Biology subjects

Serra, D.

Publications and source records attributed to Serra, D..

6 recordsLinked to original sources

bioRxiv2026

An atlas of human histological diversity

Descriptions of tissues by histopathologists rest on verbal statements limited by quantitative inaccuracies and personal cognitive biases. Here we propose an unsupervised computational framework that transposes to histology the concepts and methods of RNA-seq gene expression analysis, setting histology on an unbiased quantitative ground. Leveraging this framework and the GTEx dataset, we built an atlas surveying the histological diversity of 40 organs from 946 non-diseased individuals and documenting 11,125,747 associations between 2,560 morphemes--the histological analogs of genes in our framework--and 9 layers of patho-clinical and multi-omic molecular data, providing a rich context to interpret histology. In contrast with the ideally healthy normal specimens depicted in histology textbooks, the atlas reveals the influence of age, sex, genetics and sub-clinical pathologies on tissue structures. For example, we report that female eccrine sweat glands are surrounded by more adipocytes than their male counterparts, and that distinct calcification-associated aorta morphemes are driven by either smoking or genetic polymorphisms. Cross-organ analyses also delineate the systemic histological impact of diabetes and other conditions and establish the power of blood gene expression to predict disease-related morphemes. The atlas is released as an interactive web resource aimed at researchers.

pathology↗

bioRxiv2024

FAST-STEM: A human pluripotent stem cell engineering toolkit for rapid design-build-test-learn development of human cell-based therapeutic devices

Very recent clinical advances in stem cell derived tissue replacement and gene therapy, in addition to the rise of artificial intelligence-aided scientific discovery, have placed the possibility of sophisticated human cell-based therapies firmly within reach. However, development of such cells and testing of their engineered gene circuit components, has proven highly challenging, due to the need for generating stable cell lines for each design-build-test-learn engineering cycle. Current approaches to generating stable human induced pluripotent stem cell (hiPSC) lines are highly time-consuming and suffer from lack of control, poor integration efficiency, and limited functionality. Validation in clinically relevant stem cell derived tissues is also broadly lacking. Such drawbacks are prohibitive to repeatably conducting cutting-edge stem cell engineering with broad application within a realistic timeframe and will not scale with the future of regenerative medicine. We have developed FAST-STEM (Facile Accelerated Stem-cell Transgene integration with SynBio Tunable Engineering Modes), a hPSC engineering platform that drastically reduces the time to generate differentiation ready stem cell lines from several weeks to 5 days, exhibiting a ~612-fold improvement in transgene integration rate over previous methodologies. Additional FAST-STEM innovations include: (i) rapid and highly efficient transgene integration; (ii) copy number control; (iii) simultaneous or consecutive integration of multiple gene cassettes; (iv) library screen capability. In addition to this unique functional versatility, platform transportability and broad use case for stem cell-engineering was confirmed by differentiation into eight different cell types across nine different laboratories. This platform dramatically lowers the bar for integration of synthetic biology with regenerative medicine, enabling experiments which were previously deemed logistically impossible, thus paving the way for sophisticated human cell device development.

bioengineering↗

bioRxiv2024

DEFICIENCY OF THE NUTRIENT SENSOR CPT1c IN SF1 NEURONS DISRUPTS THE ENDOCANNABINOID SYSTEM RESULTING IN COMPROMISED SATIETY AND FUEL SELECTION UPON FAT INTAKE

The SF1 neurons of the ventromedial hypothalamus (VMH) are pivotal in governing body weight and adiposity, particularly in response to a high-fat diet (HFD). Previous studies have shown that the activation of SF1 neurons induces satiety, increases energy expenditure, and promotes the preferential use of fats as energy substrate. Furthermore, SF1 neurons are necessary for recovering from insulin-induced hypoglycemia. Here we demonstrate the essential role of the nutritional sensor CPT1c in the activation of SF1 neurons by dietary fats. Mice deficient in CPT1C in SF1 neurons (SF1-CPT1c-KO) are unable to adjust their caloric intake during the initial exposure to a HFD. This is associated with an impaired metabolic transition in the liver, muscle, and adipose tissue, despite a normal response to a glucose or insulin challenge. During chronic HFD exposure, SF1-CPT1c-KO mice are more prone to obesity and glucose intolerance than controls. CPT1c deficiency in SF1 neurons also leads to alterations in hypothalamic endocannabinoid levels and their metabolism. Our findings posit CPT1C in SF1 neurons as a sensor for dietary fats, regulating satiety responses and nutrient partitioning likely through the modulation of the endocannabinoid system.

