About

Nicholas J. Hand, Ph.D., is a Research Associate Professor of Genetics at the University of Pennsylvania's Perelman School of Medicine. He is a broadly trained molecular biologist with a long-standing interest in diseases affecting or originating in the liver, as well as in microRNAs with regulatory roles in liver development, physiology, and disease. His work is informed by discoveries from cutting-edge human genetics approaches and involves the use of disease-relevant cell types derived from human induced pluripotent stem cells (iPSC), CRISPR/Cas9 genome-editing, mouse models, primary and transformed cell lines, and next-generation sequencing to study gene expression. Dr. Hand's research includes interests in cardiometabolic disease, metabolically-associated steatotic liver disease, and pleiotropic human loci impacting lipid and lipoprotein metabolism. He leads efforts to link genetic variants to genes and functions through the functional follow-up of discoveries from genome-wide and phenome-wide association studies. His independent group focuses on cholestatic liver disease and diseases of haploinsufficiency, with particular attention to mRNA regulatory elements as potential targets for treating haploinsufficient conditions.

Research topics

• Internal medicine
• Medicine
• Genetics
• Biology

Selected publications

• G4mer: An RNA language model for transcriptome-wide identification of G-quadruplexes and disease variants from population-scale genetic data

  Nature Communications · 2025-11-20

  articleOpen access

  Abstract RNA G-quadruplexes (rG4s) are key regulatory elements in gene expression, yet the effects of genetic variants on rG4 formation remain underexplored. Here, we introduce G4mer, an RNA language model that predicts rG4 formation, classifies rG4 subtypes, and evaluates the effects of genetic variants across the transcriptome. G4mer significantly improves accuracy over existing methods and uncovers subtype-specific differences in mutational sensitivity and evolutionary constraint, highlighting sequence length and flanking motifs as important rG4 features. Applying G4mer to $${5}^{{\prime} }$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msup> <mml:mrow> <mml:mn>5</mml:mn> </mml:mrow> <mml:mrow> <mml:mo>′</mml:mo> </mml:mrow> </mml:msup> </mml:math> untranslated region (UTR) variations, we identify variants in breast cancer-associated genes that alter rG4 formation and validate their impact on structure and gene expression. These results demonstrate the potential of integrating computational models with experimental approaches to study rG4 function, especially in diseases where non-coding variants are often overlooked. To support broader applications, G4mer is available as both a web tool and a downloadable model.

  PublisherOA PDFDOI

• <i>Ppp1r3b</i> is a metabolic switch that shifts hepatic energy storage from lipid to glycogen

  Science Advances · 2025-05-16 · 6 citations

  articleOpen access

  The PPP1R3B gene, encoding PPP1R3B protein, is critical for liver glycogen synthesis and maintaining blood glucose levels. Genetic variants affecting PPP1R3B expression are associated with several metabolic traits and liver disease, but the precise mechanisms are not fully understood. We studied the effects of both Ppp1r3b overexpression and deletion in mice and cell models and found that both changes in Ppp1r3b expression result in dysregulated metabolism and liver damage, with overexpression increasing liver glycogen stores, while deletion resulted in higher liver lipid accumulation. These patterns were confirmed in humans where variants increasing PPP1R3B expression had lower liver fat and decreased plasma lipids, whereas putative loss-of-function variants were associated with increased liver fat and elevated plasma lipids. These findings support that PPP1R3B is a crucial regulator of hepatic metabolism beyond glycogen synthesis and that genetic variants affecting PPP1R3B expression levels influence if hepatic energy is stored as glycogen or triglycerides.

  PublisherDOI

• Deep metabolic phenotyping of humans with protein-altering variants in TM6SF2 using a genome-first approach

  JHEP Reports · 2024-10-11 · 7 citations

  articleOpen access

  Background & Aim: represents a good candidate for this approach due to its known association with steatotic liver disease (SLD). Methods: and evaluated their association with liver phenotypes and clinical outcomes. Results: <0.05), primarily driven by a novel rare stop-gain variant (W35X) with the same directionality. Conclusion: function and SLD and provides the basis for future mechanistic studies. Impact and implications: variants in metabolic dysfunction-associated steatotic liver disease.

