Proteomics analysis of rough endoplasmic reticulum in pancreatic beta cells

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/111127/1/pmic8033.pd

Spatiotemporal genomic analysis reveals distinct molecular features in recurrent stage I non-small cell lung cancers

Stage I non-small cell lung cancer (NSCLC) presents diverse outcomes. To identify molecular features leading to tumor recurrence in early-stage NSCLC, we perform multiregional whole-exome sequencing (WES), RNA sequencing, and plasma-targeted circulating tumor DNA (ctDNA) detection analysis between recurrent and recurrent-free stage I NSCLC patients (CHN-P cohort) who had undergone R0 resection with a median 5-year follow-up time. Integrated analysis indicates that the multidimensional clinical and genomic model can stratify the prognosis of stage I NSCLC in both CHN-P and EUR-T cohorts and correlates with positive pre-surgical deep next generation sequencing (NGS) ctDNA detection. Increased genomic instability related to DNA interstrand crosslinks and double-strand break repair processes is significantly associated with early tumor relapse. This study reveals important molecular insights into stage I NSCLC and may inform clinical postoperative treatment and follow-up strategies

YY1 directly interacts with myocardin to repress the triad myocardin/SRF/CArG box-mediated smooth muscle gene transcription during smooth muscle phenotypic modulation

Yin Yang 1 (YY1) regulates gene transcription in a variety of biological processes. In this study, we aim to determine the role of YY1 in vascular smooth muscle cell (VSMC) phenotypic modulation both in vivo and in vitro. Here we show that vascular injury in rodent carotid arteries induces YY1 expression along with reduced expression of smooth muscle differentiation markers in the carotids. Consistent with this finding, YY1 expression is induced in differentiated VSMCs in response to serum stimulation. To determine the underlying molecular mechanisms, we found that YY1 suppresses the transcription of CArG box-dependent SMC-specific genes including SM22α, SMα-actin and SMMHC. Interestingly, YY1 suppresses the transcriptional activity of the SM22α promoter by hindering the binding of serum response factor (SRF) to the proximal CArG box. YY1 also suppresses the transcription and the transactivation of myocardin (MYOCD), a master regulator for SMC-specific gene transcription by binding to SRF to form the MYOCD/SRF/CArG box triad (known as the ternary complex). Mechanistically, YY1 directly interacts with MYOCD to competitively displace MYOCD from SRF. This is the first evidence showing that YY1 inhibits SMC differentiation by directly targeting MYOCD. These findings provide new mechanistic insights into the regulatory mechanisms that govern SMC phenotypic modulation in the pathogenesis of vascular diseases

Modified carbon fabric electrodes: preparation and electrochemical behavior toward amaranth electrolysis

