Functional Genetics

We are an international interdisciplinary team of physicians, biologists, biochemists and related disciplines which share an interest for the pathophysiology of monogenic hereditary disorders.  Main topics are currently ion transport related disorders and neurodegenerative disorders like axonopathies.  To unravel the chain of events that finally result in a specific pathology we use different approaches including molecular biology, cell models, the generation of mouse models using homologous recombination and CRISPR/Cas mediated genome engineering, new sequencing technologies, and advanced microscopy techniques.

Ion transport related disorders                                

Ion transport processes also play crucial roles for neuronal excitability, signal transduction, transport across epithelia, and the homeostasis of extracellular, cytosolic, and vesicular compartments. The essential role of the molecules involved in these processes is reflected by a large number of hereditary disorders due to mutations in genes encoding ion channels or -transporters. Over the past years our group has established and analyzed several knockout-mouse models of ion channels/ -transporters to better understand their pathophysiological role in disease.

The composition of the “milieu interne” is a result of the dynamic and controlled exchange of solute and water between body cells and our surrounding environment. The equilibrium requires that the amount of water and ions excreted into the urine exactly matches the daily intake or production of various substances. The kidney plays a central role for electrolyte and water homeostasis. In humans the glomeruli filter daily very large amounts (∼180 liters) of water and of ions (e.g., 25,000 mmol of Na+, 4,300 mmol of HCO3, 720 mmol of K+). These quantities easily exceed those in the body. Accordingly, the renal tubule must absorb most substances filtered at the glomerulus to avoid their loss into urine. However, as indicated above, a small fraction of water and ions that exactly matches the daily input from diet and metabolism must also be excreted.

Net elimination of nonvolatile acid is mediated by type A-intercalated cells (A-ICs) in the connecting tubule and collecting duct (CD). To achieve proton (H+) secretion, A-ICs express V-type ATPase at the apical cell pole. Protons are generated within these cells by hydration of CO2, which is catalyzed by intracellular carbonic anhydrase type II (CAII). The resulting H2CO3 dissociates into H+ and HCO3-. Whereas H+ is secreted apically via the proton pump, HCO3- is extruded basolaterally by the chloride/bicarbonate exchanger AE1 (SLC4A1). This transport model is supported by hereditary defects, also known as distal renal tubular acidosis (dRTA), caused by mutations of either the a4 or B1 subunit of the proton pump, of CAII, or of the anion-exchanger AE1, respectively. Recently, we generated a knockin mouse model for the most common missense mutation in AE1 in patients suffering from distal renal tubular acidosis ( Our results suggest that reduced basolateral anion-exchange activity inhibits trafficking and regulation of the V-type ATPase, thus compromising luminal H+ secretion and possibly lysosomal acidification. In the past we had already shown that the KCl-cotransporer KCC4 is important for chloride recycling at the basolateral membrane of A-ICs ( and thus supports basolateral HCO3- transport via the anion-exchanger AE1 (Figure 1). With a knockout mouse model for the a4 subunit we also identified a previously unrecognized role of the a4 subunit in proximal tubule cells. We could show that a4 KO mice suffer not only from severe acidosis but also from proximal tubule dysfunction with defective endocytic trafficking, proteinuria, phosphaturia and accumulation of lysosomal material.


Figure 1: Cell types and ion transport in the distal renal tubule. Type A intercalated cells (A-ICs) secrete H+ via the apical V-type ATPase (vATPase). HCO3- is recovered basolaterally via the anion-exchanger AE1. In type B intercalated cells (B-ICs) the vATPase energizes NaCl uptake via the Pendrin/NDCBE system.


