Biology subjects

Kelly, K. P.

Publications and source records attributed to Kelly, K. P..

5 recordsLinked to original sources

bioRxiv2026

SIM2s coordinates programmed mitophagy with respiratory chain supercomplex remodeling during mammary epithelial differentiation

Lactation requires mammary epithelial cells (MECs) to rapidly expand mitochondrial function while remodeling the mitochondrial population that supports milk synthesis and secretion. Programmed mitophagy is required for MEC differentiation, yet why mitochondrial turnover is necessary during this developmental transition remains poorly understood. Using Mito-QC reporter mice, we identified developmentally regulated changes in mitolysosome burden across the transition from late pregnancy to lactation that were altered by mammary-specific gain or loss of the bhlh/PAS protein, SIM2s (single-minded 2 s). In differentiating HC11 cells, mitochondrial turnover was accompanied by increased assembly and activity of respiratory supercomplexes containing complexes I, III, and IV. Depletion of PRKN prevented acquisition of this differentiation-associated respiratory profile and impaired lactogenic differentiation. SIM2s co-migrated with higher-order respiratory assemblies, and loss of SIM2s reduced supercomplex assembly and activity in HC11 cells and mammary tissue. SIM2s also localized in close proximity to complex III in differentiated mammary epithelium, whereas loss of SIM2s reduced proximity between complexes III and IV. Together, these findings support a model in which SIM2s coordinates PRKN-dependent mitochondrial turnover with respiratory-chain remodeling during MEC differentiation. Our results suggest that programmed mitophagy does more than remove mitochondria during development; it contributes to establishment of a mitochondrial population with a respiratory-chain architecture suited to the emerging differentiated state.

cell biology↗

bioRxiv2026

Atg8 orchestrates stress-responsive chromatin programs across immunity and metabolism

Organisms must coordinate transcriptional responses to immune and metabolic stress, often within the same tissue. In Drosophila and mammals, adipose tissue integrates these signals by mounting antimicrobial defense during acute infection and remodeling lipid metabolism under chronic nutrient surplus. How one cell-biological system supports both functions, and through what molecular machinery, remains incompletely understood. Atg8/LC3, classically defined by canonical autophagy, has emerging non-canonical roles in nuclear gene regulation, raising the possibility that it contributes to stress-coordinated transcription beyond cargo turnover. Using unbiased CUT&RUN in adult Drosophila nuclei, we find that endogenous Atg8 exhibits broad chromatin occupancy at immune, metabolic, and autophagy loci, and accumulates in nuclei under prolonged high-sugar diet (HSD) and acute Gram-positive infection. We identify two conserved Atg8-interacting motifs (AIMs) within the Rel homology domain of NF-{kappa}B/Dif. Flies carrying CRISPR-engineered AIM-mutant Dif are highly susceptible to both infection and chronic HSD, establishing a physiological requirement for intact Dif AIMs. AIM-mutant Dif shows impaired infection-induced nuclear accumulation, suggesting that Atg8 contributes to both Dif cytoplasmic-to-nuclear shuttling and nuclear function. Unbiased comparison of Atg8 chromatin occupancy across HSD and infection further reveals shared and divergent motif grammar, positioning Atg8 as a stress-responsive chromatin cofactor for immune and metabolic transcription. Together, these findings expand the functional landscape of Atg8/LC3 beyond canonical autophagy and reveal that autophagy machinery contributes to stress-specific transcriptional complex assembly. AIM/LIR-mediated interactions, exemplified by Dif, represent one such interface, while additional mechanisms likely underlie Atg8s broader chromatin engagement at loci enriched for transcription factor motifs whose cognate factors lack known AIM/LIRs. We propose that Atg8/LC3-mediated coordination of immune and metabolic transcription is a general principle by which cells integrate diverse stress signals, with implications for obesity, chronic inflammation, and other disease states in which immune and metabolic dysregulation converge. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/727304v2_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@15c056dorg.highwire.dtl.DTLVardef@68493dorg.highwire.dtl.DTLVardef@a07c6corg.highwire.dtl.DTLVardef@4896c6_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LIStress drives Atg8 into nuclei, where it occupies immune and metabolic chromatin. C_LIO_LITwo conserved AIMs in NF-{kappa}B/Dif bind Atg8 and enable Dif nuclear entry. C_LIO_LIAIM-mutant Dif flies are highly susceptible to infection and chronic high-sugar diet. C_LIO_LIAtg8 occupies stress-related motifs on prolonged HSD and acute infection. C_LI

genomics↗

bioRxiv2023

Atg8-LC3 controls systemic nutrient surplus signaling from flies to humans.

