Biology subjects

Magtanong, L.

Publications and source records attributed to Magtanong, L..

5 recordsLinked to original sources

bioRxiv2026

A human transcriptomic deletion links cortical expansion and cancer

Alternative splicing represents a major source of potential evolutionary novelty in protein sequence. Despite this, relatively few studies have investigated the functional impacts of human-specific alternative splicing. Here, we analyze RNA-sequencing data from nine iPSC-derived cell types and identify dozens of human transcriptomic conserved deletions (htCONDELs): evolutionary divergence in splicing that leads to the partial or full removal of conserved protein-coding sequence from the human transcriptome. We investigated one example in detail: an htCONDEL in the gene HMMR, which encodes a centrosomal protein that binds microtubules and regulates mitosis. We found that this htCONDEL, which produces a human-specific isoform lacking a conserved microtubule-binding domain, enables cells to flexibly divide with a broader range of mitotic spindle orientations in vitro. Introducing the human HMMR isoform into mice similarly alters the orientation of cell division in the developing neocortex and increases the production of outer radial glia-like cells, the expansion of which played an essential role in increasing human brain size. Combined with previous work implicating the same HMMR isoform in carcinoma progression, our results suggest that evolution of HMMR splicing in humans increased plasticity in cell division, potentially leading to tradeoffs between advantageous effects on brain development and deleterious effects on cancer risk later in life.

evolutionary biology↗

bioRxiv2026

Adaptive loss of function accelerated the evolution of ancient and modern human cognition

Methods to detect accelerated evolution have identified many genomic regions with unexpectedly rapid evolution in the human lineage-significantly more than in chimpanzees, our closest living relatives. However, these methods focus on accelerated sequence evolution of short non-coding regions, leaving open the questions of how to identify accelerated evolution of molecular function, as opposed to sequence, and whether accelerated evolution has shaped the human genome more broadly. Here, we introduce a new approach to detect accelerated evolution: Function Aware Statistical Test for Evolutionary Rates (FASTER). In contrast to previous methods, FASTER can detect not only accelerated evolution of sequence, but also of predicted function, and can be applied to any set of genomic regions. Applying this method to humans and chimpanzees, we identified protein-coding, untranslated (UTR), and non-coding regions with accelerated evolution of function. Across all these genomic levels, we consistently found more rapid evolution in conserved sites in the human lineage compared to chimpanzee, many of which are predicted to reduce protein stability or chromatin accessibility. Multiple lines of evidence suggest this human-acceleration was driven in part by positive selection on brain development and cognition which has continued to shape human evolution even in the past several thousand years. Collectively, these results demonstrate the power of genome-wide scans for the evolution of predicted function and specifically suggest that a higher rate of reduction in function-including widespread decreases in cis-regulatory activity-may have been an important driver of both ancient and recent human evolution.

genomics↗

bioRxiv2022

Ribosome stalling during selenoprotein translation exposes a ferroptosis vulnerability in cancer

Ferroptosis is a regulated, iron-dependent form of necrosis that is triggered by the accumulation of oxidatively damaged phospholipids1-3. Glutathione peroxidase 4 (GPX4) prevents ferroptosis by converting phospholipid hydroperoxides into non-toxic lipid alcohols4, 5. Ferroptosis has been implicated in the pathology of several degenerative conditions and inhibiting GPX4 activity has emerged as a therapeutic strategy to induce cancer cell death1, 2. However, many cancer cell lines are resistant to GPX4 inhibition6, and the mechanisms that regulate GPX4 activity and ferroptosis resistance remain incompletely understood. Here, employing a synthetic lethal CRISPR-Cas9 screen in a triple negative breast cancer (TNBC) cell line, we identify LRP8 (also known as ApoER2) as a ferroptosis resistance factor. LRP8 is upregulated in cancer, and we find that it promotes ferroptosis resistance in cancer cells in both 2-dimensional (2-D) cell culture and 3-dimensional (3-D) spheroid models. Mechanistically, loss of LRP8 decreases cellular selenium levels, resulting in the reduced expression of a subset of selenoproteins, including GPX4. Remarkably, the reduction in GPX4 is not due to the classic hierarchical selenoprotein regulatory program7, 8. Instead, our findings demonstrate that the translation of GPX4 is severely impaired in the selenium-deficient LRP8 knockout (KO) cells due to extensive ribosome stalling at the inefficiently decoded GPX4 selenocysteine (SEC) UGA codon, which results in ribosome collisions and early translation termination. Thus, our findings reveal ribosome stalling and collisions during GPX4 translation as targetable ferroptosis vulnerabilities in cancer cells.

cancer biology↗

bioRxiv2019

A Compendium of Kinetic Cell Death Modulatory Profiles Identifies Ferroptosis Regulators

Cell death can be executed by regulated apoptotic and non-apoptotic pathways, including the iron-dependent process of ferroptosis. Small molecules are essential tools for studying the regulation of cell death. Using live-cell, time-lapse imaging, and a library of 1,833 small molecules including FDA-approved drugs and investigational agents, we assemble a large compendium of kinetic cell death modulatory profiles for inducers of apoptosis and ferroptosis. From this dataset we identified dozens of small molecule inhibitors of ferroptosis, including numerous investigational and FDA-approved drugs with unexpected off-target antioxidant or iron chelating activities. ATP-competitive mechanistic target of rapamycin (mTOR) inhibitors, by contrast, were on-target ferroptosis inhibitors. Further investigation revealed both mTOR-dependent and mTOR-independent mechanisms linking amino acid levels to the regulation of ferroptosis sensitivity in cancer cells. These results highlight widespread bioactive compound pleiotropy and link amino acid sensing to the regulation of ferroptosis.

systems biology↗

bioRxiv2019

Dietary Induction and Modulation of Ferroptosis in Caenorhabditis elegans

Ferroptosis is an iron-dependent form of regulated cell death associated with oxidized polyunsaturated phospholipids. Understanding the role of this process in vivo has been slowed by the lack of readily accessible model systems. Exposing the nematode Caenorhabditis elegans to the polyunsaturated fatty acid dihomogamma-linolenic acid (DGLA; 20:3n-6) causes germ cell death and sterility that is largely independent of the canonical apoptosis pathway. Here we demonstrate that DGLA-induced germ cell death is modulated by small molecule ferroptosis inhibitors, genetic manipulation of ferritin, NADPH oxidase, and glutathione peroxidases, and by dietary co-supplementation with oleic acid. Thus, DGLA-induced germ cell death in C. elegans is highly analogous to ferroptosis in mammalian cells. DGLA can also induce ferroptosis in human cells, further highlighting this omega-6 PUFA as a metabolic instigator of ferroptosis. Together, these results establish C. elegans as a powerful animal model to study the induction and modulation of ferroptosis by dietary fats.\n\nHighlights- Dietary dihomogamma-linolenic acid (DGLA)-induced germ cell death in C. elegans is alleviated by small molecule antioxidants and iron chelators\n- Dietary and endogenous oleic acid protects from DGLA-induced ferroptosis\n- Ether-lipid deficiency increases sensitivity to DGLA-induced ferroptosis\n- DGLA specifically induces ferroptosis in human cancer cells

cell biology↗