Inflammatory diseases of the central nervous system (CNS) remain enigmatic, largely because we have an incomplete understanding of how immune surveillance is coordinated between the brain and peripheral immune tissues. Recent work has challenged the notion that the brain is immune-privileged, introducing mechanisms by which antigens, immune cells, and waste traffic bidirectionally between the CNS and peripheral immune tissues. Bridging the brain and periphery are the glymphatic and meningeal lymphatic networks. A recently elucidated “glymphatic” system clears cerebrospinal fluid (CSF) and brain-parenchyma-derived solutes. This efflux subsequently enters meningeal lymphatic vessels and, to a lesser extent in humans than in other animals, nasal mucosal lymphatics and other drainage pathways. The meningeal lymphatic system is recognized as a pathway not just for waste movement, but also for the egress of immune cells from the central nervous system, after which these cells can function as messengers to the periphery. Much of this waste ultimately drains to the cervical lymph nodes. The deep cervical lymph nodes (dcLNs) are of particular interest due to their ability to respond to CNS antigens and mount responses within the CNS (1–4). The so-called efferent arm of the immune response also exists whereby lymphocytes can migrate from the periphery into the CNS and influence brain function (3, 5–7). Disruption along these pathways can occur because of inflammatory signals, aging, poor sleep quality, and alterations in vascular health, among other factors.

In this review, we synthesize current knowledge on the anatomy, physiology, and immune functions of the glymphatic system, meningeal lymphatic system, and other exit routes, as well as highlight how cervical lymph node analysis might help to reshape neuroinflammatory disease management. Our interest in lymph node analysis, however, is exploratory, and cannot currently inform therapeutic decision making in patients. Nevertheless, we draw from emerging evidence in animal models as well as in humans to demonstrate how the use of imaging, immunophenotyping, and targeted interventions could potentially influence clinical decision making in human neuroinflammatory processes.

In most tissues of the body, lymphatic vessels are the primary means by which excess fluid, proteins, and other metabolic by-products are eliminated. Since the brain’s parenchyma is devoid of conventional lymphatic vessels, waste was believed to diffuse passively into CSF-filled ventricles (8). In 2012, however, two-photon imaging of anesthetized mice revealed that the brain has an intricate system of waste clearance (9). Rather than a traditional lymphatic system, the CNS relies on a highly organized clearance mechanism that operates through glial water channels—the glymphatic system (10). This system has since been demonstrated in both mice and humans.

The glymphatic system channels CSF through specialized spaces surrounding blood vessels, called perivascular spaces. As arteries and veins course from the subarachnoid space into the brain’s parenchyma, they are first enclosed by an extension of the pia mater, forming CSF-filled perivascular spaces, known as Virchow-Robin spaces (11). These spaces around penetrating vessels are bordered externally by astrocytic endfeet. Astrocytic endfeet regulate the blood-brain barrier (BBB) and facilitate the exchange of substances between blood and brain parenchyma. As vessels venture further into the parenchyma, the perivascular space progressively narrows and is no longer discernible at the capillary level. Instead, it tightens into a basal lamina, which is porous and minimally resistant to CSF flow (11). The entry of CSF into the parenchyma is mediated directly by aquaporin-4 (AQP4) channels expressed on the astrocytic endfeet of the perivascular spaces; the channels are influenced by noradrenergic tone: reduced adrenergic signaling during sleep enhances glymphatic drainage (9, 12).

CSF that has exited the perivascular space through AQP4 channels mixes with intraparenchymal interstitial fluid (ISF), which contains diverse waste products (8). This mixing generates a directed flow, known as a vectorial convective flux (Figure 1). The movement of CSF and ISF depends largely on cerebral arterial pulsation. Mouse studies in particular have found that modifying blood pressure can increase backflow and reduce net flow in perivascular space (13), while ligating the carotid artery can reduce pulsatility and slow the rate of CSF-ISF exchange (14). This directed flow leaves the parenchyma through AQP4 channels via the astrocytic endfeet of perivenous spaces (9, 15). Tracer studies in rodents have demonstrated that 40-80% of large proteins and other solutes in extracellular space can be removed by vectorial convective flux (9).

