Personalized medicine and proteomics: lessons from non-small cell lung cancer

Personalized medicine allows the selection of treatments best suited to an individual patient and disease phenotype. To implement personalized medicine, effective tests predictive of response to treatment or susceptibility to adverse events are needed, and to develop a personalized medicine test, both high quality samples and reliable data are required. We review key features of state-of-the-art proteomic profiling and introduce further analytic developments to build a proteomic toolkit for use in personalized medicine approaches. The combination of novel analytical approaches in proteomic data generation, alignment and comparison permit translation of identified biomarkers into practical assays. We further propose an expanded statistical analysis to understand the sources of variability between individuals in terms of both protein expression and clinical variables and utilize this understanding in a predictive test.     

Rat mutations cvd and hob with cerebellar malformations map to chromosome 2.

In this paper, we executed genome mapping and comparative mapping analyses for cvd and hob, autosomal recessive mutations with cerebellar vermis defect and cerebellar dysplasia in the rat. For the linkage analysis, we produced three sets of backcross progeny, (ACI x CVD)F(1) and (F344 x CVD)F(1) females crossed to a cvd homozygous male rat, and (HOB x WKY)F(1) males crossed to hob homozygous female rats. Analysis of the segregation patterns of simple sequence length polymorphism (SSLP) markers scanning the whole rat genome allowed the mapping of these autosomal recessive mutations to rat Chromosome (Chr) 2. The most likely gene order is D2Mgh12 - D2Rat86 - D2Mit15 - D2Rat185 - cvd - D2Rat66 - D2Mgh13, and D2Mit18 - Fga -D2Mit14 - D2Rat16 - hob - D2Mgh13. Crossing test between a proven cvd heterozygous and a hob heterozygous rats demonstrated their allelism. Furthermore, comparative mapping indicated the cvd locus corresponds to mouse chromosome 3 and a strong candidate gene Unc5h3, a causative gene for the rostral cerebellar malformation mouse, was implicated.     

Pyrazolo pyrimidine-type inhibitors of SRC family tyrosine kinases promote ovarian steroid-induced differentiation of human endometrial stromal cells in vitro

Reversible protein tyrosine phosphorylation, coordinately controlled by protein tyrosine kinases and phosphatases, is a critical element in signal transduction pathways regulating a wide variety of biological processes, including cell growth, differentiation, and tumorigenesis. We have previously reported that c-Src belonging to the Src family tyrosine kinase (SFK) becomes dephosphorylated at tyrosine 530 (Y530) and thereby activated during progestin-induced differentiation of human endometrial stromal cells (i.e., decidualization). In this study, to elucidate the role of decidual c-Src activation, we examined whether 4-amino-5-(4-methylphenyl)-7-(t-butyl)pyrazolo[3,4-d]pyrimidine (PP1) and 4-amino-5-(4-chlorophenyl)-7-(t-butyl)pyrazolo[3,4-d]pyrimidine (PP2), both potent and selective SFK inhibitors, affected the ovarian steroid-induced decidualization in vitro. Unexpectedly, PP1 paradoxically increased the kinase activity of decidual c-Src together with dephosphorylation of Y530 in the presence of ovarian steroids. Concomitantly, PP1 enhanced morphological and functional decidualization, as determined by induction of decidualization markers, such as insulin-like growth factor binding protein-1 and prolactin. PP2 also advanced decidualization along with up-regulation of the active form of c-Src whose Y-530 was dephosphorylated. In contrast to PP1 and PP2, herbimycin A, a tyrosine kinase inhibitor with less specificity for SFKs, showed little enhancing effect on the expression of both IGFBP-1 and active c-Src. These results suggest that SFKs, including c-Src, may play a significant role in stromal cell differentiation, providing a clue for a possible therapeutic strategy to modulate endometrial function by targeting signaling pathway(s) involving SFKs.     

Mitochondrial DNA haplogrouping of the brown bear,Ursus arctos (Carnivora: Ursidae) in Asia,based on a newly developed APLP analysis

Sequence analyses of the complete brown bear, Ursus arctos, mitochondrial DNA (mtDNA) genome have detected scattered single nucleotide polymorphisms (SNPs) that define distinct mtDNA haplogroups in phylogeographical studies. The degraded DNA in historical samples, such as stuffed or excavated specimens, however, is often not suitable for sequence analyses. To address this problem, we developed an amplified product length polymorphism (APLP) analysis for mtDNA‐haplogrouping U. arctos specimens by detecting haplogroup‐specific SNPs. We verified the validity and utility of this method by analysing up to 170‐year‐old skin samples from U. arctos specimens collected widely across continental Eurasia. We detected some of the same haplogroups as those occurring in eastern Hokkaido (Japan) and eastern Alaska in continental Eurasia (the Altai and the Caucasus). Our results show that U. arctos in eastern Hokkaido and eastern Alaska descended from a common ancestor in continental Eurasia, and suggest that U. arctos occupied several refugia in southern Asia during the Last Glacial Maximum. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 627–635.     

