"Primer shot" fractionation with an early treatment break is theoretically superior to consecutive weekday fractionation schemes for early-stage non-small cell lung cancer

PURPOSE

Radiotherapy is traditionally given in equally spaced weekday fractions. We hypothesize that heterogeneous interfraction intervals can increase radiosensitivity via reoxygenation. Through modeling, we investigate whether this minimizes local failures and toxicity for early-stage non-small cell lung cancer (NSCLC).

METHODS

Previously, a tumor dose-response model based on resource competition and cell-cycle-dependent radiosensitivity accurately predicted local failure rates for early-stage NSCLC cohorts. Here, the model mathematically determined non-uniform inter-fraction intervals minimizing local failures at similar normal tissue toxicity risk, i.e., iso-BED3 (iso-NTCP) for fractionation schemes 18Gyx3, 12Gyx4, 10Gyx5, 7.5Gyx8, 5Gyx12, 4Gyx15. Next, we used these optimized schedules to reduce toxicity risk (BED3) while maintaining stable local failures (TCP).

RESULTS

Optimal schedules consistently favored a "primer shot" fraction followed by a 2-week break, allowing tumor reoxygenation. Increasing or decreasing the assumed baseline hypoxia extended or shortened this optimal break by up to one week. Fraction sizes of 7.5 Gy and up required a single primer shot, while smaller fractions needed one or two extra fractions for full reoxygenation. The optimized schedules, versus consecutive weekday fractionation, predicted absolute LF reductions of 4.6%-7.4%, except for the already optimal LF rate seen for 18Gyx3. Primer shot schedules could also reduce BED3 at iso-TCP with the biggest improvements for the shortest schedules (94.6Gy reduction for 18Gyx3).

CONCLUSION

A validated simulation model clearly supports non-standard "primer shot" fractionation, reducing the impact of hypoxia-induced radioresistance. A limitation of this study is that primer-shot fractionation is outside prior clinical experience and therefore will require clinical studies for definitive testing.

Outcomes of patients with high bleeding risks characteristics presenting with acute coronary syndrome undergoing percutaneous coronary intervention

Background

Patients with high bleeding risk characteristics (HBR) presenting with acute coronary syndrome (ACS) pose a clinical challenge to balance risk for recurrent ischemic events versus incurring bleeding with dual antiplatelet therapy.

Purpose

We seek to determine the incidence and predictors of short and long term ischemic and bleeding outcomes in patients with HBR factors presenting with ACS after percutaneous coronary intervention (PCI).

Method

Consecutive patients over a 1-year period, who underwent PCI for ACS were categorized as having HBR based on: age ≥75, anemia (hemoglobin<110g/L), thrombocytopenia (platelet<100x109/L), renal failure (eGFR<30umol/L) or concurrent use of oral anticoagulation. Primary outcome was major adverse cardiovascular event (MACE) defined as composite of cardiovascular death, myocardial infarction, and stroke at 1 year. Key secondary outcomes include significant bleeding defined as Bleeding Academic Research Consortium (BARC) type 3 or 5, and net adverse cardiovascular event (NACE), as a composite of MACE and significant bleeding.

Results

Of 1351 patients presented with ACS, 389 (28.8%) had at least one HBR criteria. At 1 year, patients with HBR, compared to those without, had increased MACE (11.1% vs 4.2%, p<0.001) and cardiovascular death (5.7% vs 1.7%, p<0.001). Patients with HBR had increased significant bleeding (3.6% vs 2.3%, p=0.011) and NACE (14.4% vs 5.4%, p<0.001). Multivariate analysis showed the presence of HBR and prior history of myocardial infarction were predictors for 1-year MACE (OR 2.67, CI [1.62–4.42], p<0.001 and OR 2.18, CI [1.29–3.70], p=0.004, respectively), whereas the use of second-generation antiplatelet agent was not. Increased MACE and NACE were observed in HBR patients beyond 1 month of DAPT.

Conclusion

Among patients with ACS undergoing PCI, those with HBR had higher risk for both ischemic and bleeding complications. Novel strategies need to be considered for this high-risk group. Current guidelines, recommending 1 year of DAPT for patients with ACS, should be re-evaluated among patients with HBR.