The finding that NDCBE/SLC4A8-dependent thiazide-sensitive Na⁺ reabsorption occurs in the cortical collecting duct challenges the current model of how thiazides mediate their antihypertensive action and identifies a potentially new target for antihypertensive strategies (, Moreover, basolateral NaCl exit from β-intercalated cells was independent of the Na+/K+-ATPase but critically relied on the presence of basolateral SLC4A9/AE4 (

Chloride transport by the renal tubule is critical for blood pressure (BP), acid-base, and potassium homeostasis. Chloride uptake from the urinary fluid is mediated by various apical transporters, whereas basolateral chloride exit is thought to be mediated by ClC-Ka/K1 and ClC-Kb/K2, two chloride channels from the ClC family, or by KCl cotransporters from the SLC12 gene family. Nevertheless, the localization and role of ClC-K channels is not fully resolved. Because inactivating mutations in ClC-Kb/K2 cause Bartter syndrome, a disease that mimics the effects of the loop diuretic furosemide, ClC-Kb/K2 is assumed to have a critical role in salt handling by the thick ascending limb. To dissect the role of this channel in detail, we generated a mouse model with a targeted disruption of the murine orthologue ClC-K2. Mutant mice developed a Bartter syndrome phenotype, characterized by renal salt loss, marked hypokalemia, and metabolic alkalosis. Patch-clamp analysis of tubules isolated from knockout mice suggest that ClC-K2 is the main basolateral chloride channel in the thick ascending limb and in the aldosterone-sensitive distal nephron (

Ion homeostasis is a vital homeostatic function also for the brain, because electrical activity directly depends on ion gradients. On the one hand electrical activity can result in pH changes and on the other hand is influenced by pH transients by affecting a variety of ion channels. It turned out that cation chloride cotransporters such as KCC2 ( and NKCC1 ( are crucial in the control of the electrochemical Cl- gradient that is required for “classical” hyperpolarizing postsynaptic inhibition mediated by GABAA and glycine receptors (Figure 2). We currently address the role of these and related transporters in the context of brain trauma within an international research group headed by Claudio Rivera (ACROBAT) and during cortical development (Priority program of the DFG). We also studied the role of SLC4A10 for synaptic transmission, since it localizes to glutamatergic presynapses. We could show that SLC4A10 modulates glutamate release in a pH dependent manner ( SLC4A7 is closely related and also contributes to neuronal pH homeostasis plays an essential role for the production of the cerebrospinal fluid (


Figure 2: GABA and Chloride homeostasis. In immature neurons the intracellular Cl- concentration [Cl-]i is high because of NKCC1 mediated Cl- accumulation. Hence, opening of GABAA receptors results in an influx of Cl-. During development the incipient expression of KCC2 lowers [Cl-]I and renders GABA hyperpolarizing. The expression of KCl cotransporters can change in pathological conditions such as epilepsy, brain trauma or chronic pain, thus modulating GABAergic transmission.



The axon is the long process of a neuron that carries efferent action potentials from the soma to the target cell. Because protein and lipid synthesis largely occur in the cell soma, anterograde transport is required to supply axons with the respective materials. Conversely, material intended for degradation has to be transported in a retrograde manner to the cell soma. The same logistic challenge applies to intracellular signals, both anterogradely and retrogradely. Thus, it is no surprise that neurons with long projections are particularly susceptible to impairment in cell processes such as trafficking, transport, energy utilization, and signaling and cytoskeletal organization. The term axonopathy refers to a group of neurodegenerative disorders that mainly manifests at long axons as e.g. hereditary spastic paraplegia (HSP), amyotrophic lateral sclerosis (ALS), hereditary motor and sensory neuropathies (CMT/HMSN), and hereditary sensory and autonomic neuropathies (HSAN). Our current research focus in the field is to investigate the genetic and cell-biological basis of disease in selected axonopathies. E.g. we could show that REEP1, which is mutated in autosomal dominant SPG31, is an endoplasmic reticulum (ER) resident protein, which contributes to ER structure via its RETICULON domain ( We also addressed the function of Spastizin (SPG15, and Spatacsin (SPG11, for motoneuron maintenance.  Both protein associate with a recently identified adaptor protein complex, i.e. AP-5, and are thought to be involved in the recycling of lysosomes from autolysosomes, while the role of AP-5 is largely unknown.


Figure 3: Cellular functions relevant for axonal disorders. Motoneurons and sensory neurons have particularly long axons, which are liable for neurodegeneration such as polyneuropathies or hereditary spastic paraplegia due to functional changes in mitochondria (red), ER (blue), Golgi (brown), the lysosomal/autophagic system (green) or intracellular transport.


