Cell Types

Neurons are electrically excitable cells that transmit information through electrochemical signals across synapses. As the principal functional units of the nervous system, they integrate synaptic inputs and relay outputs via axons to other neurons, muscles, or glands. Neuronal subtypes differ widely in morphology, neurotransmitter identity, connectivity, and firing properties.

Neural progenitor cells are mitotically active precursors that generate neurons and glial cells during nervous system development and, in restricted niches such as the subventricular zone and the hippocampal dentate gyrus, in the adult brain. They balance self-renewal and differentiation through tightly regulated signaling pathways. Their decline with age is associated with reduced neurogenesis.

Enteric glial cells (EGCs) are the resident glia of the enteric nervous system (ENS), the "gut brain." They resemble CNS astrocytes and are integral to gastrointestinal homeostasis. EGCs support enteric neurons, regulate intestinal barrier integrity, modulate immune responses within the gut wall, and influence motility. Their dysfunction is implicated in inflammatory bowel diseases (IBD), infections, and functional GI disorders, highlighting their role beyond mere structural support.

Enteric neurons are the functional units of the enteric nervous system (ENS), a complex network embedded in the gastrointestinal wall. They autonomously control gut functions including motility, secretion, blood flow, and immune responses. Comprising sensory neurons, interneurons, and motor neurons, they use diverse neurotransmitters (ACh, serotonin, NO, etc.). This "second brain" operates independently but communicates bidirectionally with the central nervous system.

Melanocytes are neural crest-derived cells located in the basal layer of the epidermis and in hair follicles. Their primary function is the production of melanin, a pigment that provides color to skin and hair and protects underlying cells from UV radiation damage. Melanin is synthesized in organelles called melanosomes, which are then transferred to neighboring keratinocytes via dendritic processes.

B cells are lymphocytes responsible for the humoral arm of the adaptive immune response. They develop in the bone marrow and, upon maturation, circulate in blood and lymph. When activated by antigen (often with T cell help), they proliferate and differentiate into antibody-secreting plasma cells or long-lived memory B cells. Their antibodies neutralize pathogens, opsonize them for phagocytosis, and activate the complement system.

Kupffer cells are specialized tissue-resident macrophages located within the sinusoids of the liver. They are the largest population of fixed macrophages in the body. They phagocytose pathogens, toxins, cellular debris, and aged red blood cells from the portal blood flow. They play crucial roles in liver immunity, iron recycling, lipid metabolism, and maintaining overall hepatic homeostasis. Their activation can contribute to liver inflammation and fibrosis.

Macrophages are large, phagocytic cells of the innate immune system present in all tissues (where they have specific names like Kupffer cells, microglia). They derive from blood monocytes or local progenitors. They engulf and destroy pathogens and dead cells, secrete cytokines and chemokines to regulate inflammation, present antigens, and are key players in tissue repair, remodeling, and homeostasis. They exhibit remarkable functional plasticity (M1/M2 spectra).

Monocytes are circulating white blood cells (agranulocytes) that serve as precursors for macrophages and dendritic cells. Produced in the bone marrow, they patrol the bloodstream for several days before migrating into tissues in response to inflammatory signals. In tissues, they differentiate into macrophages or dendritic cells. In blood, they can phagocytose pathogens and present antigens, acting as a bridge between innate and adaptive immunity.

Plasma B cells (or plasma cells) are the terminal, fully differentiated effector state of activated B lymphocytes. They are antibody factories, specializing in the massive secretion of antibodies of a single specificity. They possess extensive endoplasmic reticulum and a prominent Golgi apparatus to support high-rate protein synthesis. Most are short-lived, but some become long-lived plasma cells that reside in the bone marrow, providing sustained antibody levels.

T cells (T lymphocytes) are central players in cell-mediated adaptive immunity. They develop in the thymus and express T cell receptors (TCRs) that recognize peptide antigens presented by MHC molecules. Major subsets include: Helper T cells (CD4+, which secrete cytokines to help B cells and macrophages), Cytotoxic T cells (CD8+, which kill infected/cancerous cells), and Regulatory T cells (Tregs, which suppress immune responses to prevent autoimmunity).

