. To conclude, patient subgroups with varying pain phenotypes were discovered in the studies. Previous studies have highlighted the role of psychosocial factors in those with the most severe pain phenotypes. The results of these studies suggest the importance of sleep and lifestyle-related factors as well. Research into metabolomics may give new insights to why pain becomes more severe for some. Sleep is affected by multiple factors, not only pain, in patients with chronic pain.Kivun voimakkuus ensisijaisena muuttujana on kyseenalaistettu pitkäaikaisen kivun hoidossa. Voi olla tärkeä huomioida myös muut kipumuuttujat, kuten kivun laaja-alaisuus tai kuinka kipu häiritsee erilaisia toimintoja. Yhdessä eri kipumuuttujat voivat muodostaa erilaisia kivun ilmiasuja, fenotyyppejä. Hoidon kohdentamista voi auttaa se, jos ymmärrämme paremmin kuinka erilaiset kivun fenotyypit yhdistyvät esimerkiksi elintapoihin ja psykologisiin tekijöihin. Tämän väitöstutkimuksen aiheena oli tutkia kivun fenotyyppejä ja niihin yhdistyviä tekijöitä potilailla, jotka tulevat pitkäaikaisen kivun hoitoon erikoissairaanhoidossa. Aineisto tähän poikkileikkaustutkimukseen kerättiin kuudella suomalaisella kipuklinikalla. Koko kohortti koostui 473 potilaasta. Heiltä kerättiin tietoa muun muassa taustatekijöistä, aiemmista hoidoista, oheissairauksista, elintavoista sekä erilaisia psykologisia muuttujia. Kivun häiritsevyydestä muodostetut fenotyypit toivat esille, että kivun häiritsevyyden dimensiot (häiritsevyys aktiivisuuteen / affektiivisiin toimintoihin) yhdistyivät eri tekijöihin. Voimakas kivun häiritsevyys aktiivisuuteen yhdistyi vähäisempään vapaa-ajan liikuntaan, korkeampaan painoindeksiin ja esillä oli enemmän kipuun liittyvää välttelykäyttäytymistä verrattuna siihen, että kivun häiritsevyys oli heikkoa kummallakin dimensiolla. Kun sen sijaan kivun häiritsevyys affektiivisiin toimintoihin oli voimakas, esillä oli enemmän depressio-oireita, ahdistunutta ajattelua kipuun liittyen sekä vähemmän kivun hyväksymisestä kertovaa itselle tärkeisiin toimintoihin suuntautumista. Kun kivun häiritsevyys oli voimakas kummallakin dimensiolla, edellä mainitut kielteiset muutokset yhdistyivät. Lisäksi tupakointi oli yleisempää ja kipuun liittyvää ahdistusta oli enemmän, sillä kivun pelkoa ja kehollisia ahdistusreaktioita oli enemmän kuin muissa kivun häiritsevyydestä muodostetuissa fenotyypeissä. Aineistolähtöisesti erottui kolme potilasryhmää erilaisin kivun fenotyypein. Toisessa ääripäässä olevassa ryhmässä kivun voimakkuus ja kivun häiritsevyys olivat matalat, kun taas toisen ääripään ryhmässä yhdistyivät korkea kivun voimakkuus, korkea kivun häiritsevyys ja kipualueiden suuri määrä. Koneoppimisanalyysi toi esille, että uniongelmat olivat keskeinen tekijä suhteessa näihin ryhmiin. Lisäksi kivun pelko, huonoksi koettu terveydentila ja matalampi systolinen verenpaine nousivat analyysissä esille. Analyyseissä löydettiin viitteitä myös ryhmien välisistä eroista metabolomiikassa. Jatkuvista uniongelmista kärsivillä potilailla oli enemmän kipuun liittyvää ahdistusta kuin normaalisti nukkuvilla. Tutkimuksen tulokset viittasivat siihen, että kehollisilla ahdistusreaktioilla oli keskeinen rooli uniongelmissa. Uniongelmista kärsivillä potilailla oli tavallista useammin oheissairauksia (esimerkiksi astma tai depressio). Levottomien jalkojen oireet olivat uniongelmista kärsivillä selkeästi tavallisempia kuin normaalisti nukkuvilla. Uniongelmista kärsivillä oli tavallisemmin taustassaan viisi tai sitä useampi lapsuudenaikainen kuormitustekijä. Uniongelmista kärsivät käyttivät enemmän uni- ja kipulääkkeitä kuin normaalisti nukkuvat. Tutkimuksissa löytyi siis kivun fenotyyppien suhteen erilaisia potilaiden alaryhmiä. Aiemmissa tutkimuksissa on noussut etenkin psykososiaaliset tekijät suhteessa vaikeampiin kivun fenotyyppeihin. Näiden tutkimusten tulokset viittaavat siihen, että uni ja elintapoihin liittyvät tekijät ovat myös tärkeitä. Metabolomiikan tutkimus voi antaa viitteitä aineenvaihdunnallisten prosessien osuudesta kivun vaikeutumisessa. Pitkäaikaisessa kivussa uniongelmiin ei vaikuta pelkkä kipu, vaan myös monet muut tekijät