  PublisherDOI

• G4mer: An RNA language model for transcriptome-wide identification of G-quadruplexes and disease variants from population-scale genetic data

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-10-03 · 3 citations

  preprintOpen access

  ABSTRACT RNA G-quadruplexes (rG4s) are key regulatory elements in gene expression, yet the effects of genetic variants on rG4 formation remain underexplored. Here, we introduce G4mer, an RNA language model that predicts rG4 formation and evaluates the effects of genetic variants across the transcriptome. G4mer significantly improves accuracy over existing methods, highlighting sequence length and flanking motifs as important rG4 features. Applying G4mer to 5’ untranslated region (UTR) variations, we identify variants in breast cancer-associated genes that alter rG4 formation and validate their impact on structure and gene expression. These results demonstrate the potential of integrating computational models with experimental approaches to study rG4 function, especially in diseases where non-coding variants are often overlooked. To support broader applications, G4mer is available as both a web tool and a downloadable model.

  PublisherDOI

• A Nutraceutical Mechanistic Model Receives a Gut Check

  Cellular and Molecular Gastroenterology and Hepatology · 2024-01-01

  editorialOpen access1st authorCorresponding

  The recent study in Cellular and Molecular Gastroenterology and Hepatology by Sánchez et al from the Bergheim laboratory at the University of Vienna explores the mechanisms underlying the potentially pathogenic role for the depletion of liver phosphatidylcholine under metabolic stress. It has been known for some time that liver phosphatidylcholine levels are lower in human MASLD patients compared with nonsteatotic controls.1Puri P. Baillie R.A. Wiest M.M. et al.A lipidomic analysis of nonalcoholic fatty liver disease.Hepatology. 2007; 46: 1081-1090Crossref PubMed Scopus (1004) Google Scholar The effect of dietary supplementation of phosphatidylcholine and related phospholipids has been an area of active exploration in the nutriceutical space, with soy-derived polyenyl-phosphatidylcholine supplementation showing significant clinical benefit in a randomized clinical trial in a MASLD/metabolic dysfunction–associated steatohepatitis (MASH) cohort.2Maev I.V. Samsonov A.A. Palgova L.K. et al.Effectiveness of phosphatidylcholine as adjunctive therapy in improving liver function tests in patients with non-alcoholic fatty liver disease and metabolic comorbidities: real-life observational study from Russia.BMJ Open Gastroenterol. 2020; 7e000368Google Scholar Phosphatidylcholine supplementation enhances barrier function in cultured intestinal epithelial cells,3Olson A. Diebel L.N. Liberati D.M. Exogenous phosphatidylcholine supplementation improves intestinal barrier defense against Clostridium difficile toxin.J Trauma Acute Care Surg. 2014; 77 (discussion 576): 570-575Crossref PubMed Google Scholar and can rescue intestinal barrier defects and decrease inflammation in patients with ulcerative colitis.4Stremmel W. Ehehalt R. Staffer S. et al.Mucosal protection by phosphatidylcholine.Dig Dis. 2012; 30: 85-91Crossref PubMed Scopus (48) Google Scholar Despite this, the mechanisms underlying both the decrease in liver phosphatidylcholine and the protective effect of its restoration remain unclear, which are areas that Sánchez et al addressed in their recent study. Sánchez et al used a fast-food–type diet (high fat, high fructose, and high cholesterol) in female C57BL/6J mice to induce MASLD/MASH. After 8 weeks on the diet (16 weeks of age), the mouse livers showed extensive macrosteatosis and the onset of MASH, with increased alanine aminotransferase levels and increased neutrophil granulocyte infiltration, and increased myeloperoxidase activity. The authors also noted effects on the nitric oxide signaling pathway, with increased NOx and a reciprocal decrease in arginase activity (a counter-regulator of nitric oxide [NO] signaling). Relative to the standard diet group, the FFC-fed female mice showed a roughly 2-fold decrease in their liver phosphatidylcholine content. Strikingly, the markers of MASH onset were attenuated significantly by dietary co-administration of phosphatidylcholine with the FFC diet. Sánchez