T/NKT cells encompass T lymphocyte populations together with natural killer T (NKT) cells, which recognize lipid antigens presented by the non-polymorphic CD1d molecule. NKT cells bridge innate and adaptive immunity by rapidly releasing large amounts of cytokines upon activation. They are implicated in tumor surveillance, autoimmunity, and antimicrobial responses.

Pancreatic islet (islets of Langerhans) cells are the endocrine cells of the pancreas, organized into clusters scattered throughout the exocrine tissue. Major types include: Alpha cells (secrete glucagon, raises blood sugar), Beta cells (secrete insulin, lowers blood sugar), Delta cells (secrete somatostatin, inhibits other islet cells), and PP cells (secrete pancreatic polypeptide). They precisely regulate glucose homeostasis.

Alveolar type 1 (AT1) cells are thin, squamous epithelial cells that cover approximately 95% of the gas exchange surface in the lung alveoli. Their extremely flattened morphology (extending over large areas) is ideal for the passive diffusion of oxygen and carbon dioxide between the airspace and the underlying pulmonary capillaries. They are terminally differentiated and crucial for maintaining the delicate blood-air barrier.

Alveolar type 2 (AT2) cells are cuboidal epithelial cells found in the alveolar corners. They have three critical functions: (1) They synthesize and secrete pulmonary surfactant, a phospholipid-protein mixture that reduces surface tension and prevents alveolar collapse. (2) They serve as progenitor cells for both AT1 and AT2 cells, repairing the alveolar epithelium after injury. (3) They contribute to innate immune defense in the alveoli.

Cells of the thick ascending limb (TAL) of the loop of Henle in the kidney nephron. They are impermeable to water but actively reabsorb sodium, potassium, and chloride via the Na-K-2Cl cotransporter (NKCC2) on their apical membrane. This transport is critical for generating the hypertonic medullary interstitium necessary for water reabsorption in the collecting duct. They also contribute to magnesium and calcium reabsorption.

Basal cells are a layer of mitotically active epithelial progenitor/stem cells found attached to the basement membrane in stratified and pseudostratified epithelia (e.g., skin, airways, prostate). They divide to give rise to cells that differentiate and move upward to replenish the superficial layers. In the airway, they are major stem cells capable of regenerating both ciliated and secretory cells after injury.

Cholangiocytes are the epithelial cells that line the intrahepatic and extrahepatic bile ducts. They modify the composition of bile (through secretion and absorption of water, ions, and bicarbonate), form a protective barrier, and respond to hormonal signals. They express receptors and channels (e.g., CFTR) critical for bile flow. Their proliferation and dysfunction are central to cholangiopathies like primary sclerosing cholangitis (PSC).

Ciliated cells are epithelial cells characterized by the presence of motile cilia (hair-like projections) on their apical surface. They are found in the respiratory tract, oviducts, and ventricles of the brain (ependymal cells). Coordinated, rhythmic beating of cilia moves fluid or mucus over the epithelial surface. In the airways, this "mucociliary escalator" traps and propels inhaled particles and pathogens out of the lungs, a key defense mechanism.

This refers to basal cells (e.g., in skin, prostate, or airways) that are actively progressing through the cell cycle (in S, G2, or M phase). This label often comes from single-cell RNA sequencing data, indicating a transient state of proliferation. These cells are crucial for tissue turnover and regeneration, as they represent the active stem/progenitor pool that is dividing to produce new differentiated cells.

A broad categorization for any epithelial cell (from various tissues) that is captured in an active phase of the cell cycle. This label is used in genomic datasets to distinguish proliferating cells from quiescent or terminally differentiated ones. It highlights the dynamic nature of epithelia, where constant renewal and repair are driven by these cycling populations.

Enterocytes are the principal absorptive columnar epithelial cells lining the small intestine villi. Their apical surface is covered with microvilli, forming a "brush border" that dramatically increases surface area for nutrient absorption. They digest and absorb carbohydrates, peptides, amino acids, and lipids. They also secrete water and ions and form a crucial barrier between the gut lumen and the internal environment.

In the thyroid gland, follicular cells (thyrocytes) are the principal epithelial cells that form spherical follicles. They synthesize thyroglobulin and, upon stimulation by TSH, take up iodine to produce the thyroid hormones thyroxine (T4) and triiodothyronine (T3), which are stored in the colloid-filled follicle lumen and released into the blood to regulate metabolism, growth, and development.