The final publication is available at Springer via http://dx.doi.org/10.1007/s10800-014-0769-9The electrochemical behavior of non-modified, Pt-modified, and Pt/polyaniline-modified carbon fiber textile electrodes was studied through a series of electrolyses, under potentiostatic conditions, on an amaranth/sulfuric solution in the presence or absence of chloride ion. The morphology of the dispersed Pt, PANI, and PANI/Pt coatings was analyzed by scanning electron microscopy. Scanning electrochemical microscopy confirmed that the textile surface was effectively modified by the electrocatalytic material. Color removal reached values above 90 % in both electroreduction and electrooxidation processes. The amaranth electroreductions carried out with the non-modified electrode showed better charge efficiency than those with the Pt-modified textile electrode. The electrooxidations with Pt-modified textile electrodes showed a significant reduction in electrolysis time. Ultraviolet-visible and Fourier transform infrared with attenuated total reflection spectra enabled the electrochemical behavior of the non-modified and Pt/PANI-modified electrodes to be distinguished.The authors wish to acknowledge to the Spanish Ministerio de Ciencia e Innovacion (contract CTM2011-23583) and Universitat Politecnica de Valencia (Vicerrectorado de Investigacion PAID-06-10 contract 003-233) for the financial support; and as well as Carbongen S. A. (Cocentaina, Spain), who kindly donated the activated carbon fabric. J. Molina is grateful to the Conselleria d'Educacio, Formacio i Ocupacio (Generalitat Valenciana) for the Programa VALi+D Postdoctoral Fellowship. A.I. del Rio is grateful to the Spanish Ministerio de Ciencia y Tecnologia for the FPI fellowship.Fernández Sáez, J.; Del Río García, AI.; Molina Puerto, J.; Bonastre Cano, JA.; Cases Iborra, FJ. (2015). Modified carbon fabric electrodes: preparation and electrochemical behavior toward amaranth electrolysis. Journal of Applied Electrochemistry. 45(3):263-272. https://doi.org/10.1007/s10800-014-0769-9S263272453Marsh H, Reinoso FR (2000) Sciences of carbon materials. Universidad de Alicante, AlicanteKinoshita K (1998) Carbon: electrochemical and physicochemical properties. Wiley, New York, pp 293–387Burchell TD (1999) Carbon materials for advances technologies. Pergamon, AmsterdamDomínguez SD, Pardilla JA, Murcia AB, Morallón E, Amorós DC (2008) Electrochemical deposition of Pt nanoparticles on different carbon supports and conducting polymers. J Appl Electrochem 38:259–268Kezhong W, Xu M, Xindong W, Jingling L (2005) Pt–Polyaniline-modified carbon fiber electrode for the electrooxidation of methanol. Rare Met 24:33–36Wu G, Li L, Li JH, Xu BQ (2006) Methanol electrooxidation on Pt particles dispersed into PANI/SWNT composite films. J Power Sources 155:118–127Singh RN, Awasthi R, Tiwari SK (2010) Electro-catalytic activities of binary nano-composites of Pt and nano-carbon/multiwall carbon nanotube for methanol electro-electrooxidation. Open Catal J 3:50–57Zhiani M, Rezaei B, Jalili J (2010) Methanol electro-electrooxidation on Pt/C modified by polyaniline nanofibers for DMFC applications. Int J Hydrogen Energ 35:9298–9305Laborde H, Léger J-M, Lamy C (1994) Electrocatalytic electrooxidation of methanol and C1 molecules on highly dispersed electrodes. Part 1: Pt in polyaniline. J Appl Electrochem 24:219–226Niu L, Li Q, Wei F, Wu S, Liu P, Cao X (2005) Electrocatalytic behaviour of Pt-modified polyaniline electrode for methanol electrooxidation: effect of Pt deposition modes. J Electroanal Chem 578:331–337Huang LM, Tang WR, Wen TCh (2007) Spatially electrodeposited Pt in polyaniline doped with poly(styrene sulfonic acid) for methanol electrooxidation. J Power Sources 164:519–526Fernández J, Molina J, del Río AI, Bonastre J, Cases FJ (2012) Synthesis and characterization of electrochemically platinum–polyaniline modified carbon textile electrodes. Int J Electrochem Sci 7:10175–10189Snehalatha M, Ravikumar C, Sekar N, Jayakumar SV, Joe H (2008) FT–Raman, IR and UV–visible spectral investigations and ab initio computations of a nonlinear food dye amaranth. J Raman Spectrosc 39:928–936Rajendran L, Ananthi SP (2004) Analysis of positive feedback currents at the scanning electrochemical microscope. J Electroanal Chem 561:113–118Niu L, Li Q, Wei F, Chen X, Wang W (2003) Formation optimization of Pt-modified polyaniline films for the electrocatalytic electrooxidation of methanol. Synthetic Met 139:271–276Sala M, del Río AI, Molina J, Cases F, Gutierrez-Bouzán MC (2012) Influence of cell design and electrode materials on the decoloration of dyeing effluents. Int J Electrochem Sc 7:12470–12488Priyantha N, Malavipathirana S (1996) Effect of chloride ions on the electrochemical behavior of platinum surfaces. J Natn Sci Coun Sri Lanka 24:237–246Rajeev J, Nidhi Sh, Keisham R (2009) Electrochemical treatment of pharmaceutical azo dye amaranth from waste water. J Appl Electochem 39:577–582Nadupalli S, Koorbanally N, Jonnalagadda SB (2011) Kinetics and mechanism of the oxidation of amaranth with hypochlorite. J Phys Chem A 115:7948–795

