Reverse transcription-quantitative polymerase chain reaction: description of a RIN-based algorithm for accurate data normalization

<p>Abstract</p> <p>Background</p> <p>Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is the gold standard technique for mRNA quantification, but appropriate normalization is required to obtain reliable data. Normalization to accurately quantitated RNA has been proposed as the most reliable method for in vivo biopsies. However, this approach does not correct differences in RNA integrity.</p> <p>Results</p> <p>In this study, we evaluated the effect of RNA degradation on the quantification of the relative expression of nine genes (<it>18S</it>, <it>ACTB</it>, <it>ATUB</it>, <it>B2M</it>, <it>GAPDH</it>, <it>HPRT</it>, <it>POLR2L</it>, <it>PSMB6</it> and <it>RPLP0</it>) that cover a wide expression spectrum. Our results show that RNA degradation could introduce up to 100% error in gene expression measurements when RT-qPCR data were normalized to total RNA. To achieve greater resolution of small differences in transcript levels in degraded samples, we improved this normalization method by developing a corrective algorithm that compensates for the loss of RNA integrity. This approach allowed us to achieve higher accuracy, since the average error for quantitative measurements was reduced to 8%. Finally, we applied our normalization strategy to the quantification of <it>EGFR</it>, <it>HER2 </it>and <it>HER3 </it>in 104 rectal cancer biopsies. Taken together, our data show that normalization of gene expression measurements by taking into account also RNA degradation allows much more reliable sample comparison.</p> <p>Conclusion</p> <p>We developed a new normalization method of RT-qPCR data that compensates for loss of RNA integrity and therefore allows accurate gene expression quantification in human biopsies.</p

Combined cetuximab and trastuzumab are superior to gemcitabine in the treatment of human pancreatic carcinoma xenografts

Background: Pancreatic carcinoma remains a treatment-refractory cancer with a poor prognosis. Here, we compared anti-epidermal growth factor receptor (EGFR) and anti-HER2 monoclonal antibodies (2mAbs) injections with standard gemcitabine treatment on human pancreatic carcinoma xenografts. Materials and methods: Nude mice, bearing human pancreatic carcinoma xenografts, were treated with either combined anti-EGFR (cetuximab) and anti-HER2 (trastuzumab) or gemcitabine, and tumor growth was observed. Results and conclusion: In first-line therapy, mice survival was significantly longer in the 2mAbs group compared with gemcitabine (P < 0.0001 for BxPC-3, P = 0.0679 for MiaPaCa-2 and P = 0.0019 for Capan-1) and with controls (P < 0.0001). In second-line therapy, tumor regressions were observed after replacing gemcitabine by 2mAbs treatment, resulting in significantly longer animal survival compared with mice receiving continuous gemcitabine injections (P = 0.008 for BxPC-3, P = 0.05 for MiaPaCa-2 and P < 0.001 for Capan-1). Therapeutic benefit of 2mAbs was observed despite K-Ras mutation. Interestingly, concerning the mechanism of action, coinjection of F(ab′)2 fragments from 2mAbs induced significant tumor growth inhibition, compared with controls (P = 0.001), indicating that the 2mAbs had an Fc fragment-independent direct action on tumor cells. This preclinical study demonstrated a significant improvement of survival and tumor regression in mice treated with anti-EGFR/anti-HER2 2mAbs in first- and second-line treatments, compared with gemcitabine, independently of the K-Ras statu

The photometric observation of the quasi-simultaneous mutual eclipse and occultation between Europa and Ganymede on 22 August 2021

Mutual events (MEs) are eclipses and occultations among planetary natural satellites. Most of the time, eclipses and occultations occur separately. However, the same satellite pair will exhibit an eclipse and an occultation quasi-simultaneously under particular orbital configurations. This kind of rare event is termed as a quasi-simultaneous mutual event (QSME). During the 2021 campaign of mutual events of jovian satellites, we observed a QSME between Europa and Ganymede. The present study aims to describe and study the event in detail. We observed the QSME with a CCD camera attached to a 300-mm telescope at the Hong Kong Space Museum Sai Kung iObservatory. We obtained the combined flux of Europa and Ganymede from aperture photometry. A geometric model was developed to explain the light curve observed. Our results are compared with theoretical predictions (O-C). We found that our simple geometric model can explain the QSME fairly accurately, and the QSME light curve is a superposition of the light curves of an eclipse and an occultation. Notably, the observed flux drops are within 2.6% of the theoretical predictions. The size of the event central time O-Cs ranges from -14.4 to 43.2 s. Both O-Cs of flux drop and timing are comparable to other studies adopting more complicated models. Given the event rarity, model simplicity and accuracy, we encourage more observations and analysis on QSMEs to improve Solar System ephemerides.Comment: 23 pages, 5 appendixes, 16 figures, 7 table