As waste is conveyed along the perivenous spaces, it may exit the brain through several pathways, many of which remain the subject of ongoing investigation in animal studies (16–18). These routes include exit via skull foramina along cranial nerves; transport through the cribriform plate to the lymphatic channels of the nasal mucosa (19, 20); egress via dural lymphatics that course alongside the dural venous sinuses and middle meningeal arteries; and passage through the arachnoid villi of the dural venous sinuses for absorption into the bloodstream. The last possibility is still debated in humans, due to the lack of arachnoid granulations in childhood and in some adults (21, 22). Transit may also occur through the calvarial bone marrow via dura-skull channels, after which the CSF’s fate is undetermined (23, 24). Animal studies suggest that roughly 50% of CSF tracers drain into extracranial lymph, with most of the rest entering the bloodstream (25–27). Eventually, waste products transported through the lymphatic system and bloodstream converge in the liver, where they are degraded.

Several factors can influence CSF flow and fluid flux from brain to the periphery via the glymphatic system, which is predominantly active at night (28). The first, and most important, is sleep. The interstitial space, where the CSF-ISF exchange or interchange occurs, enlarges by 60% during sleep. CSF flux is the highest during slow-wave sleep in mice, while studies in humans show that sleep deprivation impairs molecular clearance (29, 30). During slow-wave deep sleep, there is a reduction in CNS noradrenergic tone and an increase in the ISF volume fraction (31). A cocktail of norepinephrine receptor antagonists in awake mice increases CSF influx almost to the level seen in sleeping mice (30). Glymphatic function is also highly active in anesthetized mice, indicating that sleep versus wakefulness, not circadian rhythm per se, regulates egress via the glymphatic system (11, 32). Finally, the lateral sleep position is better for glymphatic clearance as compared to the supine or prone positions in mice, and very early work suggests the same may hold true for humans (28, 33). The dependence of glymphatic clearance on modifiable factors like sleep, body position during sleep, and vascular health suggests that many neurodegenerative diseases could be at least in part affected by optimization of these physiological parameters.

Clearance through the glymphatic system slows with age. Contributing mechanisms include decreased vessel-wall pulsatility, loss of AQP4 channel expression, and altered polarization of AQP4 along astrocytic endfeet (34, 35). A decrease of up to 80-90% in glymphatic activity has been observed in old compared to young mice (11). AQP4 channels upregulate with sleep fragmentation in younger animals but downregulate in older animals (36).

Other modifiable factors have been shown to impact glymphatic clearance in mice as well: omega-3 polyunsaturated fatty acids, physical activity, and small amounts of alcohol exert a positive impact, while chronic stress and arterial hypertension exert a negative effect (37). Both acute and chronic inflammation, whether from systemic insults or within the CNS itself, can impact glymphatic function and CSF flow. Solutes from the glymphatic system ultimately exit along various lymphatic routes, which we discuss next.

In the setting of injury and disease in the CNS, antigens from the brain, various metabolites, and damage-associated molecular patterns (DAMPs) trigger an innate and adaptive immune response both within the CNS and in peripheral lymphoid organs (43). When human serum albumin was injected into the CSF of rats, it led to antigen-specific antibody production within cervical lymph nodes (55). Cervical lymph nodes are thus proposed to serve as hubs connecting CNS inflammation with peripheral immune responses. Many therapies focus on immune cell infiltration into the CNS and target tissue migration to minimize immune-mediated damage (22).

Research indicates that peripheral immune cells enter the CNS. Dendritic cells (DCs), a professional antigen-presenting cell (APC) type, have been shown to migrate into the CNS along several chemokine gradients (22). B-cell receptor (BCR) repertoire sequencing in MS patients has shown that clonally expanded B cells in the CNS likely have origins in dcLNs due to degree of clonal expansion (7). Studies of neutrophils in mice have shown that some neutrophils and monocytes in the mLVs come from cranial and vertebral marrow, not the blood, before subsequently infiltrating the brain’s parenchyma (56).

T cells can also infiltrate the CNS. For T cells to traverse the blood-brain barrier (BBB), the BBB must express inflammation-induced adhesion molecules that mediate transendothelial migration, a process that increases in pathological conditions (57). Moreover, during neuroinflammatory states, the BBB becomes more permissive, facilitating migration to the brain parenchyma. In mice that entirely lack mLVs, T-cell infiltration into the parenchyma is reduced (58). Although T cell homing to the CNS is increased during pathological conditions, T cells may also surveil the CNS even in non-inflammatory states. Blockade of T cell migration to the CNS using alpha-4 integrin biologics resulted in rare cases of JC virus reactivation in MS patients, implying a role for T-cell trafficking in CNS immune surveillance (59, 60).