et al next measured lipopolysaccharide from the portal blood of 4 groups of mice: control and fast-food type diet, with and without phosphatidylcholine supplementation. As expected, they found that lipopolysaccharide in portal blood was increased by a fast-food–type diet, however, interestingly, the increased lipopolysaccharide levels were not attenuated by phosphatidylcholine co-administration, suggesting that the effects on the liver markers did not reflect changes in gut permeability. With this in mind, Sánchez et al focused on the effect of phosphatidylcholine on the Toll-like receptor 4 (TLR4) pathway, which transduces the pathogenic effect of lipopolysaccharide to its output in inflammatory signaling via NO and inflammatory cytokines. In contrast to the absence of an effect on lipopolysaccharide levels in blood, the pathway downstream of TLR4 was affected by phosphatidylcholine treatment: levels of tumor necrosis factor α (TNF-α) protein of the ratio of phosphorylated-IκBα to total IκBα were both increased significantly by the FCC diet, and these effects were blunted by co-administration of phosphatidylcholine. In addition, Pparg2 messenger RNA and PPARG2 protein levels were increased by FFC, and this induction was suppressed in the fast-food–type plus phosphatidylcholine group, but there were no differences between groups with respect to the transcript levels of either Pparg1 or Nr5a2 (the latter encodes LRH-1 protein). Lastly, Sánchez et al probed the effects of known modulators of the TLR4–TNF-α axis on the protective effect of phosphatidylcholine. Using lipopolysaccharide as a stressor in the murine macrophage-like cell line, J774A.1, and in primary human macrophages, they measured TNF-α protein and NOx concentration as end points (relative to lipopolysaccharide-treated cells) and found that agonists of PPARG and LRH-1 both attenuated the protective effect of phosphatidylcholine administration (or potentiated the inflammatory effect of lipopolysaccharide). Sánchez et al are appropriately cautious both in the inferences drawn from their data and in their acknowledgment of the limitations of the study. Nonetheless, their observation that the levels of lipopolysaccharide in portal blood are unaffected by co-administration of phosphatidylcholine with the fast-food–type diet raises an interesting challenge to the dogma that phosphatidylcholine supplementation promotes intestinal barrier function and thereby secondarily decreases endotoxemia. Sánchez et al show that phosphatidylcholine affects the pathway downstream of TLR4, suggesting an alternate hypothesis in which the phosphatidylcholine-mediated rescue of intestinal barrier function instead is secondary to a primary effect in decreasing inflammation, and that the impact of phosphatidylcholine supplementation in liver therefore is separable from, but analogous to that in, the gut. Notably, the transcription factors implicated in this study are both nuclear receptors that are responsive to endogenous lipid species that are dysregulated in MASLD (PPARG to fatty acids,5Itoh T. Fairall L. Amin K. et al.Structural basis for the activation of PPARgamma by oxidized fatty acids.Nat Struct Mol Biol. 2008; 15: 924-931Crossref PubMed Scopus (370) Google Scholar LRH-1 to phospholipids6Lee J.M. Lee Y.K. Mamrosh J.L. et al.A nuclear-receptor-dependent phosphatidylcholine pathway with antidiabetic effects.Nature. 2011; 474: 506-510Crossref PubMed Scopus (183) Google Scholar), and both are central regulators in liver, intestine, and the immune system. Fortunately, a wealth of lineage-specific genetic tools and pharmacologic agents already have been developed, and these will be essential to teasing apart the implications of the current work both in healthy and disease conditions. Oral Supplementation of Phosphatidylcholine Attenuates the Onset of a Diet-Induced Metabolic Dysfunction–Associated Steatohepatitis in Female C57BL/6J MiceCellular and Molecular Gastroenterology and HepatologyPreviewChanges in phosphatidylcholine levels in the liver have been associated with the development of metabolic dysfunction–associated steatotic liver disease. Here, the effects of supplementing phosphatidylcholine on the development of early signs of metabolic dysfunction–associated steatohepatitis were assessed. Full-Text PDF Open Access

