A Sequence Listing is provided herewith as a text file, “3730176US1.txt”, created on Feb. 14, 2024 and having a size of 446,507 bytes. The contents of the text file are incorporated by reference herein in their entirety.
The World Health Organization has declared Covid-19 a global pandemic. A highly infectious coronavirus, officially called SARS-CoV-2, causes the Covid-19 disease. Even with the most effective containment strategies, the spread of the Covid-19 respiratory disease has only been slowed. The available vaccines are likely best way to prevent people from getting sick, but some refuse to be vaccinated and some vaccinated people can still suffer from Covid-19 infection. Compositions and methods to facilitate recovery from Covid-19 infection are needed.
Provided are methods and compositions useful for identifying compounds that can inhibit SARS-CoV-2 infection or the effects thereof. As illustrated herein, cardiomyocytes (CMs), are highly infectible by corona viruses, including SARS-CoV-2. Even low multiplicities of infection (MOI) of SARS-CoV-2 (e.g., about 1 virion particle per 1000 cells) can infect cardiomyocytes and support SARS-CoV-2 viral replication.
COVID-19 causes severe heart failure, but specific pathological consequences in cardiomyocytes have yet to be identified. Here the inventors describe the consequences of COVID-19 infection on cardiomyocytes, and upon the functioning of the heart. As demonstrated herein, human cardiomyocytes exposed to the virus exhibit significant myofibrillar disruption and a distinct patterns of sarcomeric fragmentation. Many cardiomyocytes exposed to coronavirus lack nuclear DNA by common detection methods, such as Hoechst or hematoxylin staining. In contrast, SARS-CoV-2 does not appear to infect induced pluripotent stem cells (iPSCs), endothelial cells, or cardiac fibroblasts. The adverse morphologic features of virally infected cardiomyocytes are distinct and potentially unique compared to other genetic or environmental stresses that are known to induce cardiomyopathy phenotypes.
Human iPSC-derived cardiac cells were used as described herein for infection with SARS-CoV-2 to reveal robust transcriptomic and morphological signatures in cardiomyocytes, which allowed identification of clear markers of viral damage in human autopsy specimens. Cardiomyocytes display a distinct pattern of sarcomere fragmentation, with specific cleavage of thick filaments, and COVID-19 autopsy samples displayed similar sarcomeric disruption. Numerous iPSC-cardiomyocytes lacked nuclear DNA. Surprisingly, enucleated cardiomyocytes were prevalent in the hearts of COVID-19 patients. These striking cytopathic features are useful for identifying new therapies for COVID-19-related heart failure.
Methods and assay mixtures are described herein that involve use of human cells, for example, cardiomyocytes or cells generated from human induced pluripotent stem cells (iPS) for identifying compounds useful for treatment of SARS-CoV-2. Screening of viral infection and cytopathic effects of such infection in cardiomyocytes can be performed in multi-well plate formats that are compatible with high-throughput screening platforms.
In some cases, cardiomyocytes derived from induced pluripotent stem cells of different genotypes are used in the assays, allowing identification of compounds for treatment of SARS-CoV-2 in patients with different genetically induced cardiac conditions.
The screening assay described herein provides multiple distinct visual indications of cytopathic effects induced by coronavirus that can be used to identify different cellular responses to coronavirus infection and to test whether compounds are useful therapeutics to attenuate adverse consequences of SARS-CoV-2 viral infection. The methods are highly sensitive and can provide information on multiple parameters useful for evaluating cytopathic effects of SARS-CoV-2 viral infection. Thus, in addition to serving as a frontline screening platform for prophylactic and therapeutic effects of the virus on cardiac cells, the methods also serve as a sensitive assay for distinct cytopathic effects that could adversely impact other human cells and tissues that are vulnerable to coronavirus infection and inflammatory responses.
The therapeutic target can, for example, be the titin protein at the M-line in relation to infection. Titin is involved in sarcomere assembly and function through its elastic adaptor and signaling domains. Titin's M-line region contains a unique kinase domain that may regulate sarcomere assembly via its substrate titin cap (T-cap). Studies indicate that the titin M-line region is required to form a continuous titin filament and to provide mechanical stability.
As illustrated herein, cardiomyocytes (CMs) can easily be infected by corona viruses, including SARS-CoV-2. Methods are described herein for identifying compounds that can inhibit or prevent such infection.
Such methods can include (a) contacting cardiomyocytes with one or more test agents either before, during or after the cardiomyocytes have been contacted (infected) with corona viruses, for example SARS-CoV-2; and (b) observing whether the cardiomyocytes are enucleated, observing whether the cardiomyocytes have cleaved cardiac myofibrils, observing whether the cardiomyocytes have cleavages in their titin proteins. The assays can also include measuring the number or reproduction rate of the corona viruses compared to a control. The measurements can be performed at one or more time points after the cardiomyocytes are contacted with the one or more test agents. The control can be untreated cardiomyocytes, meaning cardiomyocytes that were not contacted with a test agent. In some cases, the control can be cardiomyocytes contacted with a compound or biological known to inhibit or prevent corona virus infection.
The cardiomyocytes can be obtained from a variety of sources, for example, from existing cardiomyocyte cell lines, from healthy subjects, and/or from patients with cardiac conditions or cardiac diseases. In some cases, the cardiomyocytes can be obtained from induced pluripotent stem cells (iPSCs), which can be generated from cells obtained from healthy subjects or from patients with cardiac conditions or cardiac diseases. For example, cardiomyocytes can be obtained from induced pluripotent stem cells (iPSCs) generated from cells with genetic mutations, including genetic mutations that adversely affect heart function, that adversely affect immune function, or a combination thereof. The cardiomyocytes can, in another example, be obtained from induced pluripotent stem cells (iPSCs) that have mutations in one or more of their immune-related genes, for example, in their innate immune genes. Such mutations can make an individual more vulnerable to COVID-19 infection.