Our efforts on axonopathies also include neuropathies.   E.g. we studied the role of another K-Cl cotransporter, i.e. KCC3, in a knockout mouse model. Mutations in KCC3 are associated with a syndromic polyneuropathy (, Together with Ingo Kurth we were able to  identify the role of voltage-gated sodium ion channel Nav1.9 in individuals with the congenital inability to experience pain ( ). For example we identified an axonopathy caused by a defect in an enzyme involved in protein glycosylation ( loss of function mutations in FAM134B in hereditary sensory and autonomic neuropathy type 2 (HSAN2) ( Together with the group of Ivan Dikic we were later able to show that FAM134B serves as an LC3 receptor and thus triggers the autophagy of endoplasmic reticulum (ER) membranes, a process also referred to as reticulophagy or ER-phagy ( We currently try to identify additional receptors that mediate ER-phagy und how this process is regulated.


Figure 4: Reticulophagy. FAM134b loss-of-function mutations result in a neurodegenerative disorder.  FAM134B is an ER-resident receptor for LC3, which triggers ER-phagy thereby controlling ER turnover and ER size, which seems to be of special relevance for long term axonal maintenance (adapted from Khaminets et al., Nature 2015).


Selected readings


Hübner CA, Stein V, Hermans-Borgmeyer I, Meyer T, Ballanyi K, Jentsch TJ (2001) Disruption of KCC2 reveals an essential role of K-Cl-cotransport already in early synaptic inhibition. Neuron 30:515-24

Boettger T*, Hübner CA*, Maier H, Rust M, Beck FX, Jentsch TJ (2002) Deafness and renal tubular acidosis in mice lacking the K-Cl co-transporter KCC4. Nature 416:874-78

Boettger T, Rust MB, Maier H, Seidenbecher T, Schweizer M, Keating DJ, Faulhaber J, Ehmke H, Pfeffer C, Scheel O, Lemcke B, Horst J, Leuwer R, Pape HC, Völkl H, Hübner CA, Jentsch TJ (2003) Loss of K-Cl co-transporter KCC3 causes deafness, neurodegeneration and reduced seizure threshold. EMBO Journal 22:5422-34

Tyzio R, Cossart R, Khalilov I, Minlebaev M, Hübner C.A., Represa A, Ben-Ari Y, Khazipov R (2006) Maternal oxytocin triggers a transient inhibitory switch in GABA signaling in the fetal brain during delivery. Science 314:1788-92                                       

RustMB, FaulhaberJ, BudackM,Pfeffer C, MaritzenT, Didié M, BeckFX, BoettgerT, SchubertR, Ehmke H, Jentsch TJ, Hübner CA (2006) Neurogenic mechanisms contribute to hypertension in mice with disruption of the K-Cl-cotransporter KCC3.  Circulation Research 98:549-56

Rust MB,AlperSL, RudhardY, BrugnaraC, TrudelM, Jentsch TJ, Hübner CA (2007) Disruption of erythroid K-Cl co-transporters alters erythrocyte volume and partially rescues erythrocyte dehydration in SAD mice. Journal of Clinical Investigation 117:1708-17

Pfeffer C, SteinV, Keating D, MaierH, RudhardY, HentschkeM, RuneG, Jentsch TJ, Hübner CA (2009) GABA-dependent network activity contributes to early maturation of excitatory hippocampal synapses.  Journal of Neuroscience 2:3419-30

Antoine MW, Hübner CA, Arezzo JC, Hébert JM (2013) A causative link between inner ear defects and long-term striatal dysfunction. Science 341(6150):1120-3

Zonouzi M, Scafidi J, Li P, McEllin B, Edwards J, Dupree JL, Harvey L, Sun D, Hübner CA, Cull-Candy SG, Farrant M, Gallo V. GABAergic regulation of cerebellar NG2 cell development is altered in perinatal white matter injury. Nat Neurosci. 2015;18(5):674-82