Recent work in animals has shown that immune cell trafficking from the periphery to the CNS is linked to certain anatomical routes. Antigens from the posterior component of the eye, for instance, also drain to dcLNs (40). As a result, these antigens can induce immune responses in the brain involving CD4⁺ T cells, B cells, and locally produced antibodies (40, 61–64). In contrast, superficial cervical lymph nodes (scLNs), which are excluded from the dcLN system delineated above, do not receive antigens from CNS as readily, and drainage to scLNs is not enough to mount a CNS immune response in most circumstances (40, 51). These findings highlight that immune cell entry into the CNS is not random. Rather, it depends on specific anatomical structures, with dcLNs acting as a central gateway for antigen sampling and immune cell response.

A bidirectional connection between the immune and nervous system has long been recognized, but progress in understanding the mechanisms of CSF drainage from the brain has begun to elucidate how mLVs influence peripheral immune responses. In many disease states, innate and adaptive immune cells accumulate in the CNS (22). Some of these cells—including DCs, B and T cells, monocytes, neutrophils, and parenchymal border macrophages (PBMs)—can exit the CNS via the mLVs (22). These cells can subsequently enter the peripheral lymphoid organs and precipitate an autoreactive immune response (43). DCs—one of the major cells that can coordinate immunity in the periphery—are guided by chemokine gradients and lymphatic signaling molecules to dcLNs, where they can prime or induce T cell tolerance in the lymph node (22).

It is unclear whether DCs are local resident cells in the CNS or whether they infiltrate from the periphery into the CNS; however, research using bone marrow-derived, tracer-labeled DCs injected into brain parenchyma has demonstrated that DCs can drain to dcLNs (65). Importantly, the brain parenchyma contains very few conventional DCs under normal conditions. The cells with DC markers in the CNS could represent true dendritic cells, transformed microglia, or cells from the periphery (12, 65). B cells in the meninges can also drain from the mLVs to the cervical lymph nodes via the transverse and sigmoid sinuses, where they can trigger anti-inflammatory and pro-inflammatory responses in the periphery (66, 67). CD4⁺ T cells, which promote progression of neuroimmunologic diseases like multiple sclerosis (MS), similarly drain via the mLVs to the dcLNs (68). Research has shown that mLV injury results in the accumulation of T lymphocytes in the meninges (69). Changes in chemokines can also affect T cell drainage (62). Monocytes are another cell type that has been shown to leave the brain and migrate to the dcLNs via the cribriform plate (70). Neutrophils in the CNS exit via initial transport to mLVs before drainage to the neck; specific mechanisms for the bidirectional movement of neutrophils are active areas of investigation (43). Finally, PBMs have been shown to affect arterial pulsatility and therefore CSF flow (71).

In states of homeostasis, autoantigens which are involved in self-recognition and peripheral immune tolerance, drain from the CNS through the mLVs to the dcLNs. In the dcLNs, antigen-presenting cells (APCs) such as DCs, present peptides in major histocompatibility complex (MHC) II to CD4⁺ T cells, triggering a pathogenic or tolerogenic T cell response via induction of FoxP3⁺ T-regulatory cells depending on the context (72). Immune tolerance is the desired consequence of this interaction, but unrestrained autoreactive T cell activation can occur when homeostasis is altered through such processes as inflammation, infection, or injury. Research has shown that macrophages in the CNS and B cells in the dcLNs each present CNS antigens to T cells in distinct ways—which can shift the immune response from promoting tolerance to potentially increasing the risk for autoimmunity (72). Studies further suggest that the delivery of CNS antigens by migratory DCs to lymph node-resident DCs, which live in lymph nodes, can drive lymphocytic proliferation and alter adaptive immune cells in the periphery (22).

Disturbance of the glymphatic system can contribute to disease in several ways. β-amyloid, reactive oxygen species (ROS), and tau protein, among other molecules, leave the CNS through the glymphatic system (73). While low to moderate ROS may have favorable effects (a phenomenon known as hormesis), excessive levels can result in apoptosis and cellular death (74). Traumatic brain injury (TBI) has been shown to reduce glymphatic pathway function by 60% for at least a month post-injury (75). Reduced tau clearance after injury sets the stage for accumulation of that protein and perhaps higher likelihood of ensuing neurodegeneration (8, 76).