Evaluation of Polyethylene Glycol as a Water-soluble Marker: Absorption and Excretion of 14C-labeled Polyethylene Glycol in Rats

The absorbability of polyethylene glycol (PEG), a water-soluble nutritional marker, from the gastrointestinal tract of rat was examined using the [¹⁴C]-labeled compound ([¹⁴C]PEG) having a molecular weight of 4000. Intravenously injected [¹⁴C]PEG was readily excreted and recovered almost completely in the urine and neither hepatic nor renal uptake of the PEG was observed. Intragastrically administered [¹⁴C]PEG was eliminated in the urine with an average recovery of only 0.43 ± 0.13% (Mean ± S.D., n= 10) of the dose over 24 hr. From the gel column chromatographic profile of the radioactivity excreted in the urine after an oral dose, [¹⁴C]PEG was suggested to be absorbed in two forms, as an original form and as a low molecular weight component. The latter component might be the degraded product of PEG in the gastrointestinal tract. From these results it was confirmed that PEG with a molecular weight of 4000 is a satisfactory marker because of its low absorbability.     

Stress relaxation properties of the cell wall of tissue segments under different growth conditions

Stress-relaxation parameters were compared under different experimentalconditions using 5th internode segments of light-grown pea seedlingsand coleoptile segments of dark-grown Avena seedlings. The followingresults were obtained. 1. In a short incubation period at 25?C, IAA caused a decreasein the minimum relaxation time, To, of the epidermal cell wallof pea internodes when it induced elongation; the optimum concentrationof IAA for decreasing To was 10 mg/liter. 2. At all concentrations of IAA used, 0.1–1000 mg/liter,the relationship between the To value of the epidermal cellwall peeled from segments incubated for 2 hr and the subsequentelongation rate in 2–3 hr incubation was linear, indicatingthat the To value of the cell wall at a certain time regulatesthe rate of the following elongation. 3. When segments of pea epicotyls or Avena coleoptiles wereincubated in mannitol solution of various concentrations inthe presence and absence of IAA and then allowed to grow inthe absence of both mannitol and IAA, the segments extendeddifferently depending upon the mannitol concentration, whichwas less than 0.3 M, given during preincubation. 4. The T_o and b (relaxation rate, S/log t) values were smallerin the cell wall of segments which extended more, than in thosewhich extended less. In this case, 0.2 M mannitol solution wasmost effective, since it inhibited IAA-induced elongation duringpre-incubation and the segments thus incubated extended themost afterward. 5. Extensibility, mm/gr, seemed to parallel the elongation whichhad occurred during pre-incubation, indicating that this value,contrary to To, represented at least partly the result of elongation. From these results we concluded that the growth rate to followis regulated by the minimum stress relaxation time, To, andpossibly by the relaxation rate, b, of the cell wall beforeextension, and these parameters may represent certain biochemicalmodifications of the cell wall components needed for cell extension. (Received August 12, 1974; )     

Transfer of Pterosiphonia pumila Yendo to the genus Symphyocladia (Rhodomelaceae, Rhodophyta)

The red alga Pterosiphonia pumila Yendo (Rhodomelaceae, Ceramiales) has flattened thalli in which there is complete lateral fusion between branches and their parental axes during early stages of development, the laterals only becoming distally free in reproduc-tively mature plants. This results in a leaf-like organization distinct from that displayed by all other species of the genus Pterosiphonia, the members of which have terete to compressed axes that are congenitally fused along only a few (<4.5) proximal segments of the laterals. The organization of P. pumila is, thus, similar to that of species of the genus Symphyocladia, to which it is here transferred as Symphyoctadia pumila (Yendo) Uwai et Masuda, comb. nov. Symphyoctadia pumila is restricted to Japan and Korea and is distinguished from the other three described species of Symphyocladia by its small (<3 cm long) ecorticate thalli and complete lack of vegetative trichoblasts. Symphyoctadia pennata Okamura has a similar suite of characteristics, has been successfully cross-bred with S. pumila in laboratory culture and is, thus, placed in synonymy with S. pumila.     

Difference of pine ectomycorrhizal biomass in relation to forest conditions

In this study, two plots in a secondary and another two in planted Pinus densiflora stands were exposed to different forest treatments, and the ectomycorrhizal (EM) biomass and its ergosterol content was measured for a year. The unmanaged plot in the secondary stand had greater EM biomass than those in any other plots. Whereas understory cutting had less effect on EM biomass, litter and humus removal decreased pine EM biomass and its ergosterol content, suggesting that such forest treatment alters EM biomass and its structure.