Biology subjects

Adler, C. E.

Publications and source records attributed to Adler, C. E..

6 recordsLinked to original sources

bioRxiv2025

Pluripotent Stem Cell Plasticity is Sculpted by a Slit-Independent Robo Pathway in a Regenerative Animal

Whole-body regeneration requires adult stem cells with high plasticity to differentiate into missing cell types. Planarians possess a unique configuration of organs embedded in a vast pool of pluripotent stem cells. How stem cells integrate positional information with discrete fates remains unknown. Here, we use the planarian pharynx to define the cell fates that depend on the pioneer transcription factor FoxA. We find that Roundabout receptor RoboA suppresses aberrant pharynx cell fates by altering foxA expression, independent of the canonical ligand Slit. An RNAi screen for extracellular proteins identifies Anosmin-1 as a potential partner of RoboA. Perturbing global patterning demonstrates that roboA/anosmin-1 functions locally in the brain. By contrast, altering pharynx fate with foxA knockdown induces head-specific neurons in the pharynx, indicating a latent plasticity of stem cells. Our data links critical extracellular cues with cell fate decisions of highly plastic stem cells, ensuring the fidelity of organ regeneration.

developmental biology↗

bioRxiv2023

CRISPR/Cas9-based depletion of 16S ribosomal RNA improves library complexity of single-cell RNA-sequencing

BackgroundSingle-cell RNA-sequencing (scRNA-seq) relies on PCR amplification to retrieve information from vanishingly small amounts of starting material. To selectively enrich mRNA from abundant non-polyadenylated transcripts, poly(A) selection is a key step during library preparation. However, some transcripts, such as mitochondrial genes, can escape this elimination and overwhelm libraries. Often, these transcripts are removed in silico, but whether physical depletion improves detection of rare transcripts in single cells is unclear. ResultsWe find that a single 16S ribosomal RNA is widely enriched in planarian scRNA-seq datasets, independent of the library preparation method. To deplete this transcript from scRNA-seq libraries, we design 30 single-guide RNAs spanning its length. To evaluate the effects of depletion, we perform a side-by-side comparison of the effects of eliminating the 16S transcript and find a substantial increase in the number of genes detected per cell, coupled with virtually complete loss of the 16S RNA. Moreover, we systematically determine that library complexity increases with a limited number of PCR cycles following CRISPR treatment. When compared to in silico depletion of 16S, physically removing it reduces dropout rates, retrieves more clusters, and reveals more differentially-expressed genes. ConclusionsOur results show that abundant transcripts reduce the retrieval of informative transcripts in scRNA-seq and distort the analysis. Physical removal of these contaminants enables the detection of rare transcripts at lower sequencing depth, and also outperforms in silico depletion. Importantly, this method can be easily customized to deplete any abundant transcript from scRNA-seq libraries.

genomics↗

bioRxiv2022

Inhibition of the ATM kinase rescues planarian regeneration after lethal radiation

As stem cells divide, they acquire mutations that can be passed on to daughter cells. To limit the possibility of propagating mutations, cells activate the DNA damage response (DDR) network, which dictates whether cells repair DNA or undergo apoptosis. At the helm of the DDR are three PI3-like kinases including Ataxia Telangiectasia Mutated (ATM). We report here that knockdown of ATM in planarian flatworms enables stem cells, which normally undergo apoptosis after radiation exposure, to survive lethal doses of radiation. In this context, stem cells circumvent apoptosis, replicate their DNA, and recover function using homologous recombination-mediated DNA repair. Despite radiation exposure, atm knockdown animals survive long-term and regenerate new tissues. These effects occur independently of ATMs canonical downstream effector p53. Together, our results demonstrate that ATMs primary function is to drive apoptosis, and suggest that inhibition of ATM could therefore potentially favor cell survival after radiation without adverse effects.

cell biology↗

bioRxiv2020

Planarian stem cells sense the identity of missing tissues to launch targeted regeneration

In order to regenerate tissues successfully, stem cells must first detect injuries and then produce missing cell types through largely unknown mechanisms. Planarian flatworms have an extensive stem cell population responsible for regenerating any organ after amputation. Here, we compare stem cell responses to different injuries by amputation of a single organ, the pharynx, or removal of tissues from other organs by decapitation. We find that planarian stem cells adopt distinct behaviors depending on what tissue is missing: loss of non-pharyngeal tissues increases numbers of non-pharyngeal progenitors, while removal of the pharynx specifically triggers proliferation and expansion of pharynx progenitors. By pharmacologically inhibiting either proliferation or activation of the MAP kinase ERK, we identify a narrow window of time during which proliferation, followed by ERK signaling, produces pharynx progenitors necessary for regeneration. Further, unlike pharynx regeneration, eye regeneration does not depend on proliferation or ERK activation. These results indicate that stem cells tailor their proliferation and expansion to match the regenerative needs of the animal.

developmental biology↗

bioRxiv2019

Injury stimulates stem cells to resist radiation-induced apoptosis

Stem cells are continuously exposed to multiple stresses including radiation and tissue injury. Because stem cells are central drivers of tissue repair and regeneration, it is essential to understand how their behavior is influenced by these stressors. Planarians have an abundant population of stem cells that are rapidly eliminated after radiation exposure via apoptosis. Low doses of radiation eliminate the majority of these stem cells, allowing a few to remain [1]. Here, we combine radiation with injury to define how surviving stem cells respond to tissue damage. We find that injuries induce stem cells to persist, but only if injured within a defined window of time surrounding radiation, and only immediately adjacent to the wound. Stem cells persist for several days without any proliferation. Instead, they are retained near the wound due to suppression of apoptosis, which we quantify in stem cells by combining FACS with Annexin V staining. Tissue injury is known to induce apoptosis in differentiated cells [2], and we hypothesize that these dying cells confer apoptosis resistance onto nearby stem cells. Indeed, pharmacological induction of cell death with cycloheximide is sufficient to prolong survival of radiated stem cells even in the absence of injury. Together, our results suggest a model in which dying cells provide a transient protective signal to nearby stem cells, altering their susceptibility to radiation-induced apoptosis.

developmental biology↗

bioRxiv2017

PHRED-1 Is A Divergent Neurexin-1 Homolog That Organizes Muscle Fibers And Patterns Organs During Regeneration

Regeneration of body parts requires the replacement of multiple cell types. To dissect this complex process, we utilized planarian flatworms that are capable of regenerating any tissue after amputation. An RNAi screen for genes involved in regeneration of the pharynx identified a novel gene, Pharynx regeneration defective-1 (PHRED-1) as essential for normal pharynx regeneration. PHRED-1 is a predicted transmembrane protein containing EGF, Laminin G, and WD40 domains, is expressed in muscle, and has predicted homologs restricted to other lophotrochozoan species. Knockdown of PHRED-1 causes abnormal regeneration of muscle fibers in both the pharynx and body wall muscle. In addition to defects in muscle regeneration, knockdown of PHRED-1 or the bHLH transcription factor MyoD also causes defects in muscle and intestinal regeneration. Together, our data demonstrate that muscle plays a key role in restoring the structural integrity of closely associated organs, and in planarians it may form a scaffold that facilitates normal intestinal branching.\n\nGraphical Abstract\n\nHighlights-PHRED-1 is a predicted transmembrane protein that contains Laminin G, EGF and WD40 domains\n\n-PHRED-1 is required for normal muscle patterning during regeneration\n\n-phred-1 is expressed in muscle cells\n\n-Muscle forms an essential scaffold for regeneration

developmental biology↗