Funding Acknowledgement

Type of funding sources: None. Kaplan-Meier curve for 1 year MACEKaplan-Meier curve for 1 year death

The effects of ecological rehabilitation projects on the resilience of an extremely drought-prone desert riparian forest ecosystem in the Tarim River Basin, Xinjiang, China

The Tarim River Basin in Xinjiang, China, has a typical desert riparian forest ecosystem. Analysis of the resilience of this type of ecosystem under extreme drought conditions and ecological rehabilitation projects could provide a theoretical basis for understanding ecosystem stability and resistance, and provide new ecological rehabilitation measures to improve ecosystem resilience. We employed a quantitative framework to assess net primary productivity (NPP) resilience, emphasizing four aspects of NPP dynamics: NPP, NPP stability, NPP resistance, and maximum NPP potential. We compared ecosystem resilience across four time periods: before the implementation of ecological rehabilitation projects (1990-2000), during construction and partial implementation of ecological rehabilitation projects (2001-2012), during the initial project stage of ecological rehabilitation (2013-2015), and during the late project stage of ecological rehabilitation (2016-2018). There are three main finding of this research. (1) Mean NPP was increased significantly from 2013 and was decreased from 2016, especially in the main stream of the Tarim River and in the basins of eight of its nine tributary rivers. (2) Ecosystem resilience in 2013-2018 was greater than in 1990-2012, with the greatest NPP stability, mean NPP and NPP resistance, especially in part one of the river basin (the Aksu River, the Weigan-Kuche River, the Dina River, the Kaidu-Konqi River, and the main stream of the Tarim River). Ecosystem resilience in 2001-2012 was lowest when compared to 1990-2000 and 2013-2018, with lowest mean NPP, NPP stability, NPP resistance and maximum NPP potential, particularly in part two of the river basin (the Kashigr River, the Yarkand River and the Hotan River basins). Therefore, part one was most affected by ecological restoration projects. When 2013-2018 was divided into two distinct stages, 2013-2015 and 2016-2018, resilience in the latter stage was the lowest, with lowest mean NPP, NPP resistance and maximum NPP potential, especially in the main stream of the Tarim River. This may be due to unreasonable water conveyance in 2014-2015. (3) Ecological resilience has increased significantly in 2013-2015 after the implementation of ecological water transfer projects, river regulation, and natural vegetation enclosure projects. Ecosystem resilience could continue to increase even more in the future with the continued implementation of reasonable ecological water transfer projects.

Comparing clinical outcomes following 1 year of dual antiplatelet therapy in patients risk stratified by the PRECISE-DAPT and DAPT scores

Background

Dual antiplatelet therapy (DAPT) is the standard of care following PCI. DAPT reduces ischemic events but increases bleeding risk. Duration of DAPT following PCI remains controversial. Current guidelines recommend duration be individualized based on risk of ischemia and bleeding. Although multiple strategies exist to risk stratify patients, including application of the PRECISE-DAPT and DAPT scores, there is currently no standardized risk assessment protocol.

Purpose

To determine if the PRECISE-DAPT and DAPT scores can identify patients at increased risk of ischemia or bleeding in a cohort prescribed 12 months of DAPT following PCI.

Methods

We calculated the PRECISE-DAPT and DAPT scores for 469 consecutive patients at baseline after PCI. Patients were grouped based on score treatment recommendation; PRECISE-DAPT prolonged or shortened (PRECISE DAPT <25 vs. ≥25) and DAPT prolonged or shortened (DAPT ≥2 vs <2). End points included 1-year rates of major adverse cardiovascular events (MACE) and TIMI major or minor bleeding.

Results

Among 469 patients, mean age was 64.4 (SD 12.2); 102 (21.7%) were women. Index presentation consisted of a STEMI in 207 (44.1%), NSTEMI in 99 (21.1%), and UA in 60 (12.8%). At presentation, 174 (37.1%) were current smokers, 115 (24.5%) had a prior MI, 118 (25.2%) had diabetes, 249 (53.1%) had dyslipidemia and 281 (60.0%) were previously diagnosed as hypertensive. Overall, there was an increase in bleeding and no difference in MACE for patients with a PRECISE-DAPT score ≥25 (13.3% vs. 4.1% P<0.001). No difference in bleeding or MACE was present in patients stratified by the DAPT score.

Conclusion

A PRECISE-DAPT score ≥25 was associated with an increased rate of bleeding and no difference in MACE in patients prescribed 12 months of DAPT. This supports the use of the PRECISE-DAPT as a prospective tool in clinical practice.