Hepatocytes are the principal parenchymal cells of the liver, making up about 80% of its mass. They are metabolic powerhouses with functions including: protein synthesis (albumin, clotting factors), bile production, detoxification and metabolism of drugs/toxins, glycogen storage and glucose homeostasis, lipid metabolism, and cholesterol synthesis. They are arranged in plates radiating from central veins, with polarized faces facing sinusoids and bile canaliculi.

Pancreatic ductal cells form the lining of the ductal network that transports digestive enzymes from the acini and bicarbonate-rich fluid from the centroacinar cells to the duodenum. They modify the pancreatic juice by secreting bicarbonate ions (HCO3-) to neutralize gastric acid. They express CFTR, and mutations here cause cystic fibrosis-related pancreatic disease. They can also act as progenitor cells in certain contexts.

Parietal cells (or oxyntic cells) are found in the gastric glands of the stomach lining. They secrete hydrochloric acid (HCl) into the stomach lumen, creating the highly acidic environment necessary for protein digestion and killing ingested microbes. They also secrete intrinsic factor, a glycoprotein essential for vitamin B12 absorption in the ileum. They have a distinctive intracellular canaliculus system for acid secretion.

Podocytes are highly specialized epithelial cells in the Bowman's capsule of the kidney glomerulus. They wrap around capillaries with primary and secondary foot processes. The slits between these foot processes, covered by the slit diaphragm, form the final filtration barrier preventing proteins from entering the urine. Podocyte injury or loss leads to proteinuria and glomerular diseases like focal segmental glomerulosclerosis (FSGS).

In the kidney's collecting duct, principal cells are the most abundant cell type. They are responsible for the final regulation of water, sodium, and potassium balance. They express aquaporin-2 channels on their apical membrane (inserted in response to vasopressin/ADH) for water reabsorption. They also reabsorb sodium via ENaC channels and secrete potassium, processes regulated by aldosterone.

These cells line the proximal convoluted tubule (PCT) of the nephron, the first and longest segment. They are responsible for the bulk reabsorption of filtered nutrients (glucose, amino acids), ions (sodium, chloride, bicarbonate), and water (~65%). Their apical surface has a dense brush border of microvilli to increase surface area. They also actively secrete organic acids and bases into the filtrate.

Serous cells are protein-secreting epithelial cells found in exocrine glands like the salivary glands (parotid) and pancreatic acini. Their secretory granules contain enzymes (e.g., amylase in saliva, digestive enzymes in pancreas). The granules often stain darkly with H&E. They typically have a round nucleus and basophilic cytoplasm due to abundant rough ER for protein synthesis.

Urothelial cells (transitional epithelial cells) line the urinary tract from renal pelvis to urethra. They form a distensible, impermeable barrier. The superficial umbrella cells have a unique apical plaque of uroplakin proteins and can change shape (from cuboidal to squamous) as the bladder fills and stretches, preventing urine from leaking into underlying tissues. This epithelium also protects against toxic substances in urine.

Peritubular myoid cells are smooth muscle-like cells that surround the seminiferous tubules in the testes. They contract rhythmically to help move sperm and testicular fluid through the tubules. They also secrete extracellular matrix components and growth factors, providing structural support and contributing to the microenvironment necessary for spermatogenesis within the tubules.

Sertoli cells are the "nurse" or sustentacular cells within the seminiferous tubules of the testes. They create the blood-testis barrier, provide structural and nutritional support to developing sperm cells (spermatogenesis), phagocytose residual bodies, and secrete fluid, androgen-binding protein (ABP), and hormones like inhibin and anti-Müllerian hormone (AMH). They are essential for male fertility.

Ovarian surface epithelial cells (Epithelial cells) in species SP037. Single-cell UMAP atlas.

Adipocytes (fat cells) are the primary cells of adipose tissue, specialized in storing energy as triglycerides within a large, single lipid droplet (white adipocytes) or in dissipating energy as heat via uncoupling protein 1 (UCP1) in numerous smaller droplets (brown/beige adipocytes). White adipocytes also secrete hormones (leptin, adiponectin) and cytokines, making adipose tissue an important endocrine organ involved in metabolism and inflammation.