A variety of test agents (e.g., compounds and/or biological agents) can be tested to identify useful agent that reduce SARS-CoV-2 virally induced myofibrillar disruption, sarcomeric fragmentation, nuclear staining, enucleation, cardiac troponin solute levels, or a combination thereof in cardiomyocytes compared to a control assay of cardiomyocytes in the presence of SARS-CoV-2 virus without the test compound(s)/biological agents. For example, the test agents can be one or more small molecules, antibodies, nucleic acids, carbohydrates, proteins, peptides, or a combination thereof. Any such test agents can be tested and/or evaluated in the assays.
A population of cardiomyocytes for testing can be derived from essentially any source and can be heterogeneous or homogeneous. In certain embodiments, the cells to be tested as described herein are adult cells, including adult cardiomyocytes from essentially any accessible source. In other embodiments, the cells used are cardiomyocytes generated from induced pluripotent stem cells (iPSCs). The cells used to generate the iPSCs can be adult cells, adult stem cells, progenitor cells, or somatic cells obtained from healthy subjects or from patients with cardiac conditions or cardiac diseases. In still other embodiments, the cells used to generate iPSCs include any type of cell from a newborn, including, but not limited to newborn cord blood, newborn stem cells, progenitor cells, and tissue-derived cells (e.g., somatic cells). Accordingly, a starting population of cells that is used to generate iPSCs, can be essentially any live somatic cell type.
The cardiomyocytes can be autologous or allogeneic cells (relative to a subject to be treated or who may receive the cells).
In some cases, cardiomyocytes from healthy subjects are used in the test assays. In other cases, cardiomyocytes from subjects with cardiac conditions are used in the test assays. Cardiomyocyte cell lines can be used in the test assays. Alternatively, the cardiomyocytes can be isolated from a healthy subject, a subject with a cardiac condition, or the cardiomyocytes can be generated from induced pluripotent stem cells (iPSCs) from either healthy subjects or subjects with a cardiac condition. For example, cardiomyocytes can be obtained from induced pluripotent stem cells (iPSCs) generated from cells with genetic mutations, including genetic mutations that adversely affect heart function, that adversely affect immune function, or a combination thereof. The cardiomyocytes can, in another example, be obtained from induced pluripotent stem cells (iPSCs) that have mutations in one or more of their immune-related genes, for example, in their innate immune genes. Such mutations can make an individual more vulnerable to COVID-19 infection.
Cardiomyocytes can be generated from induced pluripotent stem cells (iPSCs) by any convenient method. For example, the cardiomyocytes can be generated from iPSCs using the methods described in WO 2015/038704, which is incorporated herein by reference in its entirety.
Cardiomyocytes from subjects with a variety of cardiac diseases and conditions can be used in the assays described herein. For example, the cardiomyocytes can be from any subject with any cardiac pathology or cardiac dysfunction.
The terms “cardiac pathology” or “cardiac dysfunction” are used interchangeably and refer to any impairment in the heart's pumping function. This includes, for example, impairments in contractility, impairments in ability to relax (sometimes referred to as diastolic dysfunction), abnormal or improper functioning of the heart's valves, diseases of the heart muscle (sometimes referred to as cardiomyopathies), diseases such as angina pectoris, myocardial ischemia and/or infarction characterized by inadequate blood supply to the heart muscle, infiltrative diseases such as amyloidosis and hemochromatosis, global or regional hypertrophy (such as may occur in some kinds of cardiomyopathy or systemic hypertension), and abnormal communications between chambers of the heart.
As used herein, the term “cardiomyopathy” refers to any disease or dysfunction of the myocardium (heart muscle) in which the heart is abnormally enlarged, thickened and/or stiffened. As a result, the heart muscle's ability to pump blood is usually weakened. The etiology of the disease or disorder may be, for example, inflammatory, metabolic, toxic, infiltrative, fibroplastic, hematological, genetic, or unknown in origin. There are two general types of cardiomyopathies: ischemic (resulting from a lack of oxygen) and non-ischemic.
Ischemic cardiomyopathy is a chronic disorder caused by coronary artery disease (a disease in which there is atherosclerotic narrowing or occlusion of the coronary arteries on the surface of the heart). Coronary artery disease often leads to episodes of cardiac ischemia, in which the heart muscle is not supplied with enough oxygen-rich blood.
Non-ischemic cardiomyopathy is generally classified into three groups based primarily on clinical and pathological characteristics: dilated cardiomyopathy, hypertrophic cardiomyopathy and restrictive and infiltrative cardiomyopathy.
In another embodiment, the cardiac pathology is a genetic disease such as Duchenne muscular dystrophy and Emery Dreiffuss dilated cardiomyopathy.
For example, the cardiac pathology can be selected from the group consisting of congestive heart failure, myocardial infarction, cardiac ischemia, myocarditis and arrhythmia.
Cardiac muscle is striated, like skeletal muscle, with actin and myosin arranged in sarcomeres to enable contractile function. The actin and myosin filaments have a specific and constant length of about a few micrometers. The filaments are organized into repeated subunits along the length of the myofibril. These subunits are called sarcomeres. Muscle cells are largely filled with myofibrils running parallel to each other along the long axis of the cell. The sarcomeric subunits of one myofibril are in nearly perfect alignment with those of the myofibrils next to it. This alignment provides optical properties so that cells to appear striped or striated.
Titin constitutes the third myofilament of cardiac muscle, with a single giant polypeptide spanning from Z-disk to the M-band region of the sarcomere. Titin has two general regions, an N-terminal I-band and a C-terminal A-band. An approximate 1.0 MDa region in the I-band is extensible and consists of tandemly arranged immunoglobulin (Ig)-like domains that make up proximal (near Z-disk) and distal (near A-I junction) segments, interspersed by the PEVK sequence (rich in proline, glutamate, valine, and lysine residues) and an N2B element.
The C-terminal titin region of about 2 MDa includes the A-band and is inextensible. This C-terminal region is composed of regular arrays of Ig and fibronectin type 3 (Fn3) modules forming so-called super-repeats. The A-band is thought to act as a protein-ruler and possesses kinase activity. An N-terminal Z-disc region and a C-terminal M-band region bind to the Z-line and M-line of the sarcomere, respectively, so that a single titin molecule spans half the length of a sarcomere. Titin also contains binding sites for muscle associated proteins and serves as an adhesion template for assembly of contractile machinery in muscle cells. The M-band is encoded by TTN exons 359-364.