The mLVs are known to be involved in the drainage of metabolic byproducts, cellular debris, and cells. The “debris” may include β-amyloid proteins, tau proteins, α-synuclein, TDP (transactive response DNA-binding protein)-43, glutamate, as well as senescent astrocytes and red blood cells (RBCs) (43). The elimination of senescent astrocytes, for instance, is important for homeostasis during aging (43). Similarly, RBCs from hemorrhagic stroke drain via the mLVs—a process crucial for preventing negative sequelae of infarction, hemorrhage, or both (43, 77, 78).

Failure of clearance from the extracellular space is implicated in the pathogenesis and progression of Alzheimer disease (AD), small-vessel disease, stroke, diabetes, migraine, microinfarcts, glaucoma, and glioblastoma (75, 79–87). That diverse neurological diseases share a common theme of impaired lymphatic drainage is analogous to how vascular dysfunction underlies cardiovascular diseases. The extracellular accumulation of β-amyloid is known to be part of the pathogenesis of AD and cerebral amyloid angiopathy (CAA); enhancing the function of mLVs through vascular endothelial growth factor C (VEGFC) injections has been shown to promote lymphangiogenesis and solute clearance—a promising, albeit still underexplored therapeutic avenue (43, 88, 89).

Several other proteins and metabolites play major roles in neurodegeneration. Tau protein accumulation, which is implicated in progressive supranuclear palsy, corticobasal degeneration, various frontotemporal dementias, and argyrophilic grain disease, among other tauopathies, is cleared by mLVs (43). The role of mLVs in tau clearance highlights the lymphatic system as a target for treatment in these diseases as well (43). Similarly, α-synuclein, which is involved in the pathogenesis of Parkinson disease (PD), has been shown to accumulate in the brain after cervical lymphatic ligation, with associated glial activation, inflammatory response, and dopaminergic neuronal loss (43). Two other molecules, TDP-43 and glutamate, are cleared by the mLVs. Both are implicated in the pathogenesis of amyotrophic lateral sclerosis (ALS).

Acute and chronic peripheral inflammation are key extrinsic factors that can modulate CNS clearance. In rodents, systemic administration of lipopolysaccharide impaired clearance and interstitial bulk flow of β-amyloid in a way that could either precipitate or promote AD pathology (90).

A table summarizing various brain solutes that drain from the glymphatic system through the mLVs to the dcLNs is shown below (Table 1) (32, 43). A host of regulators can affect mLVs based on animal studies, including pharmacological and physical interventions (Table 1) (43). Various pathologies can impact mLV morphology just as changes in the mLVs can affect disease (58). Thus, modulating mLV clearance to aid CNS drainage holds promise as a future therapeutic approach.

To understand the rationale behind various attempts, mainly in animal models, at pharmacologic regulation of mLV function, a basic familiarity with lymphatic endothelial cell (LEC) development beginning at the genetic level is useful. These endothelial cells develop as a result of VEGFC signaling through the VEGF receptor 3 (VEGFR3); initial lymphatic development in embryos depends on this interaction (91). Expression of Prospero-related homeobox 1 (Prox 1), a DNA-homeobox transcription factor, facilitates expression of VEGFR3, while VEGFC activity is potentiated by collagen and calcium binding endothelial growth factor 1 (CCBE1) and the zinc-dependent protease ADAMTS3 (a disintegrin-like metalloproteinase with thrombospondin type 1 motif, 3). Absence of CCBE1, VEGFC, and VEGFR3 is associated with impaired development of mLVs.

Maintenance of LECs, as well as formation of lymphatic valves—particularly in basal mLVs of the CNS—relies on multiple intermediaries in pathways that are implicated in both mLV injury and repair (42). Selected therapeutic agents and the rationale for their use, based primarily on an animal study, include exogenous VEGFC; borneol (BO), which crosses the blood–brain barrier and increases VEGF expression upstream of Forkhead box O1 (FOXO1), a factor that facilitates LEC maintenance; Yoda1, an agonist of the mechanosensitive ion channel Piezo1, which is associated with increased VEGFC expression vitamin D, which is thought to increase vascular endothelial (VE) cadherin, a calcium-dependent adhesion protein involved in maintaining lymphatic vessel integrity; Yuanzhi powder (YZP), which may aid the correct polarization of aquaporin channels at astrocytic endfeet; and DNase I, which may promote degradation of neutrophil extracellular traps (NETs) within mLVs after cerebral hemorrhage (43). Numerous other potential therapeutic agents are under investigation.