Hentschke M, Wiemann M, Hentschke S, Kurth I, Seidenbecher T, Hermans-Borgmeyer I, Jentsch TJ, Gal A, Hübner CA (2006) Mice with a targeted disruption of the Cl-/HCO3- exchanger AE3 display a reduced seizure threshold. Molecular and Cellular Biology 26:182-91

Jacobs S, Ruusuvuori E. Sipilä S, Hapaanen A, Damkier HH, Kurth I, Hentschke M, Schweizer M, Rudhard Y, Laatinkainen L, Tyynelä J, Praetorius J, Voipio J, Hübner CA (2008) Targeted gene disruption of Slc4a10 results in reduced brain ventricle size and dampens neuronal excitability. Proceedings of the National Academy of Sciences U S A 105:311-6

Leviel F*, Hübner* CA, Morla L, Houillier P, El Moghrabi S, Brideau G, Hatim H, Kurth I, Kougioumtzes A, Sinning A, Pech V, Riemondy KA, Miller RL, Hummler E, Shull GE, Aronson PS, Doucet A, Wall SM, Chambrey R, and Eladari D (2010) Identification of a novel amiloride-resistant, thiazide-sensitive NaCl reabsorption pathway in the distal nephron. Journal of Clinical Investigation 120(5):1627-35                          

Sinning A, Liebmann L, Kougioumtzes A, Westermann M, Bruehl C, Hübner CA (2011). Synaptic glutamate release is modulated by the Na+-driven Cl-/HCO₃- exchanger Slc4a8. Journal of Neuroscience 31(20):7300-11

Hilgen G, Huebner AK, Tanimoto N, Sothilingam V, Seide C, Garrido MG, Schmidt KF, Seeliger MW, Löwel S, Weiler R, Hübner CA*, Dedek K* (2012) Lack of the sodium-driven chloride bicarbonate exchanger NCBE impairs visual function in the mouse retina. PLoS One 7(10):e46155

Chambrey R, Kurth I, Peti-Peterdi J, Houillier P, Purkerson JM, Leviel F, Hentschke M, Zdebik AA, Schwartz GJ, Hübner CA, Eladari D (2013) Renal intercalated cells are rather energized by a proton than a sodium pump. Proceedings of the National Academy of Sciences U S A 110(19):7928-33       

Mumtaz R, Trepiccione F, Hennings JC, Huebner AK, Serbin B, Picard N, Ullah AKMS, Păunescu TG, Capen DE, Lashhab RM, Mouro-Chanteloup I, Alper SL, Wagner CA, Cordat E, Brown D, Eladari D, Hübner CA (2017). Intercalated Cell Depletion and Vacuolar H+-ATPase Mistargeting in an Ae1 R607H Knockin Model. J Am Soc Nephrol 28(5):1507-1520


Boettger T, Rust MB, Maier H, Seidenbecher T, Schweizer M, Keating DJ, Faulhaber J, Ehmke H, Pfeffer C, Scheel O, Lemcke B, Horst J, Leuwer R, Pape HC, Völkl H, Hübner CA, Jentsch TJ (2003) Loss of K-Cl co-transporter KCC3 causes deafness, neurodegeneration and reduced seizure threshold. EMBO Journal 22:5422-34

Hübner CA, Orth U, Senning A, Kohlschütter A, Korinthenberg R, Gal A (2005) 17 novel mutations in PLP1 causing Pelizaeus Merzbacher disease. Human Mutation 25:321-2

Hübner CA, Senning A, Zerres K, Gal A, Rudnik-Schöneborn S (2005) Mild Pelizaeus-Merzbacher disease caused by a point mutation affecting correct splicing of PLP1 mRNA. Neuroscience 132:687-701

Poët M, Kornak U, SchweizerM, ZdebikAA, ScheelO, HoelterS, Wurst  W, SchmittA,  FuhrmannJC, Planells-CasesR, Mole SE, HübnerCA, JentschTJ (2006) Lysosomal storage disease upon disruption of the neuronal chloride transport protein ClC-6. Proceedings of the National Academy of Sciences U S A 103:13854-9

