Zebrafish to humans: evolution of the alpha3-chain of type IV collagen and emergence of the autoimmune epitopes associated with Goodpasture syndrome

Identification of unique α4 chain structure and conserved antiangiogenic activity of α3NC1 type IV collagen in zebrafish

BACKGROUND

Type IV collagen is an abundant component of basement membranes in all multicellular species and is essential for the extracellular scaffold supporting tissue architecture and function. Lower organisms typically have two type IV collagen genes, encoding α1 and α2 chains, in contrast with the six genes in humans, encoding α1-α6 chains. The α chains assemble into trimeric protomers, the building blocks of the type IV collagen network. The detailed evolutionary conservation of type IV collagen network remains to be studied.

RESULTS

We report on the molecular evolution of type IV collagen genes. The zebrafish α4 non-collagenous (NC1) domain, in contrast with its human ortholog, contains an additional cysteine residue and lacks the M93 and K211 residues involved in sulfilimine bond formation between adjacent protomers. This may alter α4 chain interactions with other α chains, as supported by temporal and anatomic expression patterns of collagen IV chains during the zebrafish development. Despite the divergence between zebrafish and human α3 NC1 domain (endogenous angiogenesis inhibitor, Tumstatin), the zebrafish α3 NC1 domain exhibits conserved antiangiogenic activity in human endothelial cells.

CONCLUSIONS

Our work supports type IV collagen is largely conserved between zebrafish and humans, with a possible difference involving the α4 chain.

Structure and Function of Basement Membranes

Basement membranes (BMs) are present in every tissue of the human body. All epithelium and endothelium is in direct association with BMs. BMs are a composite of several large glycoproteins and form an organized scaffold to provide structural support to the tissue and also offer functional input to modulate cellular function. While collagen I is the most abundant protein in the human body, type IV collagen is the most abundant protein in BMs. Matrigel is commonly used as surrogate for BMs in many experiments, but this is a tumor-derived BM–like material and does not contain all of the components that natural BMs possess. The structure of BMs and their functional role in tissues are unique and unlike any other class of proteins in the human body. Increasing evidence suggests that BMs are unique signal input devices that likely fine tune cellular function. Additionally, the resulting endothelial and epithelial heterogeneity in human body is a direct contribution of cell-matrix interaction facilitated by the diverse compositions of BMs.

Phenotype as Agent for Epigenetic Inheritance

The conventional understanding of phenotype is as a derivative of descent with modification through Darwinian random mutation and natural selection. Recent research has revealed Lamarckian inheritance as a major transgenerational mechanism for environmental action on genomes whose extent is determined, in significant part, by germ line cells during meiosis and subsequent stages of embryological development. In consequence, the role of phenotype can productively be reconsidered. The possibility that phenotype is directed towards the effective acquisition of epigenetic marks in consistent reciprocation with the environment during the life cycle of an organism is explored. It is proposed that phenotype is an active agent in niche construction for the active acquisition of epigenetic marks as a dominant evolutionary mechanism rather than a consequence of Darwinian selection towards reproductive success. The reproductive phase of the life cycle can then be appraised as a robust framework in which epigenetic inheritance is entrained to affect growth and development in continued reciprocal responsiveness to environmental stresses. Furthermore, as first principles of physiology determine the limits of epigenetic inheritance, a coherent justification can thereby be provided for the obligate return of all multicellular eukaryotes to the unicellular state.

The Unicellular State as a Point Source in a Quantum Biological System

A point source is the central and most important point or place for any group of cohering phenomena. Evolutionary development presumes that biological processes are sequentially linked, but neither directed from, nor centralized within, any specific biologic structure or stage. However, such an epigenomic entity exists and its transforming effects can be understood through the obligatory recapitulation of all eukaryotic lifeforms through a zygotic unicellular phase. This requisite biological conjunction can now be properly assessed as the focal point of reconciliation between biology and quantum phenomena, illustrated by deconvoluting complex physiologic traits back to their unicellular origins.