Funding Acknowledgement

Type of funding source: None

Basic and target eco-environment water requirements of a dry inland river under typical flow frequencies in China

Analysis of eco-environmental water requirements (EEWRs) and water resource allocation strategies for arid, inland river basins can provide the theoretical basis for sustainable water utilization and management. In this paper, an optimal water resource allocation strategy is proposed for Yarkand River Basin in Xinjiang, China, on the basis of a comprehensive analysis of runoff data collected between 1970 and 2016, three ecological environmental protection goals, basic eco-environmental water requirement (BEEWR) aimed at sustaining aquatic ecosystems within the river, and target eco-environmental water requirements (TEEWR) aimed at protecting various types of riparian vegetation along the river. The results showed that: (1) after the runoff in Kaqun reach subtracting the BEEWR, the annual average river loss (recharge), and the amount of water diversion for irrigation (51.43 × 10⁸ m³) from flows along the Kaqun reach, the remaining water volume during wet years was able to meet all three TEEWRs; (2) during moderately wet years, the remaining water was capable of meeting the second and third TEEWRs; and (3) during dry and extremely dry years, there was little or no residual water available to meet TEEWRs. The proposed optimal water resource allocation strategy, based on the above findings, states that the water diversion requirement for irrigation and domestic use allocated from the total amount of runoff should not exceed the National Water Policy (Three Red Lines) standard first. Then, the BEEWR allocated from the runoff should be met second, and the annual average river loss, third. Depending on the amount of remaining water, the second and third TEEWRs can be fulfilled during wet years, but during moderately wet years, only the third TEEWR can be met. During dry and extremely dry years, only the BEEWR of the river can be met and only during the flood season.

P1933Comparing treatment recommendations for the DAPT and PRECISE-DAPT scores after percutaneous coronary intervention

Background

Dual antiplatelet therapy (DAPT), with aspirin and a P2Y12 inhibitor, is the standard therapy for patients following PCI. Duration of treatment with DAPT has been controversial despite large studies. Current guidelines recommend treatment duration be individualized based on risk of ischemia and bleeding. To facilitate treatment decisions, risk assessment tools, including the DAPT and PRECISE-DAPT scores, have been developed.

Purpose

As components of these scores differ, the variability of recommendation remains unknown. We set to evaluate inter-tool concordance in treatment recommendation in a cohort of patients after PCI.

Methods

Using data from our local PCI registry, we calculated the PRECISE-DAPT at baseline following PCI and the DAPT after 1 year of treatment for 311 consecutive patients with complete data for both scores to be calculated. Based on their DAPT and PRECISE-DAPT scores, patients were grouped into concordant for long-term treatment (DAPT ≥2 and PRECISE-DAPT <25) or concordant for shortened treatment (DAPT <2 and PRECISE- DAPT ≥25). All other patients were considered discordant. We then performed a concordance analysis using Cohen's kappa to measure degree of agreement.

Results

Among the 311 patients, mean age was 63.4 (SD 11.6); 245 (79%) were men, 93 (29.9%) had history of a prior MI, 130 (41.8%) were current smokers, 32 (10.3%) had a history of CHF or LVEF <30%, 82 (26.3%) had diabetes and 196 (63.0%) were previously diagnosed with hypertension. Index event consisted of a STEMI in 101 (32.4%), NSTEMI in 93 (29.9%), unstable angina in 27 (8.7%), stable angina in 67 (21.5%) and the remaining 23 (7.4%) had other indications for PCI. Mean DAPT score was 1.52 (SD 1.37). Mean PRECISE-DAPT was 17.65 (SD 12.73). The DAPT recommended long-term treatment for 162 (52.1%) and shortened treatment for 149 (47.9%). The PRECISE-DAPT recommended long-term treatment for 245 (78.9%) and shortened treatment for 66 (21.2%). The overall proportion of agreement between the two risk scores was 56.6% with a Cohen's kappa index of 0.110 (95% CI, 0.017 to 0.204). See Table.

Concordance Analysis PRECISE-DAPT Score Recommendation Long Term (N=245) Shortened (N=66) DAPT Score Recommendation Long Term (N=162) 136 (43.7%) 26 (8.4%) Concordant for Long Term Treatment Shortened (N=149) 109 (35%) 40 (12.8%) Concordant for Shortened Treatment

Conclusion

Comparison of the DAPT score and the PRECISE-DAPT score showed concordance in treatment recommendation in only 56.6% of patients. Given the poor agreement between these tools, prospective concurrent evaluations and correlation to outcomes will be required in future studies.

