Biology subjects

Regnier, P.

Publications and source records attributed to Regnier, P..

3 recordsLinked to original sources

bioRxiv2024

Application of the AMOCATI R workflow to tumor transcriptomic data delineates the adverse effect of immune cell infiltration in immune-privileged organs

Immune cells are present inside tumor tissue and can alter tumor growth. Expression profiles of human tumors hold transcripts from cancer cells and their microenvironment, including the infiltrating immune cells. Few standardized methods examine tumor immunobiology relying only on tumor transcriptome data. Using a new in-house developed R analysis workflow called AMOCATI, we classified 43 cancer types from 11,176 patients according to the degree of infiltration by 18 distinct immune cell subsets, measured by the abundance of their transcriptomic signature, and calculated its effect on the disease outcome. In about half of cancers affecting organs without immune privilege, immune cell infiltration has beneficial effects. In contrast, immune infiltration in cancers of immune-privileged organs (eye, testis and brain) confers poor prognosis. Moreover, transcriptional evidence of increased immune cell activity in immune-privileged cancer sites is associated with bad prognosis. Thus, our results suggest that the effect of immune infiltration may depend on the origin of the primary tumor. SIGNIFICANCEOur in-house developed computational R approach AMOCATI allows to easily download public transcriptomic and clinical data, classify and analyze them. AMOCATI permitted us to define gene expression signatures associated with short- or long-term survival from 11,176 untreated patient unsorted biopsies in 43 types of cancer. We present the level of infiltration of 18 types of immune cell subsets transcriptomic signatures and 50 immune-related pathways in all these cancers Correlation between immune infiltration of the tumor and survival establishes a link between tumor tissue of origin and the overall effect of immune infiltration on survival. Immune cell infiltration in tumors from immune privileged organs correlate with shorter survival. Contrary to what we observe in hot tumors, biological pathways of immune response are associated with a short-term survival profile in these cancers.

cancer biology↗

bioRxiv2023

Tissue-resident uterine regulatory T cells support fetal growth

Regulatory T cells (Tregs) are known to contribute to successful allogeneic pregnancy by promoting maternal-fetal tolerance. Here, phenotypic studies and parabionts identified a population of uterine tissue-resident Tregs (uTregs) with trophic functions in the non-pregnant mouse endometrium. Phenotypically, uTregs are CD25-/lo and they present characteristic phenotypic attributes of tissue-resident memory T cells with effector functions. Transcriptionally, uTregs are distinguishable from other peripheral or tissue-resident Tregs by their expression of genes related to extracellular matrix remodeling and vasculogenesis, and they express a polyclonal T cell receptor (TCR) repertoire. Pregnancy triggers the expansion of uTregs, which remain CD25-/lo, retain their polyclonal TCR repertoire, and increase the expression of genes involved in regulation of hypoxia and vasculogenesis. Functionally, we show that uTregs support the proliferation of primary uterine microvascular endothelial cells in vitro and that a specific depletion of uTregs in pregnant mice leads to fetal intra-uterine growth retardation (IUGR). Thus, a previously unidentified population of CD25-/lo uTregs promotes uterine tissue remodeling before and during pregnancy, and contributes to fetal growth.

immunology↗

bioRxiv2017

Components Of Alcohol Use And All-Cause Mortality

ImportanceCurrent recommendations for low-risk drinking are based on drinking quantity: up to one drink daily for women and two drinks daily for men. Drinking frequency has not been independently examined for its contribution to mortality.\n\nObjectiveTo evaluate the impact of drinking frequency on all-cause mortality after adjusting for drinks per day and binge drinking behavior.\n\nDesignTwo independent observational studies with self-reported alcohol use and subsequent all-cause mortality: the National Health Interview Survey (NHIS), and data from Veterans Health Administration clinics (VA).\n\nSettingEpidemiological sample (NHIS) and VA outpatient database (VA Corporate Data Warehouse).\n\nParticipants208,661 individuals from the NHIS interviewed between 1997 and 2009 at the age of 30 to 70 with mortality follow-up in the last quarter of 2011; 75,515 VA outpatients born between 1948 and 1968 who completed an alcohol survey in 2008 with mortality follow-up in June 2016.\n\nExposuresQuantity of alcohol use when not binging (1-2 drinks on typical day, 3-4 drinks on typical day), frequency of non-binge drinking (never, weekly or less, 2-3 times weekly, 4 or more times weekly), and frequency of binge drinking (never, less than weekly, 1-3 times weekly, 4 or more times weekly). Covariates included age, sex, race, and comorbidity.\n\nMain Outcomes and MeasuresAll-cause mortality.\n\nResultsAfter adjusting for binge drinking behavior, survival analysis showed an increased risk for all-cause mortality among people who typically drink 1-2 drinks four or more times weekly, relative to people who typically drink 1-2 drinks at a time weekly or less (NHIS dataset HR=1.15, 95% CI 1.06-1.26; VA dataset HR=1.31, 95% CI 1.15-1.49).\n\nConclusions and RelevanceDrinking four or more times weekly increased risk of all-cause mortality, even among those who drank only 1 or 2 drinks daily. This was seen in both a large epidemiological database and a large hospital-based database, suggesting that the results can be generalized.

epidemiology↗