In the past fifty years, research into vascular biology has dramatically changed the previously established perspectives on endothelial cells (ECs). For a long time, these cells were considered to form a passive layer that contributes to the separation of blood from tissues and allows small molecules to cross the vascular wall. Recently, ECs that line both blood and lymphatic vessels have been shown to exhibit active and fundamental functions that are often tissue-specific; profoundly influence organ function during development, as characterized by the physiological roles of organs, such as the brain, lung, kidney, liver, bone, and spleen; and contribute to tissue responses under pathological conditions, such as metabolic disorders, infections, degenerative diseases, and inflammatory injuries (Geiger, 2019). These highly diverse contributions of ECs to organ function in physiology and pathology rely on the heterogeneity these cells display at both the morphological and molecular levels.

Organ-specific ECs contribute to the distinct physiological functions of each tissue and its response to pathological hits and aging, often leading to inflammation, fibrosis, altered metabolism, and regeneration in an organ-specific way. The diverse pathological responses of organs to the same noxae rely on programmed paracrine circuits established between ECs and neighboring cells. ECs produce organ-specific angiocrine substances, which participate in a paracrine or juxtacrine fashion to affect tissue behavior and cell fitness (Butler, Kobayashi, & Rafii, 2010; Ding et al., 2010; Kusumbe, Ramasamy, & Adams, 2014; Pasquier et al., 2020).

In addition to the morphological differences between arterial, venous, and lymphatic ECs, which are mainly conditioned via blood flow and shear stress (Nerem, Levesque, & Cornhill, 1981), capillary blood ECs acquire four different phenotypes: (i) continuous endothelium ECs are connected by tight junctions, are the basis for continuous basement membranes, and are characteristic of arteries and veins and the vasculature of the nervous system, skeletal muscle, skin, heart and lung; (ii) ECs in the fenestrated endothelium are characterized by transcellular holes in the cytosol that may be traversed by a thin diaphragm in the kidneys, endocrine organs, and the choroid plexus; (iii) the ECs in discontinuous endothelium form, intracellular gaps and a fragmented basement membrane are found in the liver, spleen, and bone marrow; and (iv) ECs in endothelium of high endothelial venules in lymph nodes and tertiary lymphatic structures are cuboidal and form a thick basal membrane (Aird, 2007a, Aird, 2007b; Augustin & Koh, 2017; Hennigs, Matuszcak, Trepel, & Körbelin, 2021; Sørensen, Simon-Santamaria, McCuskey, & Smedsrød, 2015). In contrast to blood ECs, lymphatic ECs form an interrupted basement membrane, overlapping intercellular junctions, and are not covered by pericytes (Pepper & Skobe, 2003) (Fig. 1).

However, EC heterogeneity is not only a tissue trait; in contrast, it is evident within certain organs (Gomez-Salinero, Itkin, & Rafii, 2021; Koch, Lee, Goerdt, & Augustin, 2021). For example, the renal parenchyma is a paradigm of morphological intra-organotypic vascular heterogeneic ECs. In the kidney, fenestrated endothelium with (peritubular endothelium, ECs of ascending vasa recta) or without diaphragms (glomerular ECs) and continuous ECs (descending vasa recta, large vessels) exist (Molema & Aird, 2012; Stolz & Sims-Lucas, 2015).

These morphological differences reflect specialized physiological organ functions mainly associated with transport mechanisms. For instance, fenestration favors the exchange of water and small solutes, for example, in gastrointestinal or peritubular renal capillaries; in discontinuous fenestrated tissue, which acts as a sieve that allows proteins and, in some cases, blood cells to pass through the capillary wall; and in continuous endothelium, which allows only the movement of small molecules, such as gases, water, glucose, and certain hormones, and in the brain, this limited exchange is instrumental in halting the passage of circulating toxins (Geiger, 2019).

EC heterogeneity is evident not only in a morphological context but also in the different molecular functions of ECs. For instance, arterial ECs express many anticoagulant factors, while ECs in veins show both anticoagulant and procoagulant activity (Marcu et al., 2018). In addition, ephrin (EPH)B2 and its EPH receptor B4 (EPHB4) mark arterial and venous ECs, respectively, and their cell-specific distribution is required for the correct formation of the vascular tree (Gerety, Wang, Chen, & Anderson, 1999; Wang, Chen, & Anderson, 1998). In another example, Brain ECs express sodium-dependent lysophosphatidylcholine symporter 1, which blocks endothelial transcytosis, contributing to blood-brain barrier (BBB) function (Ben-Zvi et al., 2014). Moreover, many EC markers, such as CD31, von Willebrand factor, prostacyclin, and endothelial nitric oxide synthase, are heterogeneously expressed (Clark & Fuchs, 1997; Heaps, Bray, McIntosh, & Schroeder, 2019; Pusztaszeri, Seelentag, & Bosman, 2006). Furthermore, leukocyte transmigration preferentially proceeds via ECs in postcapillary venules (Aird, 2012), and EC subsets show different motogenic and mitogenic properties (Hobson & Denekamp, 1984; K. Jiang, Pichol-Thievend, Neufeld, & Francois, 2021).

The molecular mechanisms involved in EC heterogeneity and their adaptability to homeostatic changes require tissue-specific angiogenic inducers and angiocrine molecules, epigenetic changes, and regulation of specific transcriptional landscapes. This review briefly summarizes the function of paracrine and juxtacrine mechanisms (2 Organ vascularization is regulated by specific angiogenic inducers and pathways, 3 Angiocrine molecules), referring to previously published outstanding reviews for details (Augustin & Koh, 2017; Gomez-Salinero et al., 2021; Hennigs et al., 2021; Koch et al., 2021; Rafii, Butler, & Ding, 2016), and focuses on analyzing transcriptional mechanisms supporting EC heterogeneity and its impact on the most important roles played by ECs in pathophysiology processes (4 Differentiated genetic programs contribute to EC plasticity and heterogeneity, 5 Lessons from single-cell transcriptomic analysis, 6 The regulation of the endothelial transcriptional network). Because this review takes into account information from different animal species, we decided to always use gene symbols in capital for simplicity.