RustMB, FaulhaberJ, BudackM,Pfeffer C, MaritzenT, Didié M, BeckFX, BoettgerT, SchubertR, Ehmke H, Jentsch TJ, Hübner CA (2006) Neurogenic mechanisms contribute to hypertension in mice with disruption of the K-Cl-cotransporter KCC3.  Circulation Research 98:549-56

Kurth I, Pamminger T, Hennings JC, Soehendra D, Huebner AK, Rotthier A, Baets J, Senderek J, Topaloglu H, Farrel SA, Nürnberg P, De Jonghe P, Gal A, Kaether C, Timmerman V, Hübner CA (2009) Mutations in FAM134B, encoding a novel Golgi protein, cause severe sensory and autonomic neuropathy. Nature Genetics 41(11):1179-81

Beetz C, Koch N, Khundadze M, Zimmer G, Nietzsche S, Hertel N, Huebner AK, Mumtaz R, Schweizer M, Dirren E, Karle KN, Irintchev A, Alvarez V, Redies C, Westermann M, Kurth I, Deufel T, Kessels MM, Qualmann B, Hübner CA (2013) A spastic paraplegia mouse model reveals REEP1-dependent ER shaping. Journal of Clinical Investigation 123(10):4273-82

Khundadze M, Kollmann K, Koch N, Biskup C, Nietzsche S, Zimmer G, Hennings JC, Huebner AK, Symmank J, Jahic A, Ilina EI, Karle K, Schöls L, Kessels M, Braulke T, Qualmann B, Kurth I, Beetz C, Hübner CA (2013) A Hereditary Spastic Paraplegia Mouse Model Supports a Role of ZFYVE26/SPASTIZIN for the Endolysosomal System. PLoS Genetics 9(12):e1003988

Hübner CA, Kurth I. Membrane-shaping disorders: a common pathway in axon degeneration. Brain. 2014;137(Pt 12):3109-21

Leipold E, Liebmann L, Korenke GC, Heinrich T, Giesselmann S, Baets J, Ebbinghaus M, Goral RO, Stödberg T, Hennings JC, Bergmann M, Altmüller J, Thiele H, Wetzel A, Nürnberg P, Timmerman V, De Jonghe P, Blum R, Schaible HG, Weis J, Heinemann SH, Hübner CA, Kurth I (2013) A de novo gain-of-function mutation in SCN11A causes loss of pain perception. Nature Genetics 45(11):1399-404

Koehler K, Malik M, Mahmood S, Gießelmann S, Beetz C, Hennings JC, Huebner AK, Grahn A, Reunert J, Nürnberg G, Thiele H, Altmüller J, Nürnberg P, Mumtaz R, Babovic-Vuksanovic D, Basel-Vanagaite L, Borck G, Brämswig J, Mühlenberg R, Sarda P, Sikiric A, Anyane-Yeboa K, Zeharia A, Ahmad A, Coubes C, Wada Y, Marquardt T, Vanderschaeghe D, Van Schaftingen E, Kurth I, Huebner A, Hübner CA (2013) Mutations in GMPPA cause a glycosylation disorder characterized by intellectual disability and autonomic dysfunction. American Journal of Human Genetics 93(4):727-34

Khaminets A, Heinrich T, Mari M, Grumati P, Huebner AK, Akutsu M, Liebmann L, Stolz A, Nietzsche S, Koch N, Mauthe M, Katona I, Qualmann B, Weis J, Reggiori F, Kurth I*, Hübner CA*, Dikic I*. Regulation of endoplasmic reticulum turnover by selective autophagy. Nature. 2015;522(7556):354-8 *equal contribution

Varga RE, Khundadze M, Damme M, Nietzsche S, Hoffmann B, Stauber T, Koch N, Hennings JC, Franzka P, Huebner AK, Kessels MM, Biskup C, Jentsch TJ, Qualmann B, Braulke T, Kurth I, Beetz C, Hübner CA. In Vivo Evidence for Lysosome Depletion and Impaired Autophagic Clearance in Hereditary Spastic Paraplegia Type SPG11. PLoS Genet. 2015;11(8):e1005454