Life Is Simple-Biologic Complexity Is an Epiphenomenon

Life originated from unicellular organisms by circumventing the Second Law of Thermodynamics using the First Principles of Physiology, namely negentropy, chemiosmosis and homeostatic regulation of calcium and lipids. It is hypothesized that multicellular organisms are merely contrivances or tools, used by unicellular organisms as agents for the acquisition of epigenetic inheritance. The First Principles of Physiology, which initially evolved in unicellular organisms are the exapted constraints that maintain, sustain and perpetuate that process. To ensure fidelity to this mechanism, we must return to the first principles of the unicellular state as the determinants of the primary level of selection pressure during the life cycle. The power of this approach is reflected by examples of its predictive value. This perspective on life is a "game changer", mechanistically rendering transparent many dogmas, teleologies and tautologies that constrain the current descriptive view of Biology.

On the Evolution of the Mammalian Brain

Hobson and Friston have hypothesized that the brain must actively dissipate heat in order to process information (Hobson et al., 2014). This physiologic trait is functionally homologous with the first instantation of life formed by lipids suspended in water forming micelles- allowing the reduction in entropy (heat dissipation). This circumvents the Second Law of Thermodynamics permitting the transfer of information between living entities, enabling them to perpetually glean information from the environment, that is felt by many to correspond to evolution per se. The next evolutionary milestone was the advent of cholesterol, embedded in the cell membranes of primordial eukaryotes, facilitating metabolism, oxygenation and locomotion, the triadic basis for vertebrate evolution. Lipids were key to homeostatic regulation of calcium, forming calcium channels. Cell membrane cholesterol also fostered metazoan evolution by forming lipid rafts for receptor-mediated cell-cell signaling, the origin of the endocrine system. The eukaryotic cell membrane exapted to all complex physiologic traits, including the lung and brain, which are molecularly homologous through the function of neuregulin, mediating both lung development and myelinization of neurons. That cooption later exapted as endothermy during the water-land transition (Torday, 2015a), perhaps being the functional homolog for brain heat dissipation and conscious/mindful information processing. The skin and brain similarly share molecular homologies through the “skin-brain” hypothesis, giving insight to the cellular-molecular “arc” of consciousness from its unicellular origins to integrated physiology. This perspective on the evolution of the central nervous system clarifies self-organization, reconciling thermodynamic and informational definitions of the underlying biophysical mechanisms, thereby elucidating relations between the predictive capabilities of the brain and self-organizational processes.

What We Talk About When We Talk About Evolution

Currently, the biologic sciences are a Tower of Babel, having become so highly specialized that one discipline cannot effectively communicate with another. A mechanism for evolution that integrates development and physiologic homeostasis phylogenetically has been identified—cell-cell interactions. By reducing this process to ligand-receptor interactions and their intermediate down-stream signaling partners, it is possible, for example, to envision the functional homologies between such seemingly disparate structures and functions as the lung alveolus and kidney glomerulus, the skin and brain, or the skin and lung. For example, by showing the continuum of the lung phenotype for gas exchange at the cell-molecular level, being selected for increased surface area by augmenting lung surfactant production and function in lowering surface tension, we have determined an unprecedented structural-functional continuum from proximate to ultimate causation in evolution. It is maintained that tracing the changes in structure and function that have occurred over both the short-term history of the organism (as ontogeny), and the long-term history of the organism (as phylogeny), and how the mechanisms shared in common can account for both biologic stability and novelty, will provide the key to understanding the mechanisms of evolution. We need to better understand evolution from its unicellular origins as the Big Bang of biology.

Pleiotropy as the Mechanism for Evolving Novelty: Same Signal, Different Result

In contrast to the probabilistic way of thinking about pleiotropy as the random expression of a single gene that generates two or more distinct phenotypic traits, it is actually a deterministic consequence of the evolution of complex physiology from the unicellular state. Pleiotropic novelties emerge through recombinations and permutations of cell-cell signaling exercised during reproduction based on both past and present physical and physiologic conditions, in service to the future needs of the organism for its continued survival. Functional homologies ranging from the lung to the kidney, skin, brain, thyroid and pituitary exemplify the evolutionary mechanistic strategy of pleiotropy. The power of this perspective is exemplified by the resolution of evolutionary gradualism and punctuated equilibrium in much the same way that Niels Bohr resolved the paradoxical duality of light as Complementarity.

