Affinity proteomics led identification of vimentin as a potential biomarker in colon cancers: insights from serological screening and computational modelling

Proteomic analysis using multiplex affinity reagents is perhaps the most reliable strategy to capture differentially expressed proteins that are slightly or immensely modified. In addition to expressional variation, it is comprehensively evident that the immunogenicity of a protein can be a deciding factor for instigating an inflammation afflicted-carcinogenesis. Considering both these factors, a simple and systematic strategy was designed to capture the immunogenic cancer biomarkers from sera of colorectal cancer patients. The affinity reagent, in the form of an antibody repertoire against the secretome of the HT29 cell line was used to grade the sera samples on the basis of the degree of immuno-reactivity and to capture differentially expressed antigens from the patient sera. Following affinity based 2DE-MALDI-TOF; the proteins were identified as (1) soluble vimentin; and (2) TGF-beta-inhibited membrane-associated protein (PP16B), in colon cancer sera and (3) keratin, type II cytoskeletal protein in rectal cancer sera. Pathway reconstruction and protein-protein networking of identified proteins predicted only Vimentin to be physically and genetically engaged in close proximity with the most established colorectal cancer associated tumorigenic pathways. Furthermore, our findings suggest that a possible surface stoichiometric shift in the structure of protein could be due to mutations in the coding sequence of Vimentin that may elicit its enhanced secretion possibly due to protein-hyperphosphorylation. Of the three proteins identified, only Vimentin showed higher expression in sera of colon cancer patients alone. Thus, it could be argued that vimentin might help in predicting individuals at higher risk of developing colon cancers. Our data are therefore suggestive of using vimentin as an antigen for tumor vaccination in an autologous set-up for colon cancers.

Ecology, distribution mapping and conservation implications of four critically endangered endemic plants of Kashmir Himalaya

During the last few decades, human-driven activities have led to indiscriminate habitat destruction and exploitation of many plant species in Kashmir Himalaya. As a result, many species have become threatened and are struggling for survival. Of particular concern are the endemic and critically endangered species which have the highest risk of the extinction, hence warranting immediate conservation actions. Therefore the current study was carried out to understand the distribution, ecology and conservation implications of the four critically endangered endemic plants of Kashmir Himalaya. Habitat distribution modelling showed that the suitable potential areas for the species occurred from subalpine to alpine meadowlands with an elevational range of 1500-4600 m asl. The output of the MaxEnt model and field surveys have revealed that their highest potential distribution is in Panchari, Khrew, Ramnagar, Pahalgam, Gurez, Sonamarg, Gulmarg and Kishtwar forest ranges. Based on the field explorations and herbarium records, Saussurea costus (Falc.) Lipsch have 27 distribution areas, Gentiana kurroo Royle 18, Lilium polyphyllum D. Don 12 and Aconitum chasmanthum Stapf have 15. Precipitation of the driest month and annual mean temperature played an important role in the distribution of the studied species. The species started their lifecycle with the onset of the spring season, flowered in summer, fruit in autumn and senesce in the winter season. Under natural conditions, the number of days required for germination ranged from 180 to 210 where cold stratification played a pivotal role. Since last few decades, the populations of these species have been shrinking in their natural habitats due to over-exploitation for medicinal purposes and habitat destruction through amplified humanoid interferences like the expansion of agricultural land, road building, grazing and urbanization. Thus there is an urgent need to come up with positive strategies to save whatever is left and plan long term rescue measures not only to protect these species from extinction but also to reintroduce them along with framing the plans to supply sustained raw materials for medicine.

Comparative proteomics and global genome-wide expression data implicate role of ARMC8 in lung cancer

BACKGROUND

Cancer loci comprise heterogeneous cell populations with diverse cellular secretions. Therefore, disseminating cancer-specific or cancer-associated protein antigens from tissue lysates could only be marginally correct, if otherwise not validated against precise standards.

MATERIALS AND METHODS

In this study, 2DE proteomic profiles were examined from lysates of 13 lung-adenocarcinoma tissue samples and matched against the A549 cell line proteome. A549 matched-cancer-specific hits were analyzed and characterized by MALDI-TOF/MS.

RESULTS

Comparative analysis identified a total of 13 protein spots with differential expression. These proteins were found to be involved in critical cellular functions regulating pyrimidine metabolism, pentose phosphate pathway and integrin signaling. Gene ontology based analysis classified majority of protein hits responsible for metabolic processes. Among these, only a single non-predictive protein spot was found to be a cancer cell specific hit, identified as Armadillo repeat-containing protein 8 (ARMC8). Pathway reconstruction studies showed that ARMC8 lies at the centre of cancer metabolic pathways.

CONCLUSIONS

The findings in this report are suggestive of a regulatory role of ARMC8 in control of proliferation and differentiation in lung adenocarcinomas.

Effect of plant growth regulators on in vitro induction and maintenance of callus from leaf and root explants of Atropa acuminata Royal ex Lindl

Atropa acuminata, an important medicinal plant belonging to family Solanaceae is under tremendous threat of extinction in its natural habitat due to the overexploitation by pharmaceutical industries. Present study is an attempt of establishing callus cultures of this important medicinal plant as callus has considerable potential as an alternative for production of secondary metabolites for industrial use, hence reducing pressure on natural populations. Callus cultures were established from leaf and root explants of Atropa acuminate. Murashige and Skoog (MS) media containing different concentration and combinations of 6-Benzyl Amino Purine (BAP), Naphthalene Acetic Acid (NAA), Kinetin (Kn) and 2,4- Dichloropheoxyacetic acid (2,4- D) were used for callus induction. Different phytohormonal combinations resulted in different types and degrees of callus. The combination of BAP and NAA on MS media supplemented with 0.5 mg/l BAP in combination with 1.0 mg/l NAA, was found to be the most efficient for in vitro callus development from root explants and from leaf explants most effective combination and concentration was 1 mg/l of both BAP and NAA. The maximum mean fresh weight of callus formed using root explants was 33.13 mg per explant and maximum fresh weight obtained from leaf explants was 22.14 mg per explants.

Chemical-induced variations in callus regenerated Atropa acuminata plants: A study on Ethyl Methanesulfonate effects

Atropa acuminata Royle ex Lindl. a member of the solanaceae family is a critically endangered medicinal herb indigenous to the Himalayan region of Kashmir and revered for its therapeutic and economic significance. Ethyl Methanesulfonate (EMS), a chemical mutagen, is commonly used to induce mutations for plant breeding and research purposes. In this study, callus cultures derived from leaf explants of A. acuminata were cultivated on Murashige and Skoog (MS) medium supplemented with Thidiazuron (0.1 mg/l) and treated with varying concentrations of EMS (0.1%, 1.0%) over defined time intervals. The impact of EMS concentrations and exposure durations, as well as their interactions, on the characteristics of regenerated callus were rigorously examined. The proliferation of shoots exhibited a diminishing trend with escalating EMS concentrations. Additionally, EMS elicited substantial alterations in the morphological and physiological attributes of the regenerated plants. Among the fifteen traits evaluated, mutant lines designated as M10, M11, and M6 displayed the most pronounced variations in morphological and physiological parameters compared to the control. Notably, the mutant line M10 exhibited significantly elevated shoot dry weight, root fresh weight, chlorophyll, and carotenoid contents demonstrating up to 98%, 31%, 348%, and 642% enhancements respectively as compared to the control. These mutant lines hold promise for further exploitation in augmenting physiological characteristics and enhancing the yield and quality of terpene glycosides in A. acuminata.