Considerable variability exists in the I-band, the M-line, and the Z-disc regions of titin. Variability in the I-band region contributes to the differences in elasticity of different titin isoforms and, therefore, to the differences in elasticity of different muscle types. Mutations in this gene are associated with familial hypertrophic cardiomyopathy. Autoantibodies to titin are produced in patients with the autoimmune disease scleroderma.
The titin protein is encoded by the TTN gene, which is located on human chromosome 2, at NC_000002.12 (178525989..178807423, complement; see website at ncbi.nlm.nih.gov/gene?LinkName=protein_gene&from_uid=291045223). Alternative splicing of the TTN gene results in multiple transcript variants.
One example of a human titin protein sequence has UniProt accession number A0A0A0MRA3-1; this titin protein sequence is shown below as SEQ ID NO:1.
Another example of a titin protein sequence is provided by UniProt as accession number Q8WZ42.
The N2-B splice variant of titin encodes the major N2-B cardiac muscle isoform, which lacks multiple exons in the region encoding PEVK repeats. This results in a shortened PEVK region in isoform N2-B compared to isoform IC. A sequence for such a human N2-B titin isoform is shown below (NCBI accession number NP 003310.4), provided below as SEQ ID NO:2.
In some cases, SARS-CoV-2 infection can be monitored by observing cleavage of titin in the C-terminal region. For example, such cleavage can occur in the M-band (also called the M-line) region of titin. The M band is at the C-terminal end 35 of the titin protein and in the center of the A band, which is in the center of the sarcomere. The approximate 250 kilodalton M band is an attachment site for the thick filaments, and it is encoded by six exons, exons 359 to 364, which are also termed M-band exons 1 to 6 (Mex1 to Mex6). The M band region interacts with several sarcomeric proteins including myosin-binding protein C, calmodulin 1, CAPN3, obscurin, and MURF1.
Cleavage of titin can be observed within the C-terminal 2000-4000 amino acids, or the 2000-3000 amino acids of the titin protein. Such cleavage is observed when SARS-CoV-2 infection occurs. A test agent that causes a reduction in titin cleavage (e.g., compared to a control) can be useful for treating and/or preventing SARS-CoV-2 infection.
Initial descriptions of COVID-19, the pandemic disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), characterized it as a primarily respiratory syndrome (see website at pubmed.ncbi.nlm.nih.gov/32031570/). However, increasing clinical evidence now implicates multiple organ systems in COVID-19 infection, including the heart, gastrointestinal tract, and kidneys (Wang, see websites at sciencedirect.com/science/article/pii/S0140673620302117; ahajournals.org/doi/10.1161/CIRCULATIONAHA.120.047164; jamanetwork.com/journals/jama/fullarticle/2763485; jamanetwork.com/joumals/jama/fullarticle/2765184).
As illustrated herein, multiple COVID-19 patients frequently present with significant myocardial damage (see also websites at jamanetwork.com/journals/jamacardiology/fullarticle/2763845; academic.oup.com/cardiovascres/article/116/10/1666/5826160; nature.com/articles/s41569-020-0413-9), even when they exhibited no prior cardiovascular disease (CVD) (jamanetwork.com/journals/jamacardiology/fullarticle/2763524), indicating that viral infection may be directly responsible for the cardiac damage. Meta-analyses identify elevated high-sensitivity troponin-I or natriuretic peptides as the strongest predictor of mortality in hospitalized patients, eclipsing both cardiovascular disease and congestive obstructive pulmonary disease (see websites at thelancet.com/journals/lancet/article/PIIS0140-6736(20)30566-3/fulltext; pubmed.ncbi.nlm.nih.gov/32362922/; pubmed.ncbi.nlm.nih.gov/32125452/; jamanetwork.com/joumals/jamacardiology/fullarticle/2763524). Alarmingly, evidence of elevated troponin can be found even in mild cases of COVID-19, and a recent study observed that the majority of recovered patients in the studied cohort presented with impaired cardiac function, indicating that long-term heart sequelae from COVID-19 may not be limited to intensive care unit cases (see website atjamanetwork.com/joumals/jamacardiology/fullarticle/2768916).
Identifying therapeutic strategies to prevent or manage myocardial injury in COVID-19 patients is hindered by limited understanding of the mechanisms by which SARS-CoV-2 induces cardiac damage. Besides direct myocardial infection, cardiac damage may be caused by other systemic impacts of SARS-CoV-2, such as hypoxic stress due to pulmonary damage, microvascular thrombosis, and/or the systemic immune response to viral infection (see website at ncbi.nlm.nih.gov/pmc/articles/PMC7270045/). Recent histological results from deceased COVID-19 patients detect viral RNA in the myocardium without inflammatory cell infiltrates (see website at jamanetwork.com/joumals/jamacardiology/fullarticle/2768914), but whether these transcripts arise from infected myocytes, cardiac stroma, or blood vessels was previously unknown (see website at onlinelibrary.wiley.com/doi/abs/10.1002/ejhf.1828). Cardiomyocytes are known to express the primary receptor for viral entry, ACE2 (see website at sciencedirect.com/science/article/pii/S0092867420302294) and may be infectable by SARS-CoV-2 (see website at ahajournals.org/doi/full/10.1161/CIRCULATIONAHA.120.047549). Developing effective interventions for cardiac injury in COVID-19 requires identification of the key molecules and cell types involved in mediating viral infection and cellular anomalies.
As described herein, ex vivo studies employed using human cell-based models of the heart were used to afford the most direct route for the prospective and clinically relevant study of the effects of cardiac viral infection. Human induced pluripotent stem cells (iPSCs) can be used as described herein to obtain functional cardiac tissue models for disease modeling and discovery, overcoming the infeasibility of using primary human hearts. Stem-cell derived models have already demonstrated the susceptibility of hepatocytes (see website at sciencedirect.com/science/article/pii/S1934590920302824), intestinal epithelium (see website at nature.com/articles/s41591-020-0912-6; see website at ncbi.nlm.nih.gov/pmc/articles/PMC7199907/), and lung organoids (see website at biorxiv.org/content/10.1101/2020.05.05.079095v1. abstract) to SARS-CoV-2 infection.