On the evolution of development

Perhaps development is more than just morphogenesis. We now recognize that the conceptus expresses epigenetic marks that heritably affect it phenotypically, indicating that the offspring are to some degree genetically autonomous, and that ontogeny and phylogeny may coordinately determine the fate of such marks. This scenario mechanistically links ecology, ontogeny and phylogeny together as an integrated mechanism for evolution for the first time. As a functional example, the Parathyroid Hormone-related Protein (PTHrP) signaling duplicated during the Phanerozoic water-land transition. The PTHrP signaling pathway was critical for the evolution of the skeleton, skin barrier, and lung function, based on experimental evidence, inferring that physiologic stress can profoundly affect adaptation through internal selection, giving seminal insights to how and why vertebrates were able to evolve from water to land. By viewing evolution from its inception in unicellular organisms, driven by competition between pro- and eukaryotes, the emergence of complex biologic traits from the unicellular cell membrane offers a novel way of thinking about the process of evolution from its beginnings, rather than from its consequences as is traditionally done. And by focusing on the epistatic balancing mechanisms for calcium and lipid homeostasis, the evolution of unicellular organisms, driven by competition between pro- and eukaryotes, gave rise to the emergence of complex biologic traits derived from the unicellular plasma lemma, offering a unique way of thinking about the process of evolution. By exploiting the cellular-molecular mechanisms of lung evolution as ontogeny and phylogeny, the sequence of events for the evolution of the skin, kidney and skeleton become more transparent. This novel approach to the evolution question offers equally novel insights to the primacy of the unicellular state, hologenomics and even a priori bioethical decisions.

Evolution and Cell Physiology. 1. Cell signaling is all of biology

I hypothesize that the First Principles of Physiology (FPPs) were co-opted during the vertebrate transition from water to land, beginning with the acquisition of cholesterol by eukaryotes, facilitating unicellular evolution over the course of the first 4.5 billion years of the Earth's history, in service to the reduction in intracellular entropy, far from equilibrium. That mechanism was perpetuated by the advent of cholesterol in the cell membrane of unicellular eukaryotes, ultimately giving rise to the metazoan homologs of the gut, lung, kidney, skin, bone, and brain. Parathyroid hormone-related protein (PTHrP), whose cognate receptor underwent a gene duplication during the transition from fish to amphibians, facilitated gas exchange for the water-to-land transition, since PTHrP is necessary for the formation of lung alveoli: deletion of the PTHrP gene in mice causes the offspring to die within a few minutes of birth due to the absence of alveoli. Moreover, PTHrP is central to the development and homeostasis of the kidney, skin, gut, bone, and brain. Therefore, duplication of the PTHrP receptor gene is predicted to have facilitated the molecular evolution of all the necessary traits for land habitation through a common cellular and molecular motif. Subsequent duplication of the β-adrenergic receptor gene permitted blood pressure control within the lung microvasculature, allowing further evolution of the lung by increasing its surface area. I propose that such gene duplications were the result of shear stress on the microvasculature, locally generating radical oxygen species that caused DNA mutations, giving rise to duplication of the PTHrP and β-adrenergic receptor genes. I propose that one can determine the FPPs by systematically tracing the molecular homologies between the lung, skin, kidney, gut, bone, and brain across development, phylogeny, and pathophysiology as a type of "reverse evolution." By tracing such relationships back to unicellular organisms, one can use the underlying principles to predict homeostatic failure as disease, thereby also potentially forming the basis for maneuvers that can treat or even prevent such failure.