Bridging the lifecycle : A case study on facility management infrastructures and uses of BIM

Purpose - The purpose of this paper is to study the conditions of the building information modelling (BIM) implementation in facility management (FM) specifically from the point of view of different groups of FM practitioners, and the FM infrastructures already in use. Design/methodology/approach - A literature review on the gap between the uses of BIM in design and FM has been done. The key professional groups of FM in the Premises Centre of the City of Helsinki were interviewed on the information tools they use, and the needs and impediments of the BIM implementation in the FM. Cultural-historical activity theory is used as a theoretical framework. Findings - The literature discussing the BIM implementation tends to omit the analysis of the existing FM information systems and software tools in use. The challenge in the BIM implementation is in which ways the relevant information included in the BIM models could be integrated with these systems. No well-articulated problems or developmental contradictions came up that would demand the investment in the BIM implementation. Practical implications - The results call for experimenting with incremental implementation of BIM in different FM activities and in the FM information infrastructures in use. Originality/value - This paper studies empirically different FM activities and information systems used by the professional groups. Such studies are needed for a realistic view of the potential integration of the BIM information to the FM information systems.Peer reviewe

Muscle activity and acute stress in fibromyalgia

Background: Fibromyalgia (FM) patients are likely to differ from healthy controls in muscle activity and in reactivity to experimental stress. Methods: We compared psychophysiological reactivity to cognitive stress between 51 female FM patients aged 18 to 65 years and 31 age- and sex-matched healthy controls. They underwent a 20-minute protocol consisting of three phases of relaxation and two phases of cognitive stress. We recorded surface electromyography normalized to maximum voluntary muscle contraction (%EMG), the percentage of time with no muscle activity (EMG rest time), and subjective pain and stress intensities. We compared group reactivity using linear modelling and adjusted for psychological and life-style factors. Results: The FM patients had a significantly higher mean %EMG (2.2 % vs. 1.0 %, p <0.001), pain intensity (3.6 vs. 0.2, p <0.001), and perceived stress (3.5 vs. 1.4, p <0.001) and lower mean EMG rest time (26.7 % vs. 47.2 %, p <0.001). In the FM patients, compared with controls, the pain intensity increased more during the second stress phase (0.71, p = 0.028), and the %EMG decreased more during the final relaxation phase (-0.29, p = 0.036). Within the FM patients, higher BMI predicted higher %EMG but lower stress. Leisure time physical activity predicted lower %EMG and stress and higher EMG rest time. Higher perceived stress predicted lower EMG rest time, and higher trait anxiety predicted higher pain and stress overall. Conclusions: Our results suggest that repeated cognitive stress increases pain intensity in FM patients. FM patients also had higher resting muscle activity, but their muscle activity did not increase with pain. Management of stress and anxiety might help control FM flare-ups.Peer reviewe

Machine Learning and Pathway Analysis-Based Discovery of Metabolomic Markers Relating to Chronic Pain Phenotypes

Recent scientific evidence suggests that chronic pain phenotypes are reflected in metabolomic changes. However, problems associated with chronic pain, such as sleep disorders or obesity, may complicate the metabolome pattern. Such a complex phenotype was investigated to identify common metabolomics markers at the interface of persistent pain, sleep, and obesity in 71 men and 122 women undergoing tertiary pain care. They were examined for patterns in d = 97 metabolomic markers that segregated patients with a relatively benign pain phenotype (low and little bothersome pain) from those with more severe clinical symptoms (high pain intensity, more bothersome pain, and co-occurring problems such as sleep disturbance). Two independent lines of data analysis were pursued. First, a data-driven supervised machine learning-based approach was used to identify the most informative metabolic markers for complex phenotype assignment. This pointed primarily at adenosine monophosphate (AMP), asparagine, deoxycytidine, glucuronic acid, and propionylcarnitine, and secondarily at cysteine and nicotinamide adenine dinucleotide (NAD) as informative for assigning patients to clinical pain phenotypes. After this, a hypothesis-driven analysis of metabolic pathways was performed, including sleep and obesity. In both the first and second line of analysis, three metabolic markers (NAD, AMP, and cysteine) were found to be relevant, including metabolic pathway analysis in obesity, associated with changes in amino acid metabolism, and sleep problems, associated with downregulated methionine metabolism. Taken together, present findings provide evidence that metabolomic changes associated with co-occurring problems may play a role in the development of severe pain. Co-occurring problems may influence each other at the metabolomic level. Because the methionine and glutathione metabolic pathways are physiologically linked, sleep problems appear to be associated with the first metabolic pathway, whereas obesity may be associated with the second.Peer reviewe

Machine Learning and Pathway Analysis-Based Discovery of Metabolomic Markers Relating to Chronic Pain Phenotypes