While two recent reports indicated that human iPSC-cardiomyocytes are susceptible to SARS-CoV-2 infection (see websites at cell.com/cell-reports-medicine/fulltext/S2666-3791(20)30068-9, biorxiv.org/content/10.1101/2020.06.01.127605v1), clear indications of specific cardiac cytopathic features have not been identified. In addition, the relative viral tropism for other cardiac cell types that may be involved in microthrombosis or weakening of the ventricular wall has previously not been explored, nor has there been direct correlation of in vitro results to clinical pathology specimens.
Identifying phenotypic biomarkers of SARS-CoV-2 infection and cardiac cytopathy that recapitulate features of patient tissue is critical for rapidly developing novel cardioprotective therapies efficacious against COVID-19. As described herein, the inventors have examined the relative susceptibility of three iPS-derived cardiac cell types: cardiomyocytes (CMs), cardiac fibroblasts (CFs), and endothelial cells (ECs), to SARS-CoV-2 infection, and identify clear hallmarks of infection and cardiac cytopathy that predict pathologic features found in human COVID-19 tissue specimens.
The term “about” as used herein when referring to a measurable value such as an amount, a length, and the like, is meant to encompass variations of 20% or +10%, more preferably 5%, even more preferably 1%, and still more preferably 0.1% from the specified value.
Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limit of that range and any other stated or intervening value in that stated range, is encompassed within the disclosed subject matter. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges, and are also encompassed within the disclosed subject matter, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the disclosed subject matter.
As used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural reference unless the context clearly dictates otherwise. Thus, for example, a reference to “a nucleic acid” or “a protein” or “a cell” includes a plurality of such nucleic acids, proteins, or cells (for example, a solution or dried preparation of nucleic acids or expression cassettes, a solution of proteins, or a population of cells), and so forth. In this document, the term “or” is used to refer to a nonexclusive or, such that “A or B” includes “A but not B,” “B but not A,” and “A and B,” unless otherwise indicated.
“Recombinant” as used herein to describe a nucleic acid molecule means a polynucleotide of genomic, cDNA, bacterial, mammalian, semisynthetic, or synthetic origin which, by virtue of its origin or manipulation, is not associated with all or a portion of the polynucleotide with which it is associated in nature.
The term “recombinant” as used with respect to a protein or polypeptide means a polypeptide produced by expression of a recombinant polynucleotide. In general, the gene of interest is cloned and then expressed in transformed organisms. The host organism expresses the foreign gene to produce the protein under expression conditions.
As used herein, a “cell” refers to any type of cell. The cell can be in an organism or it can be maintained outside of an organism. The cell can be within a living organism and be in its normal (native) state. The term “cell” includes an individual cell or a group or population of cells. The cell(s) can be a prokaryotic, eukaryotic, or archaeon cell(s), such as a bacterial, archaeal, fungal, protist, plant, or animal cell(s). The cell(s) can be from or be within tissues, organs, and biopsies. The cell(s) can be a recombinant cell(s), a cell(s) from a cell line cultured in vitro. The cell(s) can include cellular fragments, cell components, or organelles comprising nucleic acids. In some cases, the cell(s) are human cells. The term cell(s) also encompasses artificial cells, such as nanoparticles, liposomes, polymersomes, or microcapsules encapsulating nucleic acids. The methods described herein can be performed, for example, on a sample comprising a single cell or a population of cells. The term also includes genetically modified cells.
The term “transformation” refers to the insertion of an exogenous polynucleotide into a host cell, irrespective of the method used for the insertion. For example, direct uptake, transfection, or transduction are included. The exogenous polynucleotide may be maintained as a non-integrated vector, for example, a plasmid, or alternatively, may be integrated into the host genome.
“Recombinant host cells,” “host cells”, “cells”, “cell lines”, “cell cultures”, and other such terms denoting microorganisms or higher eukaryotic cell lines cultured as unicellular entities refer to cells which can be, or have been, used as recipients for recombinant vector or other transferred DNA, and include the original progeny of the original cell which has been transfected.
A “coding sequence” or a sequence which “encodes” a selected RNA or a selected polypeptide, is a nucleic acid molecule which is transcribed (in the case of DNA) and translated (in the case of mRNA) into a polypeptide in vivo when placed under the control of appropriate regulatory sequences (or “control elements”). The boundaries of the coding sequence can be determined by a start codon at the 5′ (amino) terminus and a translation stop codon at the 3′ (carboxy) terminus. A coding sequence can include, but is not limited to, cDNA from viral, prokaryotic or eukaryotic mRNA, genomic DNA sequences from viral or prokaryotic DNA, and even synthetic DNA sequences. A transcription termination sequence may be located 3′ to the coding sequence.
Typical “control elements,” include, but are not limited to, transcription promoters, transcription enhancer elements, transcription termination signals, polyadenylation sequences (located 3′ to the translation stop codon), sequences for optimization of initiation of translation (located 5′ to the coding sequence), and translation termination sequences.
“Operably linked” refers to an arrangement of elements wherein the components so described are configured so as to perform their usual function. Thus, a given promoter operably linked to a coding sequence is capable of effecting the expression of the coding sequence when the proper enzymes are present. The promoter need not be contiguous with the coding sequence, so long as it functions to direct the expression thereof. Thus, for example, intervening untranslated yet transcribed sequences can be present between the promoter sequence and the coding sequence and the promoter sequence can still be considered “operably linked” to the coding sequence.
“Encoded by” refers to a nucleic acid sequence which codes for a polypeptide or RNA sequence. For example, the polypeptide sequence or a portion thereof contains an amino acid sequence of at least 3 to 5 amino acids, more preferably at least 8 to 10 amino acids, and even more preferably at least 15 to 20 amino acids from a polypeptide encoded by the nucleic acid sequence. The RNA sequence or a portion thereof contains a nucleotide sequence of at least 3 to 5 nucleotides, more preferably at least 8 to 10 nucleotides, and even more preferably at least 15 to 20 nucleotides.