Expression of Foxp3 in colorectal cancer but not in Treg cells correlates with disease progression in patients with colorectal cancer

Background: Regulatory T cells (Treg) expressing the transcription factor forkhead-box protein P3 (Foxp3) have been identified to counteract anti-tumor immune responses during tumor progression. Besides, Foxp3 presentation by cancer cells itself may also allow them to evade from effector T-cell responses, resulting in a survival benefit of the tumor. For colorectal cancer (CRC) the clinical relevance of Foxp3 has not been evaluated in detail. Therefore the aim of this study was to study its impact in colorectal cancer (CRC). Methods and Findings: Gene and protein analysis of tumor tissues from patients with CRC was performed to quantify the expression of Foxp3 in tumor infiltrating Treg and colon cancer cells. The results were correlated with clinicopathological parameters and patients overall survival. Serial morphological analysis demonstrated Foxp3 to be expressed in cancer cells. High Foxp3 expression of the cancer cells was associated with poor prognosis compared to patients with low Foxp3 expression. In contrast, low and high Foxp3 level in tumor infiltrating Treg cells demonstrated no significant differences in overall patient survival. Conclusions: Our findings strongly suggest that Foxp3 expression mediated by cancer cells rather than by Treg cells contribute to disease progression

Prophétiser la ville. Sociologie d’un champ urbain réformateur aux prises avec la « smart city »

By focusing on non-institutional spaces dealing with the question of the “smart city”, this PhD dissertation examines the mechanisms for establishing a desirable urban future and the modalities of its implementation by non-state actors. Through two main cases, an urban prospective think tank and a group of specialized journalists within a general media, it considers the work of these intermediaries of urban reform. They animate spaces made possible by private funding but in which we observe forms of independence, spaces that embody the relative porosity of the borders between public and private. Overall, they work to produce a forward-looking vision of the urban fabric, which is partly based on digital and technological tools but does not subscribe to the discourses of the economy of promise, promoted in particular by large technology firms. On the contrary, they produce and disseminate a vision of urban planning and management in competition with the one promoted by companies of the digital economy.By retracing the movements in the social space of the controversies surrounding the “smart city”, and by focusing on interstitial spaces at the border between the public and the private sectors, between economy, journalism, academia and politics, this research overall traces a process of qualification and disqualification of knowledge, know-how, and actors likely to participate in the production of a legitimate vision of the “city of tomorrow”, and, more broadly, actors who should participate in the government of this city.En s’intéressant à des espaces non-institutionnels saisis de la question de la « smart city », cette thèse interroge les mécanismes de fixation d’un futur urbain souhaitable et les modalités de sa mise en œuvre par des acteurs extérieurs à l’État. À partir de deux principaux cas, un think tank de prospective urbaine et un groupe de journalistes spécialisés au sein d’un média généraliste, elle invite à considérer le travail de ces intermédiaires de la réforme urbaine. Ces derniers, qui animent des espaces dans lesquels s’incarnent la relative porosité des frontières entre public et privé, œuvrent à produire une vision prospective de la fabrique urbaine. Celle-ci repose en partie sur des outils numériques et technologiques sans pour autant souscrire aux discours de l’économie de la promesse, promus notamment par les grandes firmes technologiques. Ils contribuent au contraire à produire et à diffuser une vision de l’aménagement et de la gestion urbaine en concurrence avec celle que promeuvent les entreprises de l’économie numérique.En retraçant les déplacements dans l’espace social des controverses entourant la « smart city », puis en se focalisant sur des espaces interstitiels à la frontière du public et du privé, de l’économie, du journalisme, de l’universitaire et du politique, cette recherche retrace dans l’ensemble un processus de qualification et de disqualification des savoirs et des acteurs susceptibles de participer à la production d’une vision légitime de la « ville de demain » et, plus largement, à même de participer à son gouvernement

Concilier contraintes économiques et indépendance : un journalisme à la frontière de la profession

International audienc

Prophétiser la ville. Sociologie d’un champ urbain réformateur aux prises avec la « smart city »