Fibroblasts are the most common cells of connective tissue. They synthesize and secrete the extracellular matrix (ECM) components, including collagen, elastin, and fibronectin, providing structural and biochemical support to surrounding cells. They are key players in wound healing, where they proliferate, migrate to the injury site, and differentiate into contractile myofibroblasts to close wounds. They also communicate with immune and epithelial cells.

In the liver, hepatic stellate cells (HSCs) reside in the space of Disse. In their quiescent state, they store vitamin A. Upon liver injury, they activate, proliferate, and transform into myofibroblast-like cells that produce large amounts of extracellular matrix, driving liver fibrosis and cirrhosis. Pancreatic stellate cells play a similar fibrogenic role in pancreatitis and pancreatic cancer.

Stromal cells in human. 101,901 cells across 16 tissues.

Cardiomyocytes are the striated muscle cells that constitute the cardiac muscle of the heart. They are responsible for generating the contractile force that pumps blood. They are connected end-to-end by intercalated discs containing gap junctions for electrical coupling and desmosomes for mechanical attachment. Unlike skeletal muscle, they are mononucleated or binucleated and have intrinsic automaticity (pacemaker cells).

Skeletal myonuclei are the multiple nuclei contained within a single, multinucleated skeletal muscle fiber (myofiber). They are post-mitotic and are responsible for gene expression to maintain the massive cytoplasmic volume of the myofiber. They are evenly distributed, but in some muscle types, they may be clustered near the neuromuscular junction or myotendinous junction.

Smooth muscle cells (SMCs) are involuntary, non-striated muscle cells found in the walls of hollow organs (e.g., blood vessels, gut, bladder, uterus). They are spindle-shaped with a single central nucleus. They contract slowly and can maintain tension for long periods (tonus). Contraction is regulated by the autonomic nervous system, hormones, and local factors (e.g., nitric oxide, endothelin).

Endothelial cells form a single layer (the endothelium) lining the interior surface of all blood and lymphatic vessels. They are more than a passive barrier; they actively regulate vascular tone, blood clotting (hemostasis), inflammation, immune cell trafficking, and angiogenesis. They produce key molecules like nitric oxide (vasodilation), endothelin-1 (vasoconstriction), and von Willebrand factor. Dysfunction is central to cardiovascular diseases.

Spermatocytes are developing male germ cells that undergo meiosis. Primary spermatocytes (diploid, 4N DNA) result from spermatogonial mitosis. They undergo Meiosis I to form two secondary spermatocytes (haploid, 2N DNA). Secondary spermatocytes rapidly undergo Meiosis II to produce four spermatids (haploid, 1N DNA). This process occurs within the seminiferous tubules, supported by Sertoli cells.

Spermatogonia are the undifferentiated germ stem cells located on the basement membrane of the seminiferous tubules. They undergo mitotic divisions to self-renew and produce a population of cells committed to differentiation (primary spermatocytes). Type A spermatogonia are the stem cell reservoir, while Type B spermatogonia are committed progenitors. They are the foundation of lifelong sperm production.

Intercalated cells are specialized cells found in the collecting ducts of the kidney nephron. They are critical for regulating systemic acid-base balance. There are two main types: Type A (alpha) cells secrete protons (H+) via H+-ATPase pumps and reabsorb bicarbonate, correcting acidosis. Type B (beta) cells secrete bicarbonate and reabsorb protons, correcting alkalosis. They also play a role in potassium balance.

Mesothelial cells form a monolayer (the mesothelium) that lines the body's serous cavities (pleural, pericardial, peritoneal) and covers the outer surface of internal organs. They produce a lubricating serous fluid that allows organs to move smoothly. They also provide a protective barrier, participate in immune surveillance and inflammation, and can undergo transition to a fibroblast-like phenotype (mesothelial-to-mesenchymal transition) in pathology.

Proliferating cells (Other) in species SP037. Single-cell UMAP atlas.

Cycling cells are cells actively progressing through the cell cycle (G1, S, G2, and M phases), typically identified by expression of proliferation markers such as MKI67 and TOP2A. In single-cell atlases they represent a transient proliferative state rather than a fixed lineage and can arise from multiple progenitor or stem cell populations within a tissue. Their abundance reflects the turnover and regenerative activity of the tissue sampled.