Organisms experience constant nutritional flux, and homeostatic mechanisms evolved to operate at the nexus of extreme nutritional states - scarcity and surplus. Thus, we surmised that decoding bidirectional molecular switches that operate at the interface of scarcity response and surplus signaling will enable the development of strategies to treat disorders that arise from nutrient imbalance states. Adipocytes secrete leptin, an interleukin protein, which signals nutrient surplus to the central brain to regulate feeding and energy expenditure. We report that Atg8-LC3-family proteins, best known for their role in autophagy, are required for leptin secretion in Drosophila and human adipocytes. Atg8-LC3 genetic knockdown and point mutations to the Atg8-LC3 interaction motif (AIM/LIR) of leptin, and its functional ortholog in Drosophila, Upd2, disrupt adipokine secretion and increase adipokine retention in human and fly cells. At an organismal level, Atg8-driven Upd2 retention increases organismal resilience to nutrient extremes by rewiring the transcriptome, organismal feeding behavior, and hunger response. Comparative proteomic analyses reveal that LC3 directs leptin to an exosome secretory pathway. We use genetic knockdown in primary human adipocytes to establish that LC3 is required for leptin secretion in a physiologically relevant mammalian system. Hence, we uncover a previously unknown and evolutionarily conserved role for Atg8-LC3 in promoting adipocyte-brain nutrient surplus signaling. We propose that Atg8-LC3s bidirectional role in nutrient sensing-conveying nutrient surplus and responding to nutrient deprivation-enables organisms to manage nutrient flux effectively.

physiology↗

bioRxiv2021

Fat Body Phospholipid State Dictates Hunger Driven Feeding Behavior

Diet-induced obesity (DIO) leads to dysfunctional feeding behavior. However, the precise molecular nodes underlying diet-induced dysregulation of satiety sensing and feeding motivation are poorly understood. The fruit fly is a simple genetic model system yet displays significant evolutionary conservation to mammalian nutrient sensing and energy balance. Using a longitudinal high sugar regime in Drosophila, we sought to address how lipid alteration in fat cells alters feeding behavior. We find that prolonged exposure to HSD degrades the hunger-driven feeding (HDF) response. Lipidomics analysis reveals that longitudinal exposure to HSD significantly alters whole body phospholipid profiles. By performing a systematic screen for phospholipid enzymes, we identify Pect as a critical regulator of hunger-driven feeding. Pect is a rate-limiting enzyme in the phosphatidylethanolamine (PE) biosynthesis pathway and the fly ortholog of human PCYT2. We show that disrupting Pect only in the fat body causes insulin-resistant phenotypes and a loss of hunger-driven feeding. Excitingly, we find that overexpression of Pect restores HSD-induced loss of hunger-driven feeding response. Strikingly human studies have noted a correlation between PCYT2/Pect levels and clinical obesity. Now, our unbiased studies in Drosophila provide specific genetic evidence for Pect in maintaining nutrient sensing during DIO. Our study provides novel insights into the role of phospholipids in interorgan communication of nutrient status. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=193 SRC="FIGDIR/small/472854v4_ufigA1.gif" ALT="Figure 1"> View larger version (66K): org.highwire.dtl.DTLVardef@1ecf3eorg.highwire.dtl.DTLVardef@b800f2org.highwire.dtl.DTLVardef@461a7eorg.highwire.dtl.DTLVardef@75651c_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2020

Eating breakfast and avoiding the evening snack sustains lipid oxidation

Circadian (daily) regulation of metabolic pathways implies that food may be metabolized differentially over the daily cycle. To test that hypothesis, we monitored the metabolism of older subjects in a whole-room respiratory chamber over two separate 56-h sessions in a random crossover design. In one session, one of the three daily meals was presented as breakfast whereas in the other session, a nutritionally equivalent meal was presented as a late-evening snack. The duration of the overnight fast was the same for both sessions. Whereas the two sessions did not differ in overall energy expenditure, the respiratory exchange ratio (RER) was different during sleep between the two sessions. Unexpectedly, this difference in RER due to daily meal timing was not due to daily differences in physical activity, sleep disruption, or core body temperature. Rather, we found that the daily timing of nutrient availability coupled with daily/circadian control of metabolism drives a switch in substrate preference such that the late-evening snack session resulted in significantly lower lipid oxidation compared to the breakfast session. Therefore, the timing of meals during the day/night cycle affects how ingested food is oxidized or stored in humans with important implications for optimal eating habits.

animal behavior and cognition↗