The terms “isolated,” “purified,” or “biologically pure” refer to material that is free to varying degrees from components which normally accompany it as found in its native state. “Isolate” denotes a degree of separation from original source or surroundings. “Purify” denotes a degree of separation that is higher than isolation. A “purified” or “biologically pure” protein is sufficiently free of other materials such that any impurities do not materially affect the biological properties of the protein or cause other adverse consequences. That is, a nucleic acid or peptide of this invention is purified if it is substantially free of cellular material, viral material, or culture medium when produced by recombinant DNA techniques, or chemical precursors or other chemicals when chemically synthesized. Purity and homogeneity are typically determined using analytical chemistry techniques, for example, polyacrylamide gel electrophoresis or high-performance liquid chromatography. The term “purified” can denote that a nucleic acid or protein gives rise to essentially one band in an electrophoretic gel. For a protein that can be subjected to modifications, for example, phosphorylation or glycosylation, different modifications may give rise to different isolated proteins, which can be separately purified.
“Expression” refers to detectable production of a gene product by a cell. The gene product may be a transcription product (i.e., RNA), which may be referred to as “gene expression”, or the gene product may be a translation product of the transcription product (i.e., a protein), depending on the context.
“Purified polynucleotide” refers to a polynucleotide of interest or fragment thereof which is essentially free, e.g., contains less than about 50%, preferably less than about 70%, and more preferably less than about at least 90%, of the protein and/or nucleic acids with which the polynucleotide is naturally associated. Techniques for purifying polynucleotides of interest are available in the art and include, for example, disruption of the cell containing the polynucleotide with a chaotropic agent and separation of the polynucleotide(s) and proteins by ion-exchange chromatography, affinity chromatography and sedimentation according to density.
“Substantially purified” generally refers to isolation of a substance (compound, polynucleotide, protein, polypeptide, peptide composition) such that the substance comprises the majority percent of the sample in which it resides. Typically, in a sample, a substantially purified component comprises 50%, preferably 80%-85%, more preferably 90-95% of the sample. Techniques for purifying polynucleotides and polypeptides of interest are well-known in the art and include, for example, ion-exchange chromatography, affinity chromatography and sedimentation according to density.
The term “transfection” is used to refer to the uptake of foreign DNA by a cell. A cell has been “transfected” when exogenous DNA has been introduced inside the cell membrane. A number of transfection techniques are generally known in the art. See, e.g., Graham et al. (1973) Virology, 52:456, Sambrook et al. (2001) Molecular Cloning, a laboratory manual, 3rd edition, Cold Spring Harbor Laboratories, New York, Davis et al. (1995) Basic Methods in Molecular Biology, 2nd edition, McGraw-Hill, and Chu et al. (1981) Gene 13:197. Such techniques can be used to introduce one or more exogenous DNA moieties into suitable host cells. The term refers to both stable and transient uptake of the genetic material and includes uptake of peptide-linked or antibody-linked DNAs.
The term “transduction” refers to the introduction of foreign nucleic acid to a cell through a replication-incompetent viral vector.
A “vector” is capable of transferring nucleic acid sequences to target cells (e.g., viral vectors, non-viral vectors, particulate carriers, and liposomes). Typically, “vector construct,” “expression vector,” and “gene transfer vector,” mean any nucleic acid construct capable of directing the expression of a nucleic acid of interest and which can transfer nucleic acid sequences to target cells. Thus, the term includes cloning and expression vehicles, as well as viral vectors.
“Mammalian cell” refers to any cell derived from a mammalian subject suitable for transfection with an engineered vector system comprising an expression system described herein. The cell may be xenogeneic, autologous, or allogeneic. The cell can be a primary cell obtained directly from a mammalian subject. The cell may also be a cell derived from the culture and expansion of a cell obtained from a mammalian subject. Immortalized cells are also included within this definition. In some embodiments, the cell has been genetically engineered to express a recombinant protein and/or nucleic acid.
The term “subject” includes animals, including both vertebrates and invertebrates, including, without limitation, invertebrates such as arthropods, mollusks, annelids, and cnidarians; and vertebrates such as amphibians, including frogs, salamanders, and caecillians; reptiles, including lizards, snakes, turtles, crocodiles, and alligators; fish; mammals, including human and non-human mammals such as non-human primates, including chimpanzees and other apes and monkey species; laboratory animals such as mice, rats, rabbits, hamsters, guinea pigs, and chinchillas; domestic animals such as dogs and cats; farm animals such as sheep, goats, pigs, horses and cows; and birds such as domestic, wild and game birds, including chickens, turkeys and other gallinaceous birds, ducks, geese, and the like. In some cases, the disclosed methods find use in experimental animals, in veterinary application, and in the development of animal models for disease, including, but not limited to, rodents including mice, rats, and hamsters; primates, and transgenic animals.
“Gene transfer” or “gene delivery” refers to methods or systems for reliably inserting DNA or RNA of interest into a host cell. Such methods can result in transient expression of non-integrated transferred DNA, extrachromosomal replication and expression of transferred replicons (e.g., episomes), or integration of transferred genetic material into the genomic DNA of host cells. Gene delivery expression vectors include, but are not limited to, vectors derived from bacterial plasmid vectors, viral vectors, non-viral vectors, alphaviruses, pox viruses and vaccinia viruses.
The term “derived from” is used herein to identify the original source of a molecule but is not meant to limit the method by which the molecule is made which can be, for example, by chemical synthesis or recombinant means.
A polynucleotide “derived from” a designated sequence refers to a polynucleotide sequence which comprises a contiguous sequence of approximately at least about 6 nucleotides, preferably at least about 8 nucleotides, more preferably at least about 10-12 nucleotides, and even more preferably at least about 15-20 nucleotides corresponding, i.e., identical or complementary to, a region of the designated nucleotide sequence. The derived polynucleotide will not necessarily be derived physically from the nucleotide sequence of interest, but may be generated in any manner, including, but not limited to, chemical synthesis, replication, reverse transcription or transcription, which is based on the information provided by the sequence of bases in the region(s) from which the polynucleotide is derived. As such, it may represent either a sense or an antisense orientation of the original polynucleotide.
