About

Natalia I. Krupenko, PhD, is an Associate Professor in the Department of Nutrition at the UNC Gillings School of Global Public Health. She has over 20 years of experience researching the role of folate vitamin in health and disease. Her research includes uncovering the structure of enzymes that could aid in disease treatment and prevention, as well as identifying regulatory links between cells that could lead to novel cancer therapies. Dr. Krupenko's work has contributed to understanding the molecular mechanisms underlying the potentially adverse effects of folate and exploring its role as both a friend and foe in health. She has been recognized with awards such as the 1st Place Poster Award at the 2012 Advances and Controversies in B-vitamins and Choline Conference in Leipzig, Germany.

Research topics

• Biology
• Genetics
• Cell biology
• Biochemistry
• Cancer research
• Medicine
• Bioinformatics

Selected publications

• Differential Expression of One‐Carbon Pathway Enzyme <scp>ALDH1L1</scp> Is Linked to Tumorigenicity of Low‐Grade Bladder Cancer Cells Through Metabolic Reprogramming

  Cancer Medicine · 2025-10-01

  articleOpen access

  BACKGROUND: RT4 bladder cancer cell line, derived from a nonmuscle-invasive low-grade subtype, is one of the few neoplastic cell lineages that maintain high expression of the candidate tumor suppressor ALDH1L1. Here, we investigated how differential ALDH1L1 expression affects cellular characteristics and tumorigenicity of RT4 cells as well as tumor metabotypes. METHODS: We characterized RT4 cells and two shRNA clones (sh506/low ALDH1L1 expression; sh572/ALDH1L1 is lost) for proliferation, migration, clonogenic capacity, and mitochondrial respiration. We have further evaluated the tumorigenic potential of RT4 cells and the two clones in nude mice and compared metabotypes of derived tumors using untargeted metabolomics. RESULTS: Both clones with diminished ALDH1L1 expression exhibited increased proliferation rates with doubling times of 19.4 h (sh506) and 23.2 h (sh572) versus 36.3 h for RT4 cells. Downregulation of ALDH1L1 expression also enhanced motility and clonogenic capacity. Proliferation and clonogenic capacity were highest for the sh506 clone (low ALDH1L1 expression), while motility was strongest for the sh572 clone (complete ALDH1L1 loss). Both clones showed altered energy metabolism, as indicated by a reduced basal oxygen consumption rate and enhanced maximal respiration rate following oligomycin treatment. Mouse xenograft tumors derived from ALDH1L1-deficient RT4 clones were significantly larger than RT4 cell-derived tumors. Of note, complete ALDH1L1 loss (sh572 clone) was less advantageous for tumor growth than the partial loss of the protein (sh506 clone). Untargeted metabolomics has shown that tumors with downregulated ALDH1L1 have altered the metabolism of fatty acids, amino acids, CoA, and acylcarnitines. Alterations in several key pathways, including glutathione metabolism (sh506), and TCA cycle (sh572), depend on the extent of ALDH1L1 downregulation. CONCLUSIONS: Our study underscores ALDH1L1 as a key metabolic regulator of proliferation, migration, and tumorigenicity in RT4 bladder cancer cells, suggesting that retaining low ALDH1L1 expression can provide a metabolic advantage for growth of aggressive tumors.

  PublisherOA PDFDOI

• Exploratory Metabolomics Underscores the Folate Enzyme ALDH1L1 as a Regulator of Glycine and Methylation Reactions

  UNC Libraries · 2025-07-26

  articleOpen access

  Folate (vitamin B9) is involved in one-carbon transfer reactions and plays a significant role in nucleic acid synthesis and control of cellular proliferation, among other key cellular processes. It is now recognized that the role of folates in different stages of carcinogenesis is complex, and more research is needed to understand how folate reactions become dysregulated in cancers and the metabolic consequences that occur as a result. ALDH1L1 (cytosolic 10-formyltetrahydrofolate dehydrogenase), an enzyme of folate metabolism expressed in many tissues, is ubiquitously downregulated in cancers and is not expressed in cancer cell lines. The RT4 cell line (derived from papillary bladder cancer) which expresses high levels of ALDH1L1 represents an exception, providing an opportunity to explore the metabolic consequences of the loss of this enzyme. We have downregulated this protein in RT4 cells (shRNA driven knockdown or CRISPR driven knockout) and compared metabolomes of ALDH1L1-expressing and -deficient cells to determine if metabolic changes linked to the loss of this enzyme might provide proliferative and/or survival advantages for cancer cells. In this study, cell extracts were analyzed using Ultra High Performance Liquid Chromatography High Resolution Mass Spectrometry (UHPLC-HR-MS). A total of 13,339 signals were identified or annotated using an in-house library and public databases. Supervised and unsupervised multivariate analysis revealed metabolic differences between RT4 cells and ALDH1L1-deficient clones. Glycine (8-fold decrease) and metabolites derived from S-adenosylmethionine utilizing pathways were significantly decreased in the ALDH1L1-deficient clones, compared with RT4 cells. Other changes linked to ALDH1L1 downregulation include decreased levels of amino acids, Krebs cycle intermediates, and ribose-5-phosphate, and increased nicotinic acid. While the ALDH1L1-catalyzed reaction is directly linked to glycine biosynthesis and methyl group flux, its overall effect on cellular metabolism extends beyond immediate metabolic pathways controlled by this enzyme.

