Biology subjects

Mann, F. G.

Publications and source records attributed to Mann, F. G..

7 recordsLinked to original sources

bioRxiv2022

A PAK kinase family member and the Hippo/Yorkie pathway modulate WNT signaling to functionally integrate body axes during regeneration

Successful regeneration of missing tissues requires seamless integration of positional information along the body axes. Planarians, which regenerate from almost any injury, use conserved, developmentally important signaling pathways to pattern the body axes. However, the molecular mechanisms which facilitate crosstalk between these signaling pathways to integrate positional information remain poorly understood. Here, we report a p21-activated kinase (smed-pak1) which functionally integrates the anterior-posterior (AP) and the medio-lateral (ML) axes. pak1 inhibits WNT/{beta}-catenin signaling along the AP axis and, functions synergistically with the {beta}-catenin-independent WNT signaling of the ML axis. Furthermore, this functional integration is dependent on warts and merlin - the components of the Hippo/Yorkie (YKI) pathway. Hippo/YKI pathway is a critical regulator of body size in flies and mice, but our data suggest the pathway is required to pattern body axes in planarians. Our study provides a signaling network integrating positional information which can mediate coordinated growth and patterning during planarian regeneration.

developmental biology↗

bioRxiv2022

Syrah, a Slide-seqV2 pipeline augmentation

Spatial transcriptomic techniques such as Slide-seqV2 uncover novel relationships and interactions between cell types by coupling gene expression and spatial data. Here we discuss two unexpected sources of error in Slide-seqV2 data, one physical and one computational. To address this we present an analysis pipeline augmentation, Syrah, which corrects for these errors and show that it improves both data quantity and quality over the standard pipeline alone or in combination with additional sequencing.

bioinformatics↗

bioRxiv2022

Stem cells partner with matrix remodeling cells during regeneration

Stem cells enable regeneration by self-renewing and differentiating as instructed by a local microenvironment called a niche1-3. In most cases, the repair or replacement of tissues is fueled by tissue-specific or lineage-restricted stem cells that proliferate in response to local injury and apoptosis4-11. However, in organisms that regenerate using abundant adult pluripotent stem cells, the stem cell niches that support tissue repair have not been identified or characterized. Since these adult pluripotent stem cells are often more widely distributed and plentiful than lineage-restricted stem cells of other organisms, defining their microenvironments may uncover alternative forms of stem cell regulation12-14. Here we used unbiased spatial transcriptomics to define the cellular and molecular environments that support pluripotency in the highly regenerative freshwater planarian Schmidtea mediterranea. We determined that stem cells associate with a diverse collection of differentiated cell types, and these associations are highly dynamic during regeneration. We explored associations with two distinct cell types: secretory cells we term hecatonoblasts, and intestinal cells. While both cell types regulate stem cell proliferation, their spatial relationships to stem cells defy the concept of a single regenerative niche. Thus, the planarian stem cell pool is likely maintained by a dynamic collection of distinct microenvironments that cooperatively power whole-body regeneration.

developmental biology↗

bioRxiv2021

A powerful and versatile new fixation protocol for immunohistology and in situ hybridization that preserves delicate tissues in planaria

Whole-mount in situ hybridization (WISH) is a powerful and widely used technique to visualize the expression pattern of genes in different biological systems. Here we describe a new protocol for ISH and immunostaining in the planarian Schmidtea mediterranea. The new Nitric Acid/Formic Acid (NAFA) protocol is compatible with both assays and prevents degradation of the epidermis or blastema. Instead of proteinase K digestion, formic acid treatment is used to permeabilize tissues and preserve antigen epitopes. We show that the NAFA protocol successfully permits development of chromogenic and fluorescent signals in situ, while preserving the anatomy of the animal. Further, the immunostaining of different proteins was compatible with the NAFA protocol following fluorescent in situ hybridization. Finally, we demonstrate with high resolution confocal imaging that the regeneration blastema is preserved when using the new method. This new NAFA protocol will be a valuable technique to study the process of wounding response and regeneration.

developmental biology↗

bioRxiv2021

Hox genes regulate asexual reproductive behavior and tissue segmentation in adult animals

Hox genes are highly conserved transcription factors renowned for their roles in the segmental patterning of the embryonic anterior-posterior (A/P) axis1. Emerging evidence for Hox gene expression and function in postnatally derived structures has fueled interest in their additional roles beyond embryogenesis2,3. We report novel functions for Hox genes in A/P adult tissue segmentation and transverse fission behavior underlying asexual reproduction in the planarian flatworm, Schmidtea mediterranea. Silencing of each of the planarian Hox family members identified 5 Hox genes required for asexual reproduction. Among these, silencing of hox3 genes resulted in supernumerary segments, while silencing of post2b eliminated segmentation altogether. The opposing roles of hox3 and post2b in segmentation are paralleled in their respective regulation of fission behavior. Silencing of hox3 increased the frequency of fission behavior initiation, while silencing of post2b eliminated fission behavior entirely. Furthermore, we identified a network of downstream effector genes mediating Hox gene regulation of asexual reproduction, thereby providing insight into their respective mechanisms of action. Our study establishes postembryonic roles for Hox genes in regulating the emergence of tissue segmentation and specific behaviors associated with asexual reproduction in adult animals.

developmental biology↗

bioRxiv2020

Decellularization enables functional analysis of ECM remodeling in planarian regeneration

The extracellular matrix (ECM) is a three-dimensional network of macromolecules that provides a microenvironment capable of supporting and regulating cell functions. However, only a few research organisms are available for the systematic dissection of the composition and functions of the ECM, particularly during regeneration. We utilized a free-living flatworm Schmidtea mediterranea to develop an integrative approach consisting of decellularization, proteomics, and RNA-interference (RNAi) to characterize and investigate ECM functions during tissue homeostasis and regeneration. High-quality ECM was isolated from planarians, and its matrisome profile was characterized by LC-MS/MS. The functions of identified ECM components were interrogated using RNAi. Using this approach, we discovered that heparan sulfate proteoglycan and kyphoscoliosis peptidase are essential for both tissue homeostasis and regeneration. Our strategy provides a robust experimental approach for identifying novel ECM components involved in regeneration that might not be discovered bioinformatically.

developmental biology↗

bioRxiv2020

Identification of rare transient somatic cell states induced by injury and required for whole-body regeneration

Regeneration requires functional coordination of stem cells, their progeny, and differentiated cells. Past studies have focused on regulation of stem cell identity and proliferation near to the wound-site, but less is known about contributions made by differentiated cells distant to the injury. Here, we present a comprehensive atlas of whole-body regeneration over time and identify rare, transient, somatic cell states induced by injury and required for regeneration. To characterize amputation-specific signaling across a whole animal, 299,998 single-cell transcriptomes were captured from planarian tissue fragments competent and incompetent to regenerate. Amputation-specific cell states were rare, non-uniformly distributed across tissues, and particularly enriched in muscle (mesoderm), epidermis (ectoderm), and intestine (endoderm). Moreover, RNAi-mediated knockdown of genes up-regulated in amputation-specific cell states drastically reduced regenerative capacity. These results identify novel cell states and molecules required for whole-body regeneration and indicate that regenerative capacity requires transcriptional plasticity in a rare subset of differentiated cells.

developmental biology↗