  PublisherOA PDFDOI

• PPP1R3B is a metabolic switch that shifts hepatic energy storage from lipid to glycogen

  bioRxiv (Cold Spring Harbor Laboratory) · 2023-03-04 · 4 citations

  preprintOpen access

  Summary Obesity is a growing worldwide epidemic that carries numerous metabolic complications including increased risk of type 2 diabetes (T2D), cardiovascular disease (CVD), and non-alcoholic fatty liver disease (NAFLD). Multiple genome-wide association studies (GWAS) have associated the PPP1R3B locus with cardiometabolic traits including fasting glucose and insulin levels (T2D traits), plasma lipids (CVD traits), and indications of hepatic steatosis and liver damage (NAFLD traits) 1–5 . The PPP1R3B gene encodes the glycogen regulatory protein PPP1R3B (also known as G L ) which has an established role in liver glycogen metabolism and plasma glucose homeostasis 6,7 . The metabolic and NAFLD GWAS single nucleotide polymorphisms (SNPs) in this region, which are all in high linkage disequilibrium, result in increased liver PPP1R3B expression and hepatic glycogen accumulation, but have provided conflicting results on the impacts on hepatic steatosis and liver damage. Here we investigate the consequences of both Ppp1r3b overexpression and deletion in mouse and cell models and find that dysregulated Ppp1r3b expression in either direction promotes metabolic dysfunction and liver injury. Hepatocyte overexpression of Ppp1r3b increases hepatic glycogen storage, prolongs fasting blood glucose levels, and confers protection from hepatic steatosis, but increases plasma ALT in aged animals. Conversely, deletion of hepatocyte Ppp1r3b eliminates hepatic glycogen, causes impaired glucose disposal, and results in hepatic steatosis with age or high sucrose diet. We investigated the metabolic pathways contributing to steatosis and found that Ppp1r3b deletion and diminished glycogenesis diverts the storage of exogenous glucose to hepatic triglycerides (TG), and stored liver lipids are preferentially used for energy during fasting through lipid oxidation and ketogenesis. Further, we interrogated two large human biobank cohorts and found carriers of SNPs associated with increased PPP1R3B expression have increased plasma glucose, decreased hepatic fat, and lower plasma lipids, while putative loss-of-function (pLoF) variant carriers have increased hepatic fat and elevated plasma ketones and lipids, consistent with the results seen in our mouse models. These findings suggest hepatic PPP1R3B serves as a metabolic switch favoring hepatic energy storage as glycogen instead of TG.

  PublisherOA PDFDOI

• A missense variant in human perilipin 2 (PLIN2 Ser251Pro) reduces hepatic steatosis in mice