  PublisherDOI

• Pancreatic islet protection at the expense of secretory function involves serine-linked mitochondrial one-carbon metabolism

  UNC Libraries · 2025-07-26

  articleOpen access
  PublisherDOI

• Differential Expression of One‐Carbon Pathway Enzyme ALDH1L1 Is Linked to Tumorigenicity of Low‐Grade Bladder Cancer Cells Through Metabolic Reprogramming

  UNC Libraries · 2025-12-17

  articleOpen access1st authorCorresponding

  RT4 bladder cancer cell line, derived from a nonmuscle‐invasive low‐grade subtype, is one of the few neoplastic cell lineages that maintain high expression of the candidate tumor suppressor ALDH1L1. Here, we investigated how differential ALDH1L1 expression affects cellular characteristics and tumorigenicity of RT4 cells as well as tumor metabotypes. We characterized RT4 cells and two shRNA clones (sh506/low ALDH1L1 expression; sh572/ALDH1L1 is lost) for proliferation, migration, clonogenic capacity, and mitochondrial respiration. We have further evaluated the tumorigenic potential of RT4 cells and the two clones in nude mice and compared metabotypes of derived tumors using untargeted metabolomics. Both clones with diminished ALDH1L1 expression exhibited increased proliferation rates with doubling times of 19.4 h (sh506) and 23.2 h (sh572) versus 36.3 h for RT4 cells. Downregulation of ALDH1L1 expression also enhanced motility and clonogenic capacity. Proliferation and clonogenic capacity were highest for the sh506 clone (low ALDH1L1 expression), while motility was strongest for the sh572 clone (complete ALDH1L1 loss). Both clones showed altered energy metabolism, as indicated by a reduced basal oxygen consumption rate and enhanced maximal respiration rate following oligomycin treatment. Mouse xenograft tumors derived from ALDH1L1‐deficient RT4 clones were significantly larger than RT4 cell‐derived tumors. Of note, complete ALDH1L1 loss (sh572 clone) was less advantageous for tumor growth than the partial loss of the protein (sh506 clone). Untargeted metabolomics has shown that tumors with downregulated ALDH1L1 have altered the metabolism of fatty acids, amino acids, CoA, and acylcarnitines. Alterations in several key pathways, including glutathione metabolism (sh506), and TCA cycle (sh572), depend on the extent of ALDH1L1 downregulation. Our study underscores ALDH1L1 as a key metabolic regulator of proliferation, migration, and tumorigenicity in RT4 bladder cancer cells, suggesting that retaining low ALDH1L1 expression can provide a metabolic advantage for growth of aggressive tumors.

  PublisherDOI

• Probing the metabolic regulator and candidate tumor suppressor ALDH1L1 as a target for non-small cell lung cancer gene therapy

  Molecular Therapy Oncology · 2025-08-21

  articleOpen access

  ALDH1L1, a major cytosolic folate enzyme and key regulator of one-carbon metabolism, is strongly and ubiquitously downregulated in lung adenocarcinomas (LUADs) and silenced in LUAD cell lines. Analysis of publicly available databases indicates that ALDH1L1 expression is associated with better prognosis and overall survival in LUAD patients. Here we used lentiviral delivery of ALDH1L1 to target metabolism in ALDH1L1-deficient LUAD cell lines A549 and H460. In these cells, ALDH1L1 expression led to strong inhibition of proliferation, colony formation, and migration. Untargeted metabolomic analysis has shown that ALDH1L1 knockin produces a strong effect on the metabotype of A549 cells including alterations in the tricarboxylic acid cycle intermediates and acylcarnitines, indicative of the impairment of cellular energetics. We have further demonstrated that in mice ALDH1L1, lentiviral delivery dramatically inhibits growth of subcutaneous xenograft tumors derived from A549 cells and prevents lung colonization in a tail-vein model. These effects prolonged for the duration of the experiments (6 weeks) with no noticeable decrease in ALDH1L1 protein levels at the endpoint of the study. We did not observe side effects of ALDH1L1 delivery on animal health when compared with the control group. Our study suggests that ALDH1L1 delivery could be a promising gene therapy approach for treating LUAD.

  PublisherDOI

• Aldehyde Dehydrogenases

  Elsevier eBooks · 2025-01-01

  book-chapter
  PublisherDOI

• Further delineation of the phenotypic and metabolomic profile of <i>ALDH1L2</i>‐related neurodevelopmental disorder

  Clinical Genetics · 2024-01-09 · 2 citations

  articleOpen access

  Abstract ALDH1L2, a mitochondrial enzyme in folate metabolism, converts 10‐formyl‐THF (10‐formyltetrahydrofolate) to THF (tetrahydrofolate) and CO 2 . At the cellular level, deficiency of this NADP + ‐dependent reaction results in marked reduction in NADPH/NADP + ratio and reduced mitochondrial ATP. Thus far, a single patient with biallelic ALDH1L2 variants and the phenotype of a neurodevelopmental disorder has been reported. Here, we describe another patient with a neurodevelopmental disorder associated with a novel homozygous missense variant in ALDH1L2 , Pro133His. The variant caused marked reduction in the ALDH1L2 enzyme activity in skin fibroblasts derived from the patient as probed by 10‐FDDF, a stable synthetic analog of 10‐formyl‐THF. Additional associated abnormalities in these fibroblasts include reduced NADPH/NADP + ratio and pool of mitochondrial ATP, upregulated autophagy and dramatically altered metabolomic profile. Overall, our study further supports a link between ALDH1L2 deficiency and abnormal neurodevelopment in humans.

