Biology subjects

Flanigan, W. R.

Publications and source records attributed to Flanigan, W. R..

6 recordsLinked to original sources

bioRxiv2026

Branched-chain amino acid fermentation as an alternative mammalian electron sink

Hypoxia disrupts mitochondrial respiration and increases the NADH/NAD+ ratio, causing reductive stress. To maintain redox homeostasis, mammalian cells divert electrons toward fermentation. While fermentation in mammals typically involves lactate production, we identify the fermentation of branched-chain amino acids (BCAAs) as an alternative electron sink activated by hypoxia. The resulting metabolites are excreted in urine as a distinct mechanism for alleviating reductive stress. BCAA fermentation is catalyzed by lactate dehydrogenase (LDH) enzymes and is highly responsive to the NADH/NAD+ ratio. Consequently, BCAA fermentation products are sensitive biomarkers for reductive stress in human contexts ranging from resistance exercise to severe hypoxemia. Furthermore, we find that mouse sperm have evolved highly efficient BCAA fermentation, providing a specific metabolic strategy to support the anaerobic electron flow that facilitates flagellar hypermotility across mammalian sperm. Our work highlights an under-appreciated fate of BCAAs in response to reductive stress.

cell biology↗

bioRxiv2026

Systemic hypoxia suppresses solid tumor growth

Local hypoxia is a hallmark of solid tumors and a negative prognostic factor in the progression and treatment of cancer. Here, we showed that systemic hypoxia, in contrast to localized tumor hypoxia, decreases tumor growth in vivo across multiple cancer types and preclinical models. The reduced tumor growth in systemic hypoxia was not explained by hypoglycemia, hypoinsulinemia, or HIF activation. Instead, metabolite profiling in tumors and tumor interstitial fluid revealed extensive perturbations in purine-related metabolites. Stable isotope tracing demonstrated that systemic hypoxia caused tumors to suppress de novo purine synthesis. Furthermore, tumors did not develop resistance to systemic hypoxia therapy, and when used in combination with chemotherapy or immunotherapy, systemic hypoxia dramatically suppressed tumor growth. Finally, we showed that systemic hypoxia can be achieved pharmacologically with the small molecule HypoxyStat. These findings challenge the long-held paradigm of hypoxia as a negative prognostic factor in cancer progression, and they suggest a potential therapeutic role for systemic hypoxia in suppressing solid tumor growth.

cancer biology↗

bioRxiv2026

Genome-wide CRISPRi screen identifies basigin loss as protective in cardiac hypoxia

Cardiac function depends on continuous oxidative metabolism, rendering cardiomyocytes highly vulnerable to oxygen deprivation. Here, we performed a genome-wide CRISPR interference (CRISPRi) screen in human iPSC-derived cardiomyocytes to identify genes that modulate survival during chronic hypoxia. This screen revealed that knockdown of basigin (BSG), a chaperone for the monocarboxylate transporters MCT1 and MCT4, confers robust protection. Canonically, hypoxic cells suppress pyruvate dehydrogenase (PDH) activity to reduce the oxidation of major fuel sources, thereby limiting TCA cycle flux, lowering oxygen consumption, and minimizing reactive oxygen species generated by an overly reduced electron transport chain (ETC). In contrast, we found that BSG inhibition reverses this response, prioritizing ATP maintenance during hypoxia and enhancing cardiomyocyte survival. Mechanistically, BSG loss restricts lactate efflux, leading to decreased PDH phosphorylation and increased glucose uptake for oxidation. Consistent with this, ETC subunits are more essential under hypoxia, highlighting cardiomyocytes unusual reliance on aerobic ATP production even when oxygen is limited. These findings challenge prevailing models of hypoxic adaptation by revealing cardiomyocyte-specific bioenergetic requirements and motivating future therapeutic efforts.

cell biology↗

bioRxiv2025

Genetic regulators of neuronal survival across metabolic environments

Cellular energy metabolism and oxygen availability shape neuronal function and vulnerability, yet the genetic regulators of these metabolic processes in human neurons remain incompletely understood. Here, we performed CRISPR interference (CRISPRi) screens in human induced pluripotent stem cell (iPSC)-derived neurons across four distinct metabolic conditions and at three physiologically relevant oxygen tensions. This combinatorial approach enabled systematic interrogation of gene-environment interactions that govern neuronal metabolic adaptation. We identified genes--including genes associated with Leigh syndrome and autism spectrum disorder--whose importance for cell survival is highly sensitive to environmental context, revealing potential mechanisms underlying metabolic specification and selective neuronal vulnerability in neurological disorders. Our screens also uncovered regulators of neuronal glycolysis, including KIAA1429 and MAPT among others, which are previously uncharacterized modulators of neuronal glucose utilization and metabolic flexibility. Our work nominates candidate metabolic interventions and gene targets for enhancing neuronal resilience under hypoxic or nutrient-limited conditions.

systems biology↗

bioRxiv2025

Red Blood Cells Serve as a Primary Glucose Sink to Improve Glucose Tolerance at Altitude

High altitude conditions result in improved glucose tolerance and lower diabetes risk across species, yet the underlying physiological mechanism remains unclear. Using mouse models, we found that hypoxia alone robustly improved glucose tolerance, independent of insulin sensitivity. This effect persisted for weeks after mice returned to normoxia. PET-CT imaging revealed that internal organs explained only a small fraction of increased glucose uptake in hypoxia, suggesting the presence of an unknown glucose sink. We hypothesized that increased glucose tolerance might be linked to the hypoxia-induced increase in red blood cells (RBCs), whose metabolism relies entirely on glucose. Experimental manipulation of RBC numbers through phlebotomy or transfusion directly altered blood glucose levels, demonstrating the necessity and sufficiency of RBCs as primary glucose sinks in hypoxia. Moreover, RBCs produced during systemic hypoxia exhibited a sustained [~]3-fold increase in glucose uptake, rapidly synthesizing the hemoglobin allosteric regulator 2,3-DPG that allows for increased oxygen release in hypoxia. Therapeutically, we demonstrated that both chronic hypoxia and our recently developed pharmacological hypoxia mimetic, HypoxyStat, effectively rescued hyperglycemia in mouse models of type 1 and type 2 diabetes. Our findings identify RBCs as critical regulators of systemic glucose metabolism under hypoxic conditions, illuminating a conserved physiological adaptation and suggesting novel therapeutic avenues for hyperglycemic disorders. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=184 SRC="FIGDIR/small/650365v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@b6e505org.highwire.dtl.DTLVardef@175e720org.highwire.dtl.DTLVardef@198efdborg.highwire.dtl.DTLVardef@1ab2418_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2020

SARS-CoV-2 infection of human iPSC-derived cardiac cells predicts novel cytopathic features in hearts of COVID-19 patients

Although COVID-19 causes cardiac dysfunction in up to 25% of patients, its pathogenesis remains unclear. Exposure of human iPSC-derived heart cells to SARS-CoV-2 revealed productive infection and robust transcriptomic and morphological signatures of damage, particularly in cardiomyocytes. Transcriptomic disruption of structural proteins corroborated adverse morphologic features, which included a distinct pattern of myofibrillar fragmentation and numerous iPSC-cardiomyocytes lacking nuclear DNA. Human autopsy specimens from COVID-19 patients displayed similar sarcomeric disruption, as well as cardiomyocytes without DNA staining. These striking cytopathic features provide new insights into SARS-CoV-2 induced cardiac damage, offer a platform for discovery of potential therapeutics, and raise serious concerns about the long-term consequences of COVID-19.

cell biology↗