  JHEP Reports · 2023-10-11 · 12 citations

  articleOpen access

  •NAFLD is characterised by the accumulation of lipid droplets within hepatocytes.•Lipid droplets are active storage organelles with a unique architecture.•PLIN2 plays an important role in the formation and stability of lipid droplets and lipophagy.•The PLIN2-Pro251 variant has been associated with reduced plasma levels of triglycerides and VLDLs.•The PLIN2-Pro251 variant reduced liver triglycerides and lipid droplet accumulation. Background & AimsNon-alcoholic fatty liver disease (NAFLD) is characterised by the accumulation of lipid droplets (LDs) within hepatocytes. Perilipin 2 (PLIN2) is the most abundant protein in hepatic LDs and its expression correlates with intracellular lipid accumulation. A recently discovered PLIN2 coding variant, Ser251Pro (rs35568725), was found to promote the accumulation of small LDs in embryonic kidney cells. In this study, we investigate the role of PLIN2-Ser251Pro (PLIN2-Pro251) on hepatic LD metabolism in vivo and research the metabolic phenotypes associated with this variant in humans.MethodsFor our animal model, we used Plin2 knockout mice in which we expressed either human PLIN2-Pro251 (Pro251 mice) or wild-type human PLIN2-Ser251 (Ser251 mice) in a hepatocyte-specific manner. We fed both cohorts a lipogenic high-fat, high-cholesterol, high-fructose diet for 12 weeks.ResultsPro251 mice were associated with reduced liver triglycerides (TGs) and had lower mRNA expression of fatty acid synthase and diacylglycerol O-acyltransferase-2 compared with Ser251 mice. Moreover, Pro251 mice had a reduction of polyunsaturated fatty acids-TGs and reduced expression of epoxygenase genes. For our human study, we analysed the Penn Medicine BioBank, the Million Veteran Program, and UK Biobank. Across these databases, the minor allele frequency of PLIN2-Pro251 was approximately 5%. There was no association with the clinical diagnosis of NAFLD, however, there was a trend toward reduced liver fat in PLIN2-Pro251 carriers by MRI-spectroscopy in UK Biobank subjects.ConclusionsIn mice lacking endogenous Plin2, expression of human PLIN2-Pro251 attenuated high-fat, high-fructose, high-cholesterol, diet-induced hepatic steatosis compared with human wild-type PLIN2-Ser251. Moreover, Pro251 mice had lower polyunsaturated fatty acids-TGs and epoxygenase genes expression, suggesting less liver oxidative stress. In humans, PLIN2-Pro251 is not associated with NAFLD.Impact and ImplicationsLipid droplet accumulation in hepatocytes is the distinctive characteristic of non-alcoholic fatty liver disease. Perilipin 2 (PLIN2) is the most abundant protein in hepatic lipid droplets; however, little is known on the role of a specific polymorphism PLIN2-Pro251 on hepatic lipid droplet metabolism. PLIN2-Pro251 attenuates liver triglycerides accumulation after a high-fat-high-glucose-diet. PLIN2-Pro251 may be a novel lipid droplet protein target for the treatment of liver steatosis. Non-alcoholic fatty liver disease (NAFLD) is characterised by the accumulation of lipid droplets (LDs) within hepatocytes. Perilipin 2 (PLIN2) is the most abundant protein in hepatic LDs and its expression correlates with intracellular lipid accumulation. A recently discovered PLIN2 coding variant, Ser251Pro (rs35568725), was found to promote the accumulation of small LDs in embryonic kidney cells. In this study, we investigate the role of PLIN2-Ser251Pro (PLIN2-Pro251) on hepatic LD metabolism in vivo and research the metabolic phenotypes associated with this variant in humans. For our animal model, we used Plin2 knockout mice in which we expressed either human PLIN2-Pro251 (Pro251 mice) or wild-type human PLIN2-Ser251 (Ser251 mice) in a hepatocyte-specific manner. We fed both cohorts a lipogenic high-fat, high-cholesterol, high-fructose diet for 12 weeks. Pro251 mice were associated with reduced liver triglycerides (TGs) and had lower mRNA expression of fatty acid synthase and diacylglycerol O-acyltransferase-2 compared with Ser251 mice. Moreover, Pro251 mice had a reduction of polyunsaturated fatty acids-TGs and reduced expression of epoxygenase genes. For our human study, we analysed the Penn Medicine BioBank, the Million Veteran Program, and UK Biobank. Across these databases, the minor allele frequency of PLIN2-Pro251 was approximately 5%. There was no association with the clinical diagnosis of NAFLD, however, there was a trend toward reduced liver fat in PLIN2-Pro251 carriers by MRI-spectroscopy in UK Biobank subjects. In mice lacking endogenous Plin2, expression of human PLIN2-Pro251 attenuated high-fat, high-fructose, high-cholesterol, diet-induced hepatic steatosis compared with human wild-type PLIN2-Ser251. Moreover, Pro251 mice had lower polyunsaturated fatty acids-TGs and epoxygenase genes expression, suggesting less liver oxidative stress. In humans, PLIN2-Pro251 is not associated with NAFLD.