Sample physical regulators in Table 1 are thought to modulate or stimulate mLV drainage. Transcranial near-infrared light may act at the level of mitochondrial cytochrome c oxidase (CcO), a photoreceptor whose activation has been associated with lymphatic endothelial cell (LEC) proliferation.

Since dcLNs are implicitly involved in immune response, noninvasive visualization of dcLNs could aid in diagnosing and monitoring CNS inflammation. However, these applications remain exploratory in the clinical setting at present. Various modern head and neck imaging techniques can be employed to investigate dcLNs, including computed tomography (CT) scans, magnetic resonance imaging (MRI), and positron emission tomography (PET)-CT. While most imaging protocols initially evolved for oncologic indications, we will discuss potential adaptations for neuroinflammatory conditions.

MRI provides superior soft tissue contrast and may be more sensitive than CT for revealing subtle node changes in neuroinflammatory disease. Routine MR sequences include 2D and 3D options with T1- and T2-weighted imaging, performed with and without fat saturation (FS). While the utility of various techniques is still debated, one study examining axillary lymph nodes found that T2-weighted fast spin echo (FSE) images showed the highest number of lymph nodes, while T1 fast field echo (FFE) had the most anatomical information (122). Ultrasound (US) is less favorable due to limitations in visualizing deeper nodes but can sometimes be used in children to reduce radiation exposure (50).

In practice, distinguishing a lymph node can be difficult, since many types of structures can appear similarly (50). After a lymph node is identified, it must be characterized as normal or abnormal. Normal lymph nodes are kidney-shaped with a central fatty hilum; changes in this fat can indicate nodal pathology (50). If a level I or II cervical node exceeds 15 mm, it is also considered abnormally enlarged; while size was previously the main way to distinguish a pathologic node, size is not always a clear indicator of pathology (50, 123). Instead, the most important findings are configuration, homogeneity, enhancement, loss of the normal fatty hilum, and preservation of surrounding fat planes (50).

Imaging techniques may be able to identify subtle asymmetries or changes in nodal architecture even before overt enlargement. If the lymph node is rounded, has no fatty center, or is enlarged, it should be flagged. However, lymph node size is not always positively correlated with disease severity in the context of inflammation. In MS, cervical lymph node diameter on MRI was inversely correlated with disease duration and disability progression, with node size diminishing during acute relapses (124). Quantitative T1 nodal “maps” can also reveal asymmetries. Particularly, T1 asymmetry of the lymph node cortex between affected and contralateral axilla can be ascertained by quantitative relaxation time mapping in breast cancer treatment-related lymphedema; the asymmetry increases with cancer stage (125). Ultimately, node measurements should always be considered in the context of scan technique and disease state.

An important advance in lymphatic imaging was the demonstration of glymphatic drainage to dcLNs using MR. One 3D T1-weighted in-vivo MR study showed evidence of glymphatic drainage from the brain to dcLNs, with cervical lymph node enhancement occurring at the same time as peak glymphatic enhancement (52). Similarly, 3D T2-FLAIR (fluid-attenuated, inversion recovery) MRI without contrast showed that dorsal and ventral mLVs can be visualized, in addition to their direct relationships with dcLNs (16). Another MRI study examined whether ligation of dcLNs affected CSF tracer dynamics, and found that CSF outflow into the nasal cavity was blocked, causing retention (126).

In addition to traditional MR, advanced techniques are increasingly being utilized to interrogate the glymphatic system in vivo. These include perivascular space assessment, DTI (diffusion tensor imaging) analysis along perivascular spaces (DTI-ALPS), arterial spin labeling, and chemical exchange saturation transfer, which can be used to evaluate the glymphatic system in vivo (127). Lower DTI-ALPS indices have been correlated with higher burdens of amyloid in AD, increased risk of dementia conversion in PD, and larger tumor volumes in patients with glioblastoma, brain metastases, and aggressive meningiomas (128–130). Glymphatic dysfunction as measured by DTI-ALPS and free water fraction are similar in MS and neuromyelitis optica spectrum disorder, indicating that neuroinflammatory processes, regardless of exact disease etiology, may impair glymphatic clearance in similar ways (131). Contrast-enhanced glymphatic MRI has shown that, after subarachnoid hemorrhage in humans, CSF is redistributed toward the ventricles and fluid transport in perivascular spaces is impaired, underscoring how vascular injury can disrupt glymphatic function (132). Emerging noninvasive imaging biomarkers for lymphatic function may eventually help to identify patients at increased risk for neurodegeneration, although clinical validation is still needed. If validated clinically, this development could shift the field toward earlier risk stratification and prevention.