Recent scientific evidence suggests that chronic pain phenotypes are reflected in metabolomic changes. However, problems associated with chronic pain, such as sleep disorders or obesity, may complicate the metabolome pattern. Such a complex phenotype was investigated to identify common metabolomics markers at the interface of persistent pain, sleep, and obesity in 71 men and 122 women undergoing tertiary pain care. They were examined for patterns in d = 97 metabolomic markers that segregated patients with a relatively benign pain phenotype (low and little bothersome pain) from those with more severe clinical symptoms (high pain intensity, more bothersome pain, and co-occurring problems such as sleep disturbance). Two independent lines of data analysis were pursued. First, a data-driven supervised machine learning-based approach was used to identify the most informative metabolic markers for complex phenotype assignment. This pointed primarily at adenosine monophosphate (AMP), asparagine, deoxycytidine, glucuronic acid, and propionylcarnitine, and secondarily at cysteine and nicotinamide adenine dinucleotide (NAD) as informative for assigning patients to clinical pain phenotypes. After this, a hypothesis-driven analysis of metabolic pathways was performed, including sleep and obesity. In both the first and second line of analysis, three metabolic markers (NAD, AMP, and cysteine) were found to be relevant, including metabolic pathway analysis in obesity, associated with changes in amino acid metabolism, and sleep problems, associated with downregulated methionine metabolism. Taken together, present findings provide evidence that metabolomic changes associated with co-occurring problems may play a role in the development of severe pain. Co-occurring problems may influence each other at the metabolomic level. Because the methionine and glutathione metabolic pathways are physiologically linked, sleep problems appear to be associated with the first metabolic pathway, whereas obesity may be associated with the second.Peer reviewe

Identification of transcriptional and metabolic programs related to mammalian cell size

SummaryBackgroundRegulation of cell size requires coordination of growth and proliferation. Conditional loss of cyclin-dependent kinase 1 in mice permits hepatocyte growth without cell division, allowing us to study cell size in vivo using transcriptomics and metabolomics.ResultsLarger cells displayed increased expression of cytoskeletal genes but unexpectedly repressed expression of many genes involved in mitochondrial functions. This effect appears to be cell autonomous because cultured Drosophila cells induced to increase cell size displayed a similar gene-expression pattern. Larger hepatocytes also displayed a reduction in the expression of lipogenic transcription factors, especially sterol-regulatory element binding proteins. Inhibition of mitochondrial functions and lipid biosynthesis, which is dependent on mitochondrial metabolism, increased the cell size with reciprocal effects on cell proliferation in several cell lines.ConclusionsWe uncover that large cell-size increase is accompanied by downregulation of mitochondrial gene expression, similar to that observed in diabetic individuals. Mitochondrial metabolism and lipid synthesis are used to couple cell size and cell proliferation. This regulatory mechanism may provide a possible mechanism for sensing metazoan cell size

Directed evolution of rRNA improves translation kinetics and recombinant protein yield

In bacteria, ribosome kinetics are considered rate-limiting for protein synthesis and cell growth. Enhanced ribosome kinetics may augment bacterial growth and biomanufacturing through improvements to overall protein yield, but whether this can be achieved by ribosome-specific modifications remains unknown. Here, we evolve 16S ribosomal RNAs (rRNAs) from Escherichia coli, Pseudomonas aeruginosa, and Vibrio cholerae towards enhanced protein synthesis rates. We find that rRNA sequence origin significantly impacted evolutionary trajectory and generated rRNA mutants with augmented protein synthesis rates in both natural and engineered contexts, including the incorporation of noncanonical amino acids. Moreover, discovered consensus mutations can be ported onto phylogenetically divergent rRNAs, imparting improved translational activities. Finally, we show that increased translation rates in vivo coincide with only moderately reduced translational fidelity, but do not enhance bacterial population growth. Together, these findings provide a versatile platform for development of unnatural ribosomal functions in vivo

Sleep problems in pain patients entering tertiary pain care : the role of pain-related anxiety, medication use, self-reported diseases, and sleep disorders

Peer reviewe

Thermal proteome profiling of breast cancer cells reveals proteasomal activation by CDK4/6 inhibitor palbociclib

Palbociclib is a CDK4/6 inhibitor approved for metastatic estrogen receptor-positive breast cancer. In addition to G1 cell cycle arrest, palbociclib treatment results in cell senescence, a phenotype that is not readily explained by CDK4/6 inhibition. In order to identify a molecular mechanism responsible for palbociclib-induced senescence, we performed thermal proteome profiling of MCF7 breast cancer cells. In addition to affecting known CDK4/6 targets, palbociclib induces a thermal stabilization of the 20S proteasome, despite not directly binding to it. We further show that palbociclib treatment increases proteasome activity independently of the ubiquitin pathway. This leads to cellular senescence, which can be counteracted by proteasome inhibitors. Palbociclib-induced proteasome activation and senescence is mediated by reduced proteasomal association of ECM29. Loss of ECM29 activates the proteasome, blocks cell proliferation, and induces a senescence-like phenotype. Finally, we find that ECM29 mRNA levels are predictive of relapse-free survival in breast cancer patients treated with endocrine therapy. In conclusion, thermal proteome profiling identifies the proteasome and ECM29 protein as mediators of palbociclib activity in breast cancer cells