  PublisherOA PDFDOI

• P10-029-23 ALDH1L2 Controls High-Fat Diet Induced Obesity-Linked Pathways in Female Mice

  Current Developments in Nutrition · 2023-07-01 · 1 citations

  articleOpen access
  PublisherDOI

• Pancreatic islet protection at the expense of secretory function involves serine-linked mitochondrial one-carbon metabolism

  Cell Reports · 2023-06-01 · 8 citations

  articleOpen access

  ratio increases. Activating transcription factor-4 (Atf4) is required and sufficient to activate serine-linked mitochondrial OCM genes in islets, with gain- and loss-of-function experiments showing that Atf4 reduces GSIS and is required, but not sufficient, for full DXO-mediated islet protection. In sum, we identify a reversible metabolic pathway that provides islet protection at the expense of secretory function.

  PublisherOA PDFDOI

• Abstract LB_B09: Loss of folate enzyme ALDH1L1 promotes cancer cell proliferation and xenograft tumor growth

  Molecular Cancer Therapeutics · 2023-12-01

  article

  Abstract Background: ALDH1L1 (aldehyde dehydrogenase 1 family member L1, or cytosolic 10-formyltetrahydrofolate dehydrogenase), an enzyme in folate metabolism, is abundantly expressed in several tissues. This enzyme converts 10-formyltetrahydrofolate to tetrahydrofolate (THF) and CO2 while reducing NADP+ to NADPH. ALDH1L1 is ubiquitously downregulated human cancers through DNA promoter methylation, while one cancer cell line, RT4 (derived from papillary bladder cancer), maintains high expression of ALDH1L1. Aims: We tested the hypothesis that loss of ALDH1L1 expression could provide a proliferative and survival advantage for cancer cells and tumor growth. Methods: The ALDH1L1 gene in RT4 cells was knocked down using the shRNA technique. Proliferation was evaluated using MTT assays and xCELLigence real-time cellular analysis (RTCA). Cell migration was assessed by wound healing assays. NADP+/NADPH levels and reduced folate pools were measured by ELISA and the ternary complex assays, respectively. RT4 tumors were generated in nude mice from RT4 lines by subcutaneous injections into both flanks of athymic nude mice. Tumor growth was monitored every week for 12-weeks, after which the tumors were harvested. ALDH1L1 levels in tumors were measured by Western Blot assays, while tumor proliferation was assessed by the Ki-67/H&amp;E staining of the tumor tissue sections. Results: We found that doubling time did not differ between the wild-type (RT4) and shControl (shC) cell lines. Doubling time for the sh506 and sh572 clones was shorter than the controls by 68% and 79%, respectively. Proliferation and migration were significantly increased in sh506 and sh572 cells compared to the control lines. NADP+/NADPH levels were significantly increased for only the sh572 clone. Interestingly, tumor volume and weight were increased in both sh506 and sh572 derived tumors compared to shC tumors. The sh506 and sh572 tumors also showed a slightly increased Ki-67 proliferation index. The ALDH1L1 protein expression was completely lost in sh572 tumors but only partially decreased in sh506 tumors. Conclusions: Our study indicates that RT4 clones lacking ALDH1L1 have increased cell proliferation and tumor growth compared to wild-type RT4 cells, supporting the role of ALDH1L1 as a metabolic regulator of proliferation. Citation Format: Halle M Fogle, Mikyoung You, Jaspreet Sharma, Jonathan McCormac, Natalia I Krupenko, Sergey A Krupenko. Loss of folate enzyme ALDH1L1 promotes cancer cell proliferation and xenograft tumor growth [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr LB_B09.

  PublisherDOI

Recent grants

• NIH Grant P20RR017677

  NIH · $18.2M · 2012

• NIH Grant R21DK083744

  NIH · $404k · 2013

• Ceramide signaling in the regulation of cellular response to folate stress

  NIH · $1.7M · 2015–2021

Frequent coauthors

• Sergey A. Krupenko

  University of North Carolina at Chapel Hill

  104 shared

• Susan Sumner

  University of California, Los Angeles

  31 shared

• Jaspreet Sharma

  28 shared

• Keri Barron

  20 shared

• Peter Pediaditakis

  16 shared

• Kristen A. Jeffries

  16 shared

• Kristi L. Helke

  Medical University of South Carolina

  16 shared

• Besim Öğretmen

  15 shared

Awards & honors

• 1st Place Poster Award 2012, Advances and Controversies in B…