As used herein, the terms “complementary” or “complementarity” refers to polynucleotides that are able to form base pairs with one another. Base pairs are typically formed by hydrogen bonds between nucleotide units in an anti-parallel orientation between polynucleotide strands. Complementary polynucleotide strands can base pair in a Watson-Crick manner (e.g., A to T, A to U, C to G), or in any other manner that allows for the formation of duplexes. As persons skilled in the art are aware, when using RNA as opposed to DNA, uracil (U) rather than thymine (T) is the base that is considered to be complementary to adenosine. However, when uracil is denoted in the context of the present invention, the ability to substitute a thymine is implied, unless otherwise stated. “Complementarity” may exist between two RNA strands, two DNA strands, or between an RNA strand and a DNA strand. It is generally understood that two or more polynucleotides may be “complementary” and able to form a duplex despite having less than perfect or less than 100% complementarity. Two sequences are “perfectly complementary” or “100% complementary” if at least a contiguous portion of each polynucleotide sequence, comprising a region of complementarity, perfectly base pairs with the other polynucleotide without any mismatches or interruptions within such region. Two or more sequences are considered “perfectly complementary” or “100% complementary” even if either or both polynucleotides contain additional non-complementary sequences as long as the contiguous region of complementarity within each polynucleotide is able to perfectly hybridize with the other. “Less than perfect” complementarity refers to situations where less than all of the contiguous nucleotides within such region of complementarity are able to base pair with each other. Determining the percentage of complementarity between two polynucleotide sequences is a matter of ordinary skill in the art.
The following example illustrate some of the experiments used in the development of the invention and some features of the invention.
This Example describes some of the materials and methods used in developing and practicing the invention.
hiPSC Maintenance; iPS-Cardiomyocyte Differentiation and Purification
Human iPS cells (WTC11 line; see website at ncbi.nlm.nih.gov/pmc/articles/PMC4063274/) were maintained in mTESR or mTESR+(STEMCELL Technologies) on Matrigel (8 μg/ml, BD Biosciences)-coated cell culture plates at 37° C., 5% CO2. Cells were passaged every 3 days using Relesr (STEMCELL Technologies) and supplemented with Rock Inhibitor Y-27632 (SelleckChem) for 24 hours after each passaging. hiPSCs were differentiated into cardiomyocytes following a modified Wnt pathway modulation-based GiWi protocol (see website at ncbi.nlm.nih.gov/pmc/articles/PMC3612968/). Briefly, hiPSCs cultures were harvested using Accutase (STEMCELL Technologies) and seeded onto Matrigel-coated 12-well plates. Three days later, cells were exposed to 12 uM CHIR99021 (Tocris) in RPMI1640 (Gibco, 11875093) supplemented with B27 without insulin (Gibco, A1895601) (R/B media) for 24 hours. After an additional 48 hours, media was changed to R/B media supplemented with 5 uM IWP2 (Tocris) for 48 hours. On day 7, media was changed to RPMI1640 medium supplemented with B27 with insulin (Gibco, 17504044) (R/B*) and refreshed every 3 days thereafter. Beating was generally observed around day 8-11. At day 15, cells were cryopreserved using CryoStor CS10 (STEMCELL Technologies). After thawing, cell cultures were enriched for iPS-cardiomyocytes following metabolic switch purification (see website at pubmed.ncbi.nlm.nih.gov/23168164/). Briefly, cells were washed once with saline buffer and incubated in DMEM (without glucose, without sodium pyruvate; Gibco, 11966025) supplemented with GlutaMax (Gibco, 35050061), MEM Non-Essential Amino Acids (Gibco, 11140050) and sodium L-lactate (4 mM, Sigma-Aldrich). Lactate media was refreshed every other day for a total of 6 days. Four to six days later (day 28-30), iPS-CMs were replated into assay plates for infection using 0.25% Trypsin (Gibco, 15050065) at a density of approximately 60,000 cells/cm2.
scRNAseq Analysis of SARS-CoV-2 Entry Factors
A historic single cell RNA sequencing data set consisting of iPSC-derived cardiomyocytes, primary fetal cardiac fibroblasts, and iPSC-derived endothelial cells was re-analyzed to compare relative expression levels of SARS-CoV-2 relevant receptors and proteases (GSE155226) (see web at biorxiv.org/content/10.1101/2020.07.06.190504v1). Briefly, day 30 lactate purified cardiomyocytes were force aggregated either alone or with a single supporting cell type. The cardiomyocytes were then cultured in suspension culture. Aggregates were dissociated and libraries prepared using the Chromium 3′ v2 library preparation platform (10× Genomics). Libraries were sequenced on a NextSeq 550 sequencer (Illumina) to a depth of at least 30 million reads per sample. Samples were demultiplexed and aligned to GRCh38 with CellRanger v3.0.2. Samples were normalized and clustered with Seurat v3.2.0, yielding four primary clusters corresponding to each cell type, which were used to profile cell-type specific expression of SARS-CoV-2 relevant factors.
Second heart field-derived cardiac fibroblasts (SHF-CFs) were differentiated following the GiFGF protocol, as described by (website at nature.com/articles/s41467-019-09831-5). Briefly, hiPSCs were seeded at 15,000 cells/cm2 in mTeSR1 medium. Once they reached 100% confluency, they were treated with R/B media supplemented with 12 μM CHIR99021 (day 0) and refreshed with R/B media 24 hours later (day 1). From days 2-20, cells were fed every 2 days with cardiac fibroblast basal media (CFBM) (Lonza, CC-3131) supplemented with 75 ng/mL bFGF. On day 20, CFs were singularized with Accutase for 10 minutes and replated at 7,000 cells/cm2 onto tissue culture plastic 10 cm dishes in FibroGRO medium (Millipore Sigma, SCMF001). FibroGRO media was changed every two days until the CFs reached approximately 80-90% confluency, at which point they were passaged with Accutase. SHF-CFs were validated to be >80% double-positive for TE-7 and vimentin by flow cytometry.