Suitable oasis scales under a government plan in the Kaidu-Konqi River Basin of northwest arid region, China

The Yanqi Basin and the Konqi River Basin of the Kaidu-Konqi River Basin were chosen as the study sites in this paper in order to investigate suitable scales of natural and artificial oases with a specified water resource and water quantity planned by the local government. Combined with remote-sensing images from 2013, water resources in 2013, 2025 and 2035, and weather and socioeconomic data, suitable scales of oases were analyzed. The results showed that: (1) The total available water quantities in the Yanqi Basin and the Konqi River Basin without river base flow, and the input of water into Bosten Lake and Tarim River, over high-, normal and low-flow periods, in 2025 and 2035, were 19.04 × 10⁸ m³, 10.52 × 10⁸ m³, 4.95 × 10⁸ m³, 9.95 × 10⁸ m³ and 9.95 × 10⁸ m³, as well as 21.77 × 10⁸ m³, 13.95 × 10⁸ m³, 10.11 × 10⁸ m³, 12.50 × 10⁸ m³, and 9.74 × 10⁸ m³. (2) The water demand of the natural oasis in the Yanqi Basin and the Konqi River Basin was 2.59 × 10⁸ m³, and 4.59 × 10⁸ m³, respectively. (3) The total water consumption of the artificial oasis in 2013, 2025, and 2035 were 10.51 × 10⁸ m³, 10.99 × 10⁸ m³ and 10.74 × 10⁸ m³ in the Yanqi Basin, respectively, and 18.59 × 10⁸ m³, 14.07 × 10⁸ m³ and 13.30 × 10⁸m³ in the Kongqi River Basin, respectively. (4) Under government planning, the optimal area in 2025 and 2035 should be 5,100.06 km² and 5,096.15 km² in the Yanqi Basin oases, and 6,008.53 km² and 4,691.36 km² in the Konqi River Basin oases, respectively, under the different inflow variations, and 4,972.71 km² and 4,969.22 km² in the Yanqi Basin oases, and 5,975.17 km² and 4,665.67 km² in the Kongqi River Basin oases, respectively, under the appropriate proportion. (5) The artificial oases in these basins should be greatly decreased in the future due to limited water resources.

Experimental study on water transport observations of desert riparian forests in the lower reaches of the Tarim River in China

Studying the water use processes of desert riparian vegetation in arid regions and analyzing the response and adaptation strategies of plants to drought stress are of great significance for developing ecological restoration measures. Based on field monitoring and test analyses of physiological ecological indicators of dominant species (Populus euphratica and Tamarix chinensis) in the desert riparian forest in the lower reaches of the Tarim River, the water relations of P. euphratica and T. chinensis under drought stress are discussed and some water use strategies put forward. The results show that (1) concerning plant water uptake, desert riparian forests depend mainly on groundwater to survive under long-term water stress. (2) Concerning plant water distribution, the survival of P. euphratica and nearby shallow root plants is mainly due to the hydraulic lift and water redistribution of P. euphratica under drought stress. (3) Concerning plant water transport, P. euphratica sustains the survival of competitive and advantageous branches by improving their ability to acquire water while restraining the growth of inferior branches. (4) Concerning plant transpiration, the sap flow curves of daily variations of P. euphratica and T. chinensis were wide-peak sin and narrower-peak respectively. T. chinensis has better environmental adaptability.

The Plastid Terminal Oxidase is a Key Factor Balancing the Redox State of Thylakoid Membrane

Mitochondria possess oxygen-consuming respiratory electron transfer chains (RETCs), and the oxygen-evolving photosynthetic electron transfer chain (PETC) resides in chloroplasts. Evolutionarily mitochondria and chloroplasts are derived from ancient α-proteobacteria and cyanobacteria, respectively. However, cyanobacteria harbor both RETC and PETC on their thylakoid membranes. It is proposed that chloroplasts could possess a RETC on the thylakoid membrane, in addition to PETC. Identification of a plastid terminal oxidase (PTOX) in the chloroplast from the Arabidopsis variegation mutant immutans (im) demonstrated the presence of a RETC in chloroplasts, and the PTOX is the committed oxidase. PTOX is distantly related to the mitochondrial alternative oxidase (AOX), which is responsible for the CN-insensitive alternative RETC. Similar to AOX, an ubiquinol (UQH2) oxidase, PTOX is a plastoquinol (PQH2) oxidase on the chloroplast thylakoid membrane. Lack of PTOX, Arabidopsis im showed a light-dependent variegation phenotype; and mutant plants will not survive the mediocre light intensity during its early development stage. PTOX is very important for carotenoid biosynthesis, since the phytoene desaturation, a key step in the carotenoid biosynthesis, is blocked in the white sectors of Arabidopsis im mutant. PTOX is found to be a stress-related protein in numerous research instances. It is generally believed that PTOX can protect plants from various environmental stresses, especially high light stress. PTOX also plays significant roles in chloroplast development and plant morphogenesis. Global physiological roles played by PTOX could be a direct or indirect consequence of its PQH2 oxidase activity to maintain the PQ pool redox state on the thylakoid membrane. The PTOX-dependent chloroplast RETC (so-called chlororespiration) does not contribute significantly when chloroplast PETC is normally developed and functions well. However, PTOX-mediated RETC could be the major force to regulate the PQ pool redox balance in the darkness, under conditions of stress, in nonphotosynthetic plastids, especially in the early development from proplastids to chloroplasts.