By focusing on non-institutional spaces dealing with the question of the “smart city”, this PhD dissertation examines the mechanisms for establishing a desirable urban future and the modalities of its implementation by non-state actors. Through two main cases, an urban prospective think tank and a group of specialized journalists within a general media, it considers the work of these intermediaries of urban reform. They animate spaces made possible by private funding but in which we observe forms of independence, spaces that embody the relative porosity of the borders between public and private. Overall, they work to produce a forward-looking vision of the urban fabric, which is partly based on digital and technological tools but does not subscribe to the discourses of the economy of promise, promoted in particular by large technology firms. On the contrary, they produce and disseminate a vision of urban planning and management in competition with the one promoted by companies of the digital economy.By retracing the movements in the social space of the controversies surrounding the “smart city”, and by focusing on interstitial spaces at the border between the public and the private sectors, between economy, journalism, academia and politics, this research overall traces a process of qualification and disqualification of knowledge, know-how, and actors likely to participate in the production of a legitimate vision of the “city of tomorrow”, and, more broadly, actors who should participate in the government of this city.En s’intéressant à des espaces non-institutionnels saisis de la question de la « smart city », cette thèse interroge les mécanismes de fixation d’un futur urbain souhaitable et les modalités de sa mise en œuvre par des acteurs extérieurs à l’État. À partir de deux principaux cas, un think tank de prospective urbaine et un groupe de journalistes spécialisés au sein d’un média généraliste, elle invite à considérer le travail de ces intermédiaires de la réforme urbaine. Ces derniers, qui animent des espaces dans lesquels s’incarnent la relative porosité des frontières entre public et privé, œuvrent à produire une vision prospective de la fabrique urbaine. Celle-ci repose en partie sur des outils numériques et technologiques sans pour autant souscrire aux discours de l’économie de la promesse, promus notamment par les grandes firmes technologiques. Ils contribuent au contraire à produire et à diffuser une vision de l’aménagement et de la gestion urbaine en concurrence avec celle que promeuvent les entreprises de l’économie numérique.En retraçant les déplacements dans l’espace social des controverses entourant la « smart city », puis en se focalisant sur des espaces interstitiels à la frontière du public et du privé, de l’économie, du journalisme, de l’universitaire et du politique, cette recherche retrace dans l’ensemble un processus de qualification et de disqualification des savoirs et des acteurs susceptibles de participer à la production d’une vision légitime de la « ville de demain » et, plus largement, à même de participer à son gouvernement

Prophétiser la ville. Sociologie d’un champ urbain réformateur aux prises avec la « smart city »

By focusing on non-institutional spaces dealing with the question of the “smart city”, this PhD dissertation examines the mechanisms for establishing a desirable urban future and the modalities of its implementation by non-state actors. Through two main cases, an urban prospective think tank and a group of specialized journalists within a general media, it considers the work of these intermediaries of urban reform. They animate spaces made possible by private funding but in which we observe forms of independence, spaces that embody the relative porosity of the borders between public and private. Overall, they work to produce a forward-looking vision of the urban fabric, which is partly based on digital and technological tools but does not subscribe to the discourses of the economy of promise, promoted in particular by large technology firms. On the contrary, they produce and disseminate a vision of urban planning and management in competition with the one promoted by companies of the digital economy.By retracing the movements in the social space of the controversies surrounding the “smart city”, and by focusing on interstitial spaces at the border between the public and the private sectors, between economy, journalism, academia and politics, this research overall traces a process of qualification and disqualification of knowledge, know-how, and actors likely to participate in the production of a legitimate vision of the “city of tomorrow”, and, more broadly, actors who should participate in the government of this city.En s’intéressant à des espaces non-institutionnels saisis de la question de la « smart city », cette thèse interroge les mécanismes de fixation d’un futur urbain souhaitable et les modalités de sa mise en œuvre par des acteurs extérieurs à l’État. À partir de deux principaux cas, un think tank de prospective urbaine et un groupe de journalistes spécialisés au sein d’un média généraliste, elle invite à considérer le travail de ces intermédiaires de la réforme urbaine. Ces derniers, qui animent des espaces dans lesquels s’incarnent la relative porosité des frontières entre public et privé, œuvrent à produire une vision prospective de la fabrique urbaine. Celle-ci repose en partie sur des outils numériques et technologiques sans pour autant souscrire aux discours de l’économie de la promesse, promus notamment par les grandes firmes technologiques. Ils contribuent au contraire à produire et à diffuser une vision de l’aménagement et de la gestion urbaine en concurrence avec celle que promeuvent les entreprises de l’économie numérique.En retraçant les déplacements dans l’espace social des controverses entourant la « smart city », puis en se focalisant sur des espaces interstitiels à la frontière du public et du privé, de l’économie, du journalisme, de l’universitaire et du politique, cette recherche retrace dans l’ensemble un processus de qualification et de disqualification des savoirs et des acteurs susceptibles de participer à la production d’une vision légitime de la « ville de demain » et, plus largement, à même de participer à son gouvernement