  PublisherOA PDFDOI

• Comparison of the structure-function properties of wild-type human apoA-V and a C-terminal truncation associated with elevated plasma triglycerides

  medRxiv · 2023-02-23 · 1 citations

  preprintOpen access

  Abstract Background Plasma triglycerides (TGs) are causally associated with coronary artery disease and acute pancreatitis. Apolipoprotein A-V (apoA-V, gene APOA5 ) is a liver-secreted protein that is carried on triglyceride-rich lipoproteins and promotes the enzymatic activity of lipoprotein lipase (LPL), thereby reducing TG levels. Little is known about apoA-V structure-function; naturally occurring human APOA5 variants can provide novel insights. Methods We used hydrogen-deuterium exchange mass spectrometry to determine the secondary structure of human apoA-V in lipid-free and lipid-associated conditions and identified a C-terminal hydrophobic face. Then, we used genomic data in the Penn Medicine Biobank to identify a rare variant, Q252X, predicted to specifically eliminate this region. We interrogated the function of apoA-V Q252X using recombinant protein in vitro and in vivo in apoa5 knockout mice. Results Human apoA-V Q252X carriers exhibited elevated plasma TG levels consistent with loss of function. Apoa5 knockout mice injected with AAV vectors expressing wildtype and variant APOA5 -AAV recapitulated this phenotype. Part of the loss of function is due to reduced mRNA expression. Functionally, recombinant apoA-V Q252X was more readily soluble in aqueous solutions and more exchangeable with lipoproteins than WT apoA-V. Despite lacking the C- terminal hydrophobic region (a putative lipid binding domain) this protein also decreased plasma TG in vivo . Conclusions Deletion of apoA-V’s C-terminus leads to reduced apoA-V bioavailability in vivo and higher TG levels. However, the C-terminus is not required for lipoprotein binding or enhancement of intravascular lipolytic activity. WT apoA-V is highly prone to aggregation, and this property is markedly reduced in recombinant apoA-V lacking the C-terminus.

  PublisherOA PDFDOI

• A multiancestry genome-wide association study of unexplained chronic ALT elevation as a proxy for nonalcoholic fatty liver disease with histological and radiological validation

  Nature Genetics · 2022 · 188 citations

  • Biology
  • Internal medicine
  • Genetics
  PublisherOA PDFDOI

• Sortilin restricts secretion of apolipoprotein B-100 by hepatocytes under stressed but not basal conditions

  DOAJ (DOAJ: Directory of Open Access Journals) · 2022-03-01 · 21 citations

  article

  Genetic variants at the SORT1 locus in humans, which cause increased SORT1 expression in the liver, are significantly associated with reduced plasma levels of LDL cholesterol and apolipoprotein B (apoB). However, the role of hepatic sortilin remains controversial, as genetic deletion of sortilin in mice has resulted in variable and conflicting effects on apoB secretion. Here, we found that Sort1-KO mice on a chow diet and several Sort1-deficient hepatocyte lines displayed no difference in apoB secretion. When these models were challenged with high-fat diet or ER stress, the loss of Sort1 expression resulted in a significant increase in apoB-100 secretion. Sort1-overexpression studies yielded reciprocal results. Importantly, carriers of SORT1 variant with diabetes had larger decreases in plasma apoB, TG, and VLDL and LDL particle number as compared with people without diabetes with the same variants. We conclude that, under basal nonstressed conditions, loss of sortilin has little effect on hepatocyte apoB secretion, whereas, in the setting of lipid loading or ER stress, sortilin deficiency leads to increased apoB secretion. These results are consistent with the directionality of effect in human genetics studies and suggest that, under stress conditions, hepatic sortilin directs apoB toward lysosomal degradation rather than secretion, potentially serving as a quality control step in the apoB secretion pathway in hepatocytes.

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Frequent coauthors

• Daniel J. Rader

  University of Pennsylvania

  41 shared

• Joshua R. Friedman

  41 shared

• Zankhana R. Master

  University of Missouri

  25 shared

• Claire L. Le Guen

  Temple University Hospital

  13 shared

• LaTasha A. Boateng

  Children's Hospital of Philadelphia

  13 shared

• Donna Conlon

  University of Pennsylvania

  10 shared

• Amber M. Horner

  10 shared

• Robert C. Bauer

  Columbia University Irving Medical Center

  9 shared

Labs

• Nicholas J. Hand LabPI

Education

• PhD, Molecular Biology

  Princeton University

  2002

• B.A.(Mod), Genetics (Natural Sciences II)

  University of Dublin Trinity College

  1992