Interstitial lung diseases-can pathologists arrive at an etiology-based diagnosis? A critical update

Interstitial lung diseases (ILD) encompass a group of diseases with a wide range of etiologies and a variety of tissue reactions within the lung. In many instances, a careful evaluation of the tissue reactions will result in a specific diagnosis or at least in a narrow range of differentials, which will assist the clinician to arrive at a definite diagnosis, when combining our interpretation with the clinical presentation of the patient and high-resolution computed tomography. In this review, we will exclude granulomatous pneumonias as well as vascular diseases (primary arterial pulmonary hypertension and vasculitis); however, pulmonary hypertension as a complication of interstitial processes will be mentioned. Few entities of pneumoconiosis presenting as an interstitial process will be included, whereas those with granulomatous reactions will be excluded. Drug reactions will be touched on within interstitial pneumonias, but will not be a major focus. In contrast to the present-day preferred descriptive pattern recognition, it is the author's strong belief that pathologists should always try to dig out the etiology from a tissue specimen and not being satisfied with just a pattern description. It is the difference of sorting tissue reactions into boxes by their main pattern, without recognizing minor or minute reactions, which sometimes will guide one to the correct etiology-oriented interpretation. In the author's personal perspective, tissue reactions can even be sorted by their timeliness, and therefore, ordered by the time of appearance, providing an insight into the pathogenesis and course of a disease. Also, underlying immune mechanisms will be discussed briefly as far as they are essential to understand the disease.

A cell-molecular approach predicts vertebrate evolution

In contrast to the conventional use of genes to determine the evolution of phenotypes, we have functionally integrated epithelial-mesenchymal interactions that have facilitated lung phylogeny and ontogeny in response to major geologic epochs. As such, this model reveals the underlying principles of lung physiology based on the evolutionary interactions between internal and external selection pressures, providing a novel understanding of lung biology. As a result, it predicts how cell-molecular changes in this process can cause disease and offers counterintuitive insights to diagnosis and treatment based on evolutionary principles.

Basement membrane diseases in zebrafish

Basement membranes (BMs) are a complex, sheet-like network of specialized extracellular matrix that underlies epithelial cells and surrounds muscle cells. They provide adherence between neighboring tissues, permit some flexibility of these adherent structures, and can act as a store for growth factors and as a guide for cell migration. The BM is not just a static structure; its deposition and remodeling are important for many processes including embryonic development, immune response, and wound healing. To date, dysfunction in BM deposition or remodeling has been linked to many human congenital disorders and diseases, affecting many different tissues in the body, including malformations, dystrophies, and cancer. However, many questions remain to be answered on the role BM proteins, and their mutations, play in the pathogenesis of human disease. In recent years, the zebrafish (Danio rerio) has emerged as a powerful animal model for human development and disease. In the first part of this chapter, we provide an overview of described defects caused by BM dysfunction in zebrafish, including development and function of notochord, muscle, central nervous system, skin, cardiovascular system, and kidney. In the second part, we will describe details of methods used to visualize and assess the structure of the BM in zebrafish, and to functionally analyze its different components.

Cell-cell signaling drives the evolution of complex traits: introduction-lung evo-devo