WTC11 iPSCs were directed towards an endothelial cell (EC) lineage by the addition of E8 media supplemented with BMP4 (5 ng/ml) and Activin A (25 ng/ml) for 48 hours followed by E7BVi media, consisting of E6 medium supplemented with bFGF (50 ng/ml), VEGF-A (50 ng/ml), BMP4 (50 ng/ml) and a TGFβ inhibitor, SB431542, (5 μM) for 72 hours. After 5 days of successive media changes, ECs were split and plated at high density in EGM media (Lonza, CC-3162) on tissue culture flasks coated with fibronectin (1:100, Sigma Aldrich F0895). On day 8, all cells were cryo-preserved and a fraction of ECs were assayed for >95% purity by flow cytometry using antibodies against mature EC markers CD31 and CDH5.
Mixed cultures of induced pluripotent stem cell derived cardiomyocytes (iPS-CMs), induced pluripotent stem cell derived endothelial cells (iPS-ECs), and induced pluripotent stem cell derived cardiac fibroblasts (iPS-CFs) were created by combining single cell suspensions of each cell types in a ratio of 60:30:10 CM:EC:CF at a density of 200,000 cells/mL. The mixed suspension was replated onto Matrigel-coated tissue culture plates 48 hours prior to infection at a density of 62,500 cells/cm2.
The WA-1 strain (BEI resources) of SARS-CoV-2 was used for all experiments. SARS-CoV-2 stocks were passaged in Vero cells (ATCC) and titer was determined via plaque assay on Vero cells as previously described (Honko et al ref). Briefly, virus was diluted 1:102-1:106 and incubated for 1 hour on Vero cells before an overlay of Avicel and complete DMEM (Sigma Aldrich, SLM-241) was added. After incubation at 37° C. for 72 hours, the overlay was removed and cells were fixed with 10% formalin, stained with crystal violet, and counted for plaque formation. SARS-CoV-2 infections of iPS-derived cardiac cells were done at a multiplicity of infection of 0.006 for 48 hours unless otherwise specified. For heat inactivation, SARS-CoV-2 stocks were incubated at 85° C. for 5 min.
Infected and mock-treated cell cultures were washed with Phosphate Buffered Solution (PBS) and fixed in 4% paraformaldehyde (PFA) overnight, followed by blocking and permeabilization with 0.1% Triton-X 100 (T8787, Sigma) and 5% BSA (A4503, Sigma) for one hour at RT. Antibody dilution buffer (Ab buffer) was comprised of PBS supplemented with 0.1% Triton-X 100 and 1% BSA. Samples were incubated with primary antibodies overnight at 4° C. (Table 1), followed by 3 washes with PBS and incubation with fluorescent-conjugated secondary antibodies at 1:250 in Ab buffer for 1 hour at room temperature (Table 1). For immunofluorescence staining, epitopes were retrieved through 35 min incubation at 95° C. in citrate solution (pH 6) or TE buffer (pH 9) and coverslips were mounted onto SuperFrost Slides (FisherBrand, 12-550-15) with ProLong Antifade mounting solution with DAPI (Invitrogen, P36931). Primary antibodies and nuclear stains were used as follows: J2 (Absolute Antibody Ab02199-2.0, 1:200), Spike (Ms, BEI Resources NR-616, 1:200), ACE2 (ProteinTech 21115-1-AP, 1:200), TNNT2 (Abcam ab45932, 1:400), ACTN2 (Sigma A7732, 1:200), PECAM-1 (Santa Cruz sc1506, 1:50), GFP (Abcam ab13970, 1:200), MTCO2 (Abcam ab110258, 1:200), Hoechst 33342 (ThermoFisher 62249, 1:10,000). Images were acquired with a Zeiss Axio Observer Z.1 Spinning Disk Confocal (Carl Zeiss) or with an ImageXpress Micro Confocal High-Content Imaging System (Molecular Devices) and processed using ZenBlue and ImageJ.
Paraffin sections of healthy and COVID-19 patient hearts were deparaffinized using xylene, re-hydrated through a decrease series of ethanol solutions (100%, 100%, 95%, 80%, 70%) and rinsed in PB1X. Hematoxylin and eosin staining was performed according manufacturer instructions and the slides were mounted with Cytoseal 60 (Richard-Allan Scientific) and glass coverslips. For immunofluorescence staining, epitopes were retrieved by immersing slides through 35 min incubation at 95° C. in citrate buffer (Vector Laboratories, pH 6) or Tris-EDTA buffer (Cellgro, pH 9). Slides were cooled for 20 min at RT and washed with PBS. Samples were permeabilized in 0.2% Triton X-100 (Sigma) in PBS by slide immersion and washed in PBS. Blocking was performed in 1.5% normal donkey serum (NDS; Jackson ImmunoResearch) and PBS solution for 1 h at RT. Primary and secondary antibody cocktails were diluted in blocking solution (Table 1). PBS washes were performed after primary (overnight, 4° C.) and secondary antibody (1 h, RT) incubations. Nuclei were stained with Hoechst and coverslips were mounted on slides using ProLong™ Gold Antifade Mountant. Samples were imaged on the Zeiss Axio Observer Z1.
Cultured cells were lysed with Qiagen buffer RLT (Qiagen, 79216) supplemented with 1% β-mercaptoethanol (Bio-Rad, 1610710) and RNA was isolated using the RNeasy Mini Kit (Qiagen 74104) or Quick-RNA MicroPrep (ThermoFisher, 50444593) and quantified using the NanoDrop 2000c (ThermoFisher). Viral load was measured by detection of the viral Nucleocapsid (N5) transcript through one-step quantitative real-time PCR, performed using PrimeTime Gene Expression Master Mix (Integrated DNA Technologies, 1055772) with primers and probes specific to N5 and RPP30 as in internal reference. RT-qPCR reactions were performed on a CFX384 (BioRad) and delta cycle threshold (ΔCt) was determined relative to RPP30 levels. Viral detection levels in pharmacologically treated samples were normalized to DMSO-treated controls.
For generating libraries for RNA-sequencing, RNA isolate quality was assessed with an Agilent Bioanalyzer 2100 on using the RNA Pico Kit (Agilent, 5067-1513). 10 ng of each RNA isolate was then prepared using the Takara SMARTer Stranded Total RNA-Seq Kit v2—Pico Input Mammalian (Takara, 634412). Transcripts were fragmented for 3.5 minutes and amplified for 12 cycles. Library concentrations were quantified with the Qubit dsDNA HS Assay Kit (Thermo Fisher, Q32851) and pooled for sequencing. Sequencing was performed on an Illumina NextSeq 550 system, using the NextSeq 500/550 High Output Kit v2.5 (150 Cycles) (Illumina, 20024907) to a depth of at least 10 million reads per sample.