From endoplasmic-reticulum stress to the inflammatory response

The endoplasmic reticulum is responsible for much of a cell's protein synthesis and folding, but it also has an important role in sensing cellular stress. Recently, it has been shown that the endoplasmic reticulum mediates a specific set of intracellular signalling pathways in response to the accumulation of unfolded or misfolded proteins, and these pathways are collectively known as the unfolded-protein response. New observations suggest that the unfolded-protein response can initiate inflammation, and the coupling of these responses in specialized cells and tissues is now thought to be fundamental in the pathogenesis of inflammatory diseases. The knowledge gained from this emerging field will aid in the development of therapies for modulating cellular stress and inflammation.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62741/1/nature07203.pd

Unfolded protein response in cancer: the Physician's perspective

The unfolded protein response (UPR) is a cascade of intracellular stress signaling events in response to an accumulation of unfolded or misfolded proteins in the lumen of the endoplasmic reticulum (ER). Cancer cells are often exposed to hypoxia, nutrient starvation, oxidative stress and other metabolic dysregulation that cause ER stress and activation of the UPR. Depending on the duration and degree of ER stress, the UPR can provide either survival signals by activating adaptive and antiapoptotic pathways, or death signals by inducing cell death programs. Sustained induction or repression of UPR pharmacologically may thus have beneficial and therapeutic effects against cancer. In this review, we discuss the basic mechanisms of UPR and highlight the importance of UPR in cancer biology. We also update the UPR-targeted cancer therapeutics currently in clinical trials

The evolution of lung cancer and impact of subclonal selection in TRACERx

Lung cancer is the leading cause of cancer-associated mortality worldwide. Here we analysed 1,644 tumour regions sampled at surgery or during follow-up from the first 421 patients with non-small cell lung cancer prospectively enrolled into the TRACERx study. This project aims to decipher lung cancer evolution and address the primary study endpoint: determining the relationship between intratumour heterogeneity and clinical outcome. In lung adenocarcinoma, mutations in 22 out of 40 common cancer genes were under significant subclonal selection, including classical tumour initiators such as TP53 and KRAS. We defined evolutionary dependencies between drivers, mutational processes and whole genome doubling (WGD) events. Despite patients having a history of smoking, 8% of lung adenocarcinomas lacked evidence of tobacco-induced mutagenesis. These tumours also had similar detection rates for EGFR mutations and for RET, ROS1, ALK and MET oncogenic isoforms compared with tumours in never-smokers, which suggests that they have a similar aetiology and pathogenesis. Large subclonal expansions were associated with positive subclonal selection. Patients with tumours harbouring recent subclonal expansions, on the terminus of a phylogenetic branch, had significantly shorter disease-free survival. Subclonal WGD was detected in 19% of tumours, and 10% of tumours harboured multiple subclonal WGDs in parallel. Subclonal, but not truncal, WGD was associated with shorter disease-free survival. Copy number heterogeneity was associated with extrathoracic relapse within 1 year after surgery. These data demonstrate the importance of clonal expansion, WGD and copy number instability in determining the timing and patterns of relapse in non-small cell lung cancer and provide a comprehensive clinical cancer evolutionary data resource