Basiliximab with delayed introduction of calcineurin inhibitors as a renal-sparing protocol following liver transplantation in children with renal impairment

Renal impairment is frequently compromised in patients with end-stage liver disease and is associated with increased long-term mortality post-LT. In contrast to CNI, basiliximab is an immunosuppressive agent with minimal nephrotoxic potential. This study reviews the experience of a single pediatric liver transplant center's renal-sparing approach with the use of basiliximab and MMF to compensate for delayed entry of CNI in children with renal impairment at the time of organ availability. There were no differences in renal function between pediatric patients with and without pre-LT renal impairment within the first year (cGFR: 135 mL/min/1.73 m2 vs. 144 mL/min/1.73 m2 ; p = 0.56) or at 5-8 yr following LT, (129 mL/min/1.73 m2 vs. 130 mL/min/1.73 m2 ; p = 0.97). In addition, there was no difference in ACR rates (50% vs. 43%, p = 0.62) between patients in the basiliximab group and those patients receiving standard CNI and steroid strategies. The utilization of a renal-sparing approach with basiliximab alongside delayed entry and lower early target trough levels of CNI in children with renal impairment at the time of LT is safe and maintains excellent long-term kidney function.

An environmental epigenetic study of ADRB2 5'-UTR methylation and childhood asthma severity

BACKGROUND

Beta-2 adrenergic receptor (ADRB2) is the primary target of both short- and long-acting beta-agonist asthma medications. ADRB2 5'-UTR methylation changes in blood have the potential to act as a surrogate biomarker of responsiveness to beta-agonist treatment and childhood asthma severity.

OBJECTIVE

To study the association between ADRB2 5'-UTR methylation, NO (2) exposure and childhood asthma severity.

METHODS

We compared ADRB2 5'-UTR methylation levels in blood between 60 children with mild asthma and 122 children with severe asthma using methylation-specific PCR. We also investigated potential joint effects between NO (2) exposure and ADRB2 5'-UTR methylation.

RESULTS

We found a significant association between intermediate (OR: 4.11, 95% CI: 1.58-10.73) and high levels (OR: 7.63, 95% CI: 3.02-19.26) of ADRB2 methylation and severe childhood asthma. In addition, we found a significant association between indoor exposure to NO (2) , an air pollutant and known asthmogen, and severe asthma among children exhibiting high ADRB2 methylation (OR: 4.59, 95% CI: 1.03-20.55) but no association among children exhibiting low levels of ADRB2 methylation (OR: 0.35, 95% CI: 0.01-14.13).

CONCLUSIONS AND CLINICAL RELEVANCE

These findings support the potential use of ADRB2 5'-UTR methylation as a biomarker of both asthma severity and risk for NO (2) -associated asthma exacerbations in children, and present the first evidence of an epigenetic link between an important environmental exposure and childhood asthma severity.

Distribution pattern of plant species diversity in the mountainous region of Ili River Valley, Xinjiang

In this paper, detrended canonical correspondence analysis was performed to analyze the relationships between diversity indices and environmental gradients, generalized additive model was employed to modal the response curves of diversity indices to the elevation, based on data from field investigation in the mountainous region of the Ili River Valley and a survey of 94 sample plots. Two hundred fifty-nine plant species were recorded in the 94 sample plots investigated, up to 235 species all appeared in the herb layer, and the species of woody plants were very limited. The communities with a complicated vertical structure presented higher values of indices. The distribution pattern of plant species diversity on the northern slope was affected by such factors as elevation, slope aspect, slope gradient, total nitrogen, total potassium, soil water content, organic matter, and that on the southern slope was mainly affected by such factors as slope gradient, elevation, available phosphorus, and soil water content. On the northern slope, Patrick index and Shannon-Wiener index of the plant communities presented a bimodality pattern along altitude; Simpson index and Pielou index showed a partially unimodal pattern. On the southern slope all the distribution pattern of species diversity indices showed two peaks, though Patrick index's bimodality pattern was not an obvious one. These altitudinal patterns were formed by the synthetic action of a variety of environmental factors with elevation playing an important role.