Physiology integrates biology with the environment through cell–cell interactions at multiple levels. The evolution of the respiratory system has been “deconvoluted” (Torday and Rehan in Am J Respir Cell Mol Biol 31:8–12, 2004) through Gene Regulatory Networks (GRNs) applied to cell–cell communication for all aspects of lung biology development, homeostasis, regeneration, and aging. Using this approach, we have predicted the phenotypic consequences of failed signaling for lung development, homeostasis, and regeneration based on evolutionary principles. This cell–cell communication model predicts other aspects of vertebrate physiology as adaptational responses. For example, the oxygen-induced differentiation of alveolar myocytes into alveolar adipocytes was critical for the evolution of the lung in land dwelling animals adapting to fluctuating Phanarezoic oxygen levels over the past 500 million years. Adipocytes prevent lung injury due to oxygen radicals and facilitate the rise of endothermy. In addition, they produce the class I cytokine leptin, which augments pulmonary surfactant activity and alveolar surface area, increasing selection pressure for both respiratory oxygenation and metabolic demand initially constrained by high-systemic vascular pressure, but subsequently compensated by the evolution of the adrenomedullary beta-adrenergic receptor mechanism. Conserted positive selection for the lung and adrenals created further selection pressure for the heart, which becomes progressively more complex phylogenetically in tandem with the lung. Developmentally, increasing heart complexity and size impinges precociously on the gut mesoderm to induce the liver. That evolutionary-developmental interaction is significant because the liver provides regulated sources of glucose and glycogen to the evolving physiologic system, which is necessary for the evolution of the neocortex. Evolution of neocortical control furthers integration of physiologic systems. Such an evolutionary vertical integration of cell-to-tissue-to-organ-to-physiology of intrinsic cell–cell signaling and extrinsic factors is the reverse of the “top-down” conventional way in which physiologic systems are usually regarded. This novel mechanistic approach, incorporating a “middle-out” cell–cell signaling component, will lead to a readily available algorithm for integrating genes and phenotypes. This symposium surveyed the phylogenetic origins of such vertically integrated mechanisms for the evolution of cell–cell communication as the basis for complex physiologic traits, from sponges to man.

Lung evolution as a cipher for physiology

In the postgenomic era, we need an algorithm to readily translate genes into physiologic principles. The failure to advance biomedicine is due to the false hope raised in the wake of the Human Genome Project (HGP) by the promise of systems biology as a ready means of reconstructing physiology from genes. like the atom in physics, the cell, not the gene, is the smallest completely functional unit of biology. Trying to reassemble gene regulatory networks without accounting for this fundamental feature of evolution will result in a genomic atlas, but not an algorithm for functional genomics. For example, the evolution of the lung can be "deconvoluted" by applying cell-cell communication mechanisms to all aspects of lung biology development, homeostasis, and regeneration/repair. Gene regulatory networks common to these processes predict ontogeny, phylogeny, and the disease-related consequences of failed signaling. This algorithm elucidates characteristics of vertebrate physiology as a cascade of emergent and contingent cellular adaptational responses. By reducing complex physiological traits to gene regulatory networks and arranging them hierarchically in a self-organizing map, like the periodic table of elements in physics, the first principles of physiology will emerge.

Keeping your vascular integrity: What can we learn from fish?

The cardiovascular system has the life-providing task of delivering oxygen and any flaw in this system can be life-threatening. This has encouraged extensive studies to elucidate the mechanisms behind cardiovascular development/homeostasis. The zebrafish has emerged as a formidable tool to speed up this quest, as illustrated in a recent issue of Nature Genetics.1 Baculovirus IAP repeat c2 (BIRC2), also termed cellular inhibitor of apoptosis (cIAP)-1, was found to specifically prevent endothelial cells (ECs, lining the inside of vessels) from going into suicide mode ('apoptosis') and so preserve vessel integrity. Here, we summarize the factors determining vascular integrity and elaborate on the suitability of the zebrafish to study this phenomenon.

Natural anti-GBM antibodies from normal human sera recognize α3(IV)NC1 restrictively and recognize the same epitopes as anti-GBM antibodies from patients with anti-GBM disease

Anti-GBM disease is a rare autoimmune condition characterized by autoantibodies targeting the alpha3 chain non-collagen 1 domain of type IV collagen (alpha3(IV)NC1). Recently, we isolated IgG reacting with alpha3(IV)NC1 from normal healthy human sera. The current study examined the antigen and epitope specificity of these natural autoantibodies (NAA) using recombinant human alpha1, 3, 5(IV)NC1 and three constructs expressing, previously defined epitope regions designated E(A), E(B) and S2, in the alpha1(IV)NC1 background. The NAA preparations reacted with recombinant human alpha3(IV)NC1 to the same extent as with purified bovine alpha(IV)NC1, but not with recombinant human alpha1 and alpha5(IV)NC1. NAA preparations recognized the three chimeric proteins (E(A), E(B) and S2) yielding similar absorbance values. We conclude that anti-GBM NAA recognize the same major epitopes as anti-GBM antibodies from patients with Goodpasture's disease.