The evolution of non-small cell lung cancer metastases in TRACERx

Metastatic disease is responsible for the majority of cancer-related deaths. We report the longitudinal evolutionary analysis of 126 non-small cell lung cancer (NSCLC) tumours from 421 prospectively recruited patients in TRACERx who developed metastatic disease, compared with a control cohort of 144 non-metastatic tumours. In 25% of cases, metastases diverged early, before the last clonal sweep in the primary tumour, and early divergence was enriched for patients who were smokers at the time of initial diagnosis. Simulations suggested that early metastatic divergence more frequently occurred at smaller tumour diameters (less than 8 mm). Single-region primary tumour sampling resulted in 83% of late divergence cases being misclassified as early, highlighting the importance of extensive primary tumour sampling. Polyclonal dissemination, which was associated with extrathoracic disease recurrence, was found in 32% of cases. Primary lymph node disease contributed to metastatic relapse in less than 20% of cases, representing a hallmark of metastatic potential rather than a route to subsequent recurrences/disease progression. Metastasis-seeding subclones exhibited subclonal expansions within primary tumours, probably reflecting positive selection. Our findings highlight the importance of selection in metastatic clone evolution within untreated primary tumours, the distinction between monoclonal versus polyclonal seeding in dictating site of recurrence, the limitations of current radiological screening approaches for early diverging tumours and the need to develop strategies to target metastasis-seeding subclones before relapse

Genomic–transcriptomic evolution in lung cancer and metastasis

Intratumour heterogeneity (ITH) fuels lung cancer evolution, which leads to immune evasion and resistance to therapy. Here, using paired whole-exome and RNA sequencing data, we investigate intratumour transcriptomic diversity in 354 non-small cell lung cancer tumours from 347 out of the first 421 patients prospectively recruited into the TRACERx study. Analyses of 947 tumour regions, representing both primary and metastatic disease, alongside 96 tumour-adjacent normal tissue samples implicate the transcriptome as a major source of phenotypic variation. Gene expression levels and ITH relate to patterns of positive and negative selection during tumour evolution. We observe frequent copy number-independent allele-specific expression that is linked to epigenomic dysfunction. Allele-specific expression can also result in genomic–transcriptomic parallel evolution, which converges on cancer gene disruption. We extract signatures of RNA single-base substitutions and link their aetiology to the activity of the RNA-editing enzymes ADAR and APOBEC3A, thereby revealing otherwise undetected ongoing APOBEC activity in tumours. Characterizing the transcriptomes of primary–metastatic tumour pairs, we combine multiple machine-learning approaches that leverage genomic and transcriptomic variables to link metastasis-seeding potential to the evolutionary context of mutations and increased proliferation within primary tumour regions. These results highlight the interplay between the genome and transcriptome in influencing ITH, lung cancer evolution and metastasis

Antibodies against endogenous retroviruses promote lung cancer immunotherapy

B cells are frequently found in the margins of solid tumours as organized follicles in ectopic lymphoid organs called tertiary lymphoid structures (TLS). Although TLS have been found to correlate with improved patient survival and response to immune checkpoint blockade (ICB), the underlying mechanisms of this association remain elusive. Here we investigate lung-resident B cell responses in patients from the TRACERx 421 (Tracking Non-Small-Cell Lung Cancer Evolution Through Therapy) and other lung cancer cohorts, and in a recently established immunogenic mouse model for lung adenocarcinoma. We find that both human and mouse lung adenocarcinomas elicit local germinal centre responses and tumour-binding antibodies, and further identify endogenous retrovirus (ERV) envelope glycoproteins as a dominant anti-tumour antibody target. ERV-targeting B cell responses are amplified by ICB in both humans and mice, and by targeted inhibition of KRAS(G12C) in the mouse model. ERV-reactive antibodies exert anti-tumour activity that extends survival in the mouse model, and ERV expression predicts the outcome of ICB in human lung adenocarcinoma. Finally, we find that effective immunotherapy in the mouse model requires CXCL13-dependent TLS formation. Conversely, therapeutic CXCL13 treatment potentiates anti-tumour immunity and synergizes with ICB. Our findings provide a possible mechanistic basis for the association of TLS with immunotherapy response