Genome-wide association study for type 2 diabetes in Indians identifies a new susceptibility locus at 2q21.

Indians undergoing socioeconomic and lifestyle transitions will be maximally affected by epidemic of type 2 diabetes (T2D). We conducted a two-stage genome-wide association study of T2D in 12,535 Indians, a less explored but high-risk group. We identified a new type 2 diabetes-associated locus at 2q21, with the lead signal being rs6723108 (odds ratio 1.31; P = 3.32 × 10⁻⁹). Imputation analysis refined the signal to rs998451 (odds ratio 1.56; P = 6.3 × 10⁻¹²) within TMEM163 that encodes a probable vesicular transporter in nerve terminals. TMEM163 variants also showed association with decreased fasting plasma insulin and homeostatic model assessment of insulin resistance, indicating a plausible effect through impaired insulin secretion. The 2q21 region also harbors RAB3GAP1 and ACMSD; those are involved in neurologic disorders. Forty-nine of 56 previously reported signals showed consistency in direction with similar effect sizes in Indians and previous studies, and 25 of them were also associated (P < 0.05). Known loci and the newly identified 2q21 locus altogether explained 7.65% variance in the risk of T2D in Indians. Our study suggests that common susceptibility variants for T2D are largely the same across populations, but also reveals a population-specific locus and provides further insights into genetic architecture and etiology of T2D

Novel modulators of non-selective and selective autophagy

På samme måte som søppel dannes fra vårt daglige forbruk, produserer cellene i kroppen vår avfallsprodukter som transporteres til cellens resykleringsstasjon (lysosomet), hvor det brytes ned og gjenvinnes. Dette skjer via en prosess kalt autofagi, som involverer oppsamling av kargo/søppel i en vesikkel (et autofagosom) som smelter sammen med lysosomet. Autofagi oppreguleres ved stress, f.eks sult, men et basalt nivå av autofagi er viktig i alle celler for å beskytte mot sykdommer som kreft og nevrodegenerering. Dannelsen av autofagosomer er vist å involvere en rekke proteinkomplekser og lipider, men de eksakte mekanismene involvert i regulering av autofagi er ikke kjent. I denne avhandlingen har Benan John Mathai og medarbeidere vist at proteinet HS1BP3 er en negativ regulator av autofagi. De fant at HS1BP3 inhiberer autofagi ved å hemme aktiviteten til det lipid-modifiserende enzymet PLD1, som igjen er viktig for å lage lipidet fosfatidsyre (PA) som er vist å være viktig for autofagi. Mathai fant at den regulatoriske rollen til HS1BP3 i autofagi er konservert i zebrafisk larver som uttrykker en fluoreserende markør for autofagi (LC3). Selektiv nedbryting av spesialavfall (som dysfunksjonelle mitokondrier eller protein aggregater) ved autofagi krever spesielle autofagi-reseptorer (f.eks p62) som binder kargo. Benan John Mathai og medarbeidere har identifisert et «eat-me signal» på mitokondrier som gjenkjennes av slike autofagi reseptorer. Ved depolarisering av mitokondriene akkumulerer matriksproteinene NIPSNAP1 og NIPSNAP2 på overflaten av mitokondriene hvor de binder autofagireseptorer, som fører til nedbrytning av de ødelagte mitokondriene (mitofagi). NIPSNAP1/2-mediert mitofagi er avhengig av proteinene PINK1 og PARKIN, som begge er assosiert med Parkinsons sykdom. Mathai fant at zebrafisk larver som mangler Nipsnap1 har økt oksidativt stress, redusert nivå av dopaminerge nevroner og redusert bevegelse. Dette doktorgradsarbeidet er et viktig bidrag til vår forståelse av de molekylære mekanismene involvert i regulering og dannelse av autofagosomer og gir innsikt i betydningen av disse prosessene i å hindre utvikling av sykdom

Studying Autophagy in Zebrafish

Autophagy is an evolutionarily conserved catabolic process which allows lysosomal degradation of complex cytoplasmic components into basic biomolecules that are recycled for further cellular use. Autophagy is critical for cellular homeostasis and for degradation of misfolded proteins and damaged organelles as well as intracellular pathogens. The role of autophagy in protection against age-related diseases and a plethora of other diseases is now coming to light; assisted by several divergent eukaryotic model systems ranging from yeast to mice. We here give an overview of different methods used to analyse autophagy in zebrafish—a relatively new model for studying autophagy—and briefly discuss what has been done so far and possible future directions

GAK and PRKCD kinases regulate basal mitophagy.