neuroscience↗

bioRxiv2023

A Flexible Transgene Integration Landing-Pad Toolkit in Human Induced Pluripotent Stem Cells Enables Facile Cellular Engineering, Gene Zygosity Control, and Parallel Transgene Integration

Development of a repeatable method for delivering transgene payloads to human induced pluripotent stem cells (hiPSCs) without risking unintended off-target effects is not fully realized. Yet, such methods are indispensable to fully unlocking the potential for applying synthetic biological approaches to regenerative medicine, delivering quantum impacts to cell-based therapeutics development. Here we present a toolkit for engineering hiPSCs centred on the development of two core landing-pad cell-lines, facilitating rapid high-efficiency delivery of transgenes to the AAVS1 safe-harbour locus using the Bxb1 large-serine recombinase. We developed two landing-pad cell lines expressing green and red fluorescent reporters respectively, both retaining stemness whilst fully capable of differentiation into all three germ layers. A fully selected hiPSC population can be isolated within 1-2 weeks after landing-pad recombinase-mediated cassette exchange. We demonstrate the capability for investigator-controlled homozygous or heterozygous transgene configurations in these cells. As such, the toolkit of vectors and protocols associated with this landing-pad hiPSC system has the potential to accelerate engineering workflows for researchers in a variety of disciplines.

synthetic biology↗

bioRxiv2020

Challenges in Undergraduate Synthetic Biology Training: Insights from a Canadian iGEM Student Perspective

The last two decades have seen vigorous activity in synthetic biology research and ever-increasing applications of synthetic biology technologies. However, pedagogical research on synthetic biology is scarce, especially when compared to some scientific and engineering disciplines. Within Canada, there are only three universities that formally teach synthetic biology programs; two of which are at the undergraduate level. Many Canadian undergraduate students are instead introduced to synthetic biology through participation in the annual International Genetically Engineered Machine (iGEM) competition where they work in design teams to conceive of and execute a synthetic biology project that they present at an international jamboree. We surveyed the Canadian landscape of synthetic biology education through the experience of students from the Canadian iGEM teams of 2019. Using a thematic codebook analysis, we gathered insights to generate recommendations that could empower future iGEM team operations and inform educators about best practices in teaching undergraduate synthetic biology.

scientific communication and education↗

bioRxiv2020

Renal tubule Cpt1a overexpression mitigates kidney fibrosis by restoring mitochondrial homeostasis

Chronic kidney disease (CKD) remains a major epidemiological, clinical and biomedical challenge. During CKD, renal tubular epithelial cells (TECs) suffer a persistent inflammatory and profibrotic response. Fatty acid oxidation (FAO), the main source of energy for TECs, is reduced in kidney fibrosis and contributes to its pathogenesis. To determine if FAO gain-of-function (FAO-GOF) could protect from fibrosis, we generated a conditional transgenic mouse model with overexpression of the fatty acid shuttling enzyme carnitine palmitoyl-transferase 1 A (CPT1A) in TECs. Cpt1a knock-in (CPT1A KI) mice subjected to three different models of renal fibrosis (unilateral ureteral obstruction, folic acid nephropathy-FAN and adenine induced nephrotoxicity) exhibited decreased expression of fibrotic markers, a blunted pro-inflammatory response and reduced epithelial cell damage and macrophage influx. Protection from fibrosis was also observed when Cpt1a overexpression was induced after FAN. FAO-GOF restituted oxidative metabolism and mitochondrial number and enhanced bioenergetics increasing palmitate oxidation and ATP levels, changes also recapitulated in TECs exposed to profibrotic stimuli. Studies in patients evidenced decreased CPT1 levels and increased accumulation of short and middle chain acyl-carnitines, reflecting impaired FAO in human CKD. We propose that strategies based on FAO-GOF may constitute powerful alternatives to combat fibrosis inherent to CKD. Graphical abstractOverexpression of CPT1A impedes tubular epithelial renal cell dedifferentiation and a pro-fibrotic phenotype by restoring mitochondrial metabolic bioenergetics. O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

biochemistry↗