The integration of conventional and advanced MRI protocols can allow for not only anatomical, but also functional and quantitative assessment of dcLNs and glymphatic system activity. Leveraging these approaches with CSF assays and immunophenotyping of nodal tissue can yield powerful biomarkers and help to develop a stronger understanding of neuroimmune dynamics.

The limitations of imaging are those not infrequently encountered in general clinical practice. Nodal anatomy is variable; imaging protocols must be standardized (and uniquely tailored to identify nodes); and artifactual findings are inevitable (133–135).

The deep cervical lymph nodes (dcLNs) could highlight immunologic processes occurring in the CNS, especially when CSF findings are inconclusive. Though lymph node study as a diagnostic or monitoring tool is still experimental, with unproven reproducibility in clinical settings, the avenue holds promise. Immunophenotyping of nodal tissue could identify unique immune cell populations that might not be evident in peripheral blood or CSF. A study in rats found that bone marrow-derived myeloid DCs injected into the CSF infiltrated the brain parenchyma and trafficked to the cervical lymph nodes in an EAE model, compared to controls—all of which is thought to then elicit both local (CNS) and systemic immune responses (136).

As dcLN groups IIA and IIB (see Figure 2) are the sites particularly relevant to CNS glymphatic drainage in humans, they are an optimal choice to assess. When imaging nodes, clinicians should note shape, enhancement patterns, hilum appearance, cortical thickness, and nodal architecture, as well as evidence of necrosis or calcification. After imaging with MR, percutaneous ultrasound-guided fine-needle aspiration (FNA) or core-needle biopsy can be used for sampling (Figure 3). FNA is often preferred because it is minimally invasive, relatively fast, and has a lower complication rate than other options. The sample consists of small tissue fragments and individual cells. The material from FNA sampling can then be used for cytology, flow cytometry, or molecular analysis. Flow cytometry may identify expanded or atypical lymphocyte clones, while immunohistochemistry can distinguish specific immune subsets and activation states. For tissue sampling and better diagnostic accuracy, however, either a core needle biopsy or examination of a whole dcLN is superior, albeit far more invasive.

Immunophenotyping can indicate subsets of T cells, B cells, monocytes, DCs, inter alia. An overlap in B-cell or T-cell receptor sequences between dcLN and CSF samples can show whether immune clones are spreading from the periphery into the CNS or vice versa. Unlike CSF sampling (e.g., of cytokines) which captures a single timepoint, dcLN immunophenotyping may reveal the dynamic trajectory of an immune response. As a result, for example, clinicians could distinguish resolving inflammation from progressive autoimmunity and thereby select personalized and more precise therapies.

Histopathologic and immunophenotypic assessment has been conducted in MS patients (120, 137). The minimal amount of tissue required for definitive analysis might be debated; the first of the cited studies examined whole lymph nodes, whereas the second involved FNA. Fine-needle samples may not suffice in characterizing the nature of an adaptive immune response originating in dcLNs. Nevertheless, the value of combined histologic and immunophenotypic lymph node analysis lies in the ability to detect changes in T- and B-cell populations that occur particularly in the context of MS relapse—and presumably in other forms of active neuroinflammation—along with alterations in nodal germinal center (GC) reactions, which reflect antigen-specific T- and B-cell interactions. Within GCs, B-cell hypermutation, as occurs in MS, is dependent on follicular T helper (Tfh) cells and an increased ratio of Tfh to T follicular regulatory (Tfr) cells, as was learned from whole-node analysis. Notably, even fine-needle aspiration (FNA) samples subjected to single-cell RNA sequencing or combined transcriptomic and epitope indexing were sufficient to identify disease-specific changes in clonal B-cell populations, including those of GC origin.