The removal of mitochondria in a programmed or stress-induced manner is essential for maintaining cellular homeostasis. To date, much research has focused upon stress-induced mitophagy that is largely regulated by the E3 ligase PRKN, with limited insight into the mechanisms regulating basal “housekeeping” mitophagy levels in different model organisms. Using iron chelation as an inducer of PRKN-independent mitophagy, we recently screened an siRNA library of lipid-binding proteins and determined that two kinases, GAK and PRKCD, act as positive regulators of PRKN-independent mitophagy. We demonstrate that PRKCD is localized to mitochondria and regulates recruitment of ULK1-ATG13 upon induction of mitophagy. GAK activity, by contrast, modifies the mitochondrial network and lysosomal morphology that compromise efficient transport of mitochondria for degradation. Impairment of either kinase in vivo blocks basal mitophagy, demonstrating the biological relevance of our findings

Phenotypic Characterization of Larval Zebrafish (Danio rerio) with Partial Knockdown of the cacna1a Gene

The CACNA1A gene encodes the pore-forming α1 subunit of voltage-gated P/Q type Ca2+ channels (Cav2.1). Mutations in this gene, among others, have been described in patients and rodents suffering from absence seizures and episodic ataxia type 2 with/without concomitant seizures. In this study, we aimed for the first time to assess phenotypic and behavioral alterations in larval zebrafish with partial cacna1aa knockdown, placing special emphasis on changes in epileptiform-like electrographic discharges in larval brains. Whole-mount in situ hybridization analysis revealed expression of cacna1aa in the optic tectum and medulla oblongata of larval zebrafish at 4 and 5 days post-fertilization. Next, microinjection of two antisense morpholino oligomers (individually or in combination) targeting all splice variants of cacna1aa into fertilized zebrafish eggs resulted in dose-dependent mortality and decreased or absent touch response. Over 90% knockdown of cacna1aa on protein level induced epileptiform-like discharges in the optic tectum of larval zebrafish brains. Incubation of morphants with antiseizure drugs (sodium valproate, ethosuximide, lamotrigine, topiramate) significantly decreased the number and, in some cases, cumulative duration of epileptiform-like discharges. In this context, sodium valproate seemed to be the least effective. Carbamazepine did not affect the number and duration of epileptiform-like discharges. Altogether, our data indicate that cacna1aa loss-of-function zebrafish may be considered a new model of absence epilepsy and may prove useful both for the investigation of Cacna1a-mediated epileptogenesis and for in vivo drug screening

NIPSNAP1 and NIPSNAP2 Act as “Eat Me” Signals for Mitophagy

The clearance of damaged or dysfunctional mitochondria by selective autophagy (mitophagy) is important for cellular homeostasis and prevention of disease. Our understanding of the mitochondrial signals that trigger their recognition and targeting by mitophagy is limited. Here, we show that the mitochondrial matrix proteins 4-Nitrophenylphosphatase domain and non-neuronal SNAP25-like protein homolog 1 (NIPSNAP1) and NIPSNAP2 accumulate on the mitochondria surface upon mitochondrial depolarization. There, they recruit proteins involved in selective autophagy, including autophagy receptors and ATG8 proteins, thereby functioning as an “eat me” signal for mitophagy. NIPSNAP1 and NIPSNAP2 have a redundant function in mitophagy and are predominantly expressed in different tissues. Zebrafish lacking a functional Nipsnap1 display reduced mitophagy in the brain and parkinsonian phenotypes, including loss of tyrosine hydroxylase (Th1)-positive dopaminergic (DA) neurons, reduced motor activity, and increased oxidative stress

Data from: HS1BP3 negatively regulates autophagy by modulation of phosphatidic acid levels

A fundamental question is how autophagosome formation is regulated. Here we show that the PX domain protein HS1BP3 is a negative regulator of autophagosome formation. HS1BP3 depletion increased the formation of LC3-positive autophagosomes and degradation of cargo both in human cell culture and in zebrafish. HS1BP3 is localized to ATG16L1- and ATG9-positive autophagosome precursors and we show that HS1BP3 binds phosphatidic acid (PA) through its PX domain. Furthermore, we find the total PA content of cells to be significantly upregulated in the absence of HS1BP3, as a result of increased activity of the PA-producing enzyme phospholipase D (PLD) and increased localization of PLD1 to ATG16L1-positive membranes. We propose that HS1BP3 regulates autophagy by modulating the PA content of the ATG16L1-positive autophagosome precursor membranes through PLD1 activity and localization. Our findings provide key insights into how autophagosome formation is regulated by a novel negative-feedback mechanism on membrane lipids

Compiled Lipidomics Data_NCOMMS-16-13893-A

Raw data of MS lipidomics datasets used in Fig. 5a and Supplementary Fig. 4c. Data are from HEK cells treated with non-targeting (Control) or HS1BP3 siRNA starved for 2 hrs (mean +/- SEM., n = 6). See the Methods section for a full description of the Methods used