Electro-acupuncture-mediated gene transfer

Gene transfer is one of the key techniques in gene therapy application. Unfortunately, it seems that by now, there still exists no approach with simplicity, easiness, efficiency and safety. A novel method for gene delivery, electro-acupuncture needle-mediated gene transfer which combined the Chinese traditional acupuncture with modem gene introduction, was developed. With acupuncture needle carrying exogenous gene into muscle after direct electronic stimuli, efficient gene delivery was achieved.

Polymorphisms and haplotypes in the bovine neuropeptide Y, growth hormone receptor, ghrelin, insulin-like growth factor 2, and uncoupling proteins 2 and 3 genes and their associations with measures of growth, performance, feed efficiency, and carcass merit in beef cattle1

Genes that regulate metabolism and energy partitioning have the potential to influence economically important traits in farm animals, as do polymorphisms within these genes. In the current study, SNP in the bovine neuropeptide Y (NPY), growth hormone receptor (GHR), ghrelin (GHRL), uncoupling proteins 2 and 3 (UCP2 and UCP3), IGF2, corticotrophin-releasing hormone (CRH), cocaine and amphetamine regulated transcript (CART), melanocortin-4 receptor (MC4R), proopiomelanocortin (POMC), and GH genes were evaluated for associations with growth, feed efficiency, and carcass merit in beef steers. In total, 24 SNP were evaluated for associations with these traits and haplotypes were constructed within each gene when 2 or more SNP showed significant associations. An A/G SNP located in intron 4 of the GHR gene had the largest effects on BW of the animals (dominance effect P < 0.01) and feed efficiency (allele substitution effect P < 0.05). Another A/G SNP located in the promoter region of GHR had similar effects but the haplotypes of these 2 SNP reduced the effects of the SNP located in intron 4. Three SNP in the NPY gene showed associations to marbling (P < 0.001) as well as with ADG, BW, and feed conversion ratio (FCR; P < 0.05). The combination of these 3 SNP into haplotypes generally improved the association or had a similar scale of association as each single SNP. Only 1 SNP in UCP3, an A/G SNP in intron 3, was associated with ADG (P = 0.025), partial efficiency of growth, and FCR (P < 0.01). Three SNP in UCP2 gene were in almost complete linkage disequilibrium and showed associations with lean meat yield, yield grade, DMI, and BW (P < 0.05). Haplo-types between the SNP in UCP3 and UCP2 generally reduced the associations seen individually in each SNP. An A/G SNP in the GHRL gene tended to show effects on residual feed intake, FCR, and partial efficiency of growth (P < 0.10). The IGF2 SNP most strongly affected LM area (P < 0.01), back fat, ADG, and FCR (P < 0.05). The SNP in the CART, MC4R, POMC, GH, and CRH genes did not show associations at P < 0.05 with any of the traits. Although most of the SNP that showed associations do not cause amino acid changes, these SNP could be linked to other yet to be detected causative mutations or nearby QTL. It will be very important to verify these results in other cattle populations.

Global gene expression patterns spanning 3T3-L1 preadipocyte differentiation

Adipogenesis is of significant relevance from an agricultural perspective. Traits such as subcutaneous fat thickness, marbling and waste fat are of substantial economic importance in animal production. In order to discover more about the genetic basis of this process, a study was undertaken to examine the changes that occur daily in global gene expression as 3T3-L1 cells differentiate from preadipocyte to adipocyte. Duplicate RNA samples were collected daily during the differentiation process and probed with the Affymetrix U74Av2 GeneChip® microarray to allow the time-course analysis of the gene expression profile in these differentiating cells. Self-organizing maps (SOM) clustering was performed to extract patterns of expression over the course of the experiment (day 0 to day 6). The clustering generated nine distinct expression patterns containing between 74 and 420 genes/ESTs. Functional clusters and important chronological changes in the expression of key genes and gene groups were identified. The pattern of expression observed for many genes not only confirmed what has been shown previously for the early stages of differentiation, but also expanded this pattern to cover the whole differentiation process thus giving a very comprehensive overview of patterns and changes in gene expression over the time course of adipocyte differentiation. Key words: Adipocyte differentiation, gene expression, SOM clustering