Samples were demultiplexed using bcl2fastq v2.20.0 and aligned to both GRCh38 and the SARS-CoV-2 reference sequence (NC_045512) using hisat2 v2.1.0 (see website at nature.com/articles/nmeth.3317). Aligned reads were converted to counts using featureCounts v1.6.2 (see website at pubmed.ncbi.nlm.nih.gov/24227677/). Cell-type clustering, gene loadings, and technical replication were assessed using the PCA and MDS projections implemented in scikit-learn v0.23.1 (see website at scikit-learn.org/stable/about.html#citing-scikit-leam). Differential expression analysis was performed using limma v3.44.3 with voom normalization (see website at genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-2-r29) and GO term enrichment analysis was performed using clusterProfiler v3.16.0 (see website at liebertpub.com/doi/10.1089/omi.2011.0118). Unbiased GO term selection was performed by non-negative matrix factorization using scikit-learn.
Cells grown on gridded 35 mm MatTek glass-bottom dishes (MatTek Corp., Ashland, MA, USA) were fixed in 2.5% glutaraldehyde and 2.5% paraformaldehyde in 0.1M sodium cacodylate buffer, pH 7.4 (EMS, Hatfield, PA, USA) following fluorescence imaging. Samples were rinsed 3×5 min at RT in 0.1M sodium cacodylate buffer, pH 7.2, and immersed in 1% osmium tetroxide with 1.6% potassium ferricyanide in 0.1M sodium cacodylate buffer for 30 minutes. Samples were rinsed (3×5 min, RT) in buffer and briefly washed with distilled water (1×1 min, RT) before sample were then subjected to an ascending ethanol gradient (7 min; 35%, 50%, 70%, 80%, 90%) followed by pure ethanol. Samples were progressively infiltrated (using ethanol as the solvent) with Epon resin (EMS, Hatfield, PA, USA) and polymerized at 60° C. for 24-48 hours. Care was taken to ensure only a thin amount of resin remained within the glass bottom dishes to enable the best possible chance for separation of the glass coverslip. Following polymerization, the glass coverslips were removed using ultra-thin Personna razor blades (EMS, Hatfield, PA, USA) and liquid nitrogen exposure as needed. The regions of interest, identified by the gridded alpha-numerical labeling, were carefully removed and mounted with cyanoacrylate glue for sectioning on a blank block. Serial thin sections (100 nm) were cut using a Leica UC 6 ultramicrotome (Leica, Wetzlar, Germany) from the surface of the block until approximately 4-5 microns in to ensure complete capture of the cell volumes. Section-ribbons were then collected sequentially onto formvar-coated 50 mesh copper grids. The grids were post-stained with 2% uranyl acetate followed by Reynold's lead citrate, for 5 min each. The sections were imaged using a Tecnai 12 120 kV TEM (FEI, Hillsboro, OR, USA), data were recorded using an UltraScan 1000 with Digital Micrograph 3 software (Gatan Inc., Pleasanton, CA, USA), and montaged datasets were collected with SerialEM (bio3d.colorado.edu/SerialEM) and reconstructed using IMOD eTOMO (bio3d.colorado.edu/imod).
The relative infectability of different cardiac cell types had not previously been characterized for SARS-CoV-2, leading to ambiguity over the sources of cardiac damage and relevant therapeutic targets. The inventors determined the tropism of SARS-CoV-2 for different cardiac cell types by infecting cardiomyocytes (CMs), cardiac fibroblasts (CFs), endothelial cells (ECs), or a mix of all three with SARS-CoV-2 at a relatively low MOI (MOI=0.006).
Viral infection load was measured by qPCR detection of the SARS-CoV-2 nucleocapsid transcript (N5) at 48 hours (
Viral replication measured in each cell type after 48 h largely correlated with corresponding ACE2 expression levels. Undifferentiated iPSCs were not infectable (
To further study if cardiac cells enable productive infection by SARS-CoV-2, plaque assays were performed on Vero cells from the supernatants of exposed cells that confirmed CFs, ECs, and iPSCs did not support productive infection, but CMs robustly produced new replication competent virions (
Immunostaining for replicating virus in the form of double-stranded viral RNA (dsRNA) or Spike protein further confirmed that infected CMs support viral replication. Positive dsRNA and Spike staining were only detected throughout infected CM cultures. Consistent with our qPCR results and plaque assays, CFs and ECs showed no dsRNA or Spike staining. However, all three cultures showed significant cytopathic effects after 48 hours of viral exposure, characterized by significant cell loss in all cell types (
Replication of (+)ssRNA viruses, including SARS-CoV and MERS-CoV, involves budding of double-membrane vesicles (DMVs) from the endoplasmic reticulum, with viral particle assembly occurring in the ER-Golgi intermediate compartment (ERGIC) cisternae (see website at biorxiv.org/content/10.1101/2020.06.23.167064v1). In CMs infected with SARS-CoV-2, dsRNA and Spike signals initially (24 h post infection) accumulated near the nucleus in small perinuclear puncta, closely matching the typical location of this ERGIC region, indicating potential active centers of replication. After 48 h post infection, an increase in the number of cells was observed with dsRNA signals throughout their cytoplasm, potentially correlating with breakdown of the ER-Golgi membrane as viral replication accelerates and the cell deteriorates, as evidenced by a decrease in sarcomeric integrity and intensity. By 72 h post infection, SARS-CoV-2 had spread throughout the culture and large swathes of the CMs had died, with the remaining cells displaying dispersed viral stain localization, dissociation from neighboring cells, and heavily reduced sarcomeric signal (
Using transmission electron microscopy of infected CMs, the inventors readily identified the remnants of the ER-Golgi membranes and large vesicles in the proximity of the nucleus (
These results demonstrate that SARS-CoV-2 is able to readily infect, replicate in, and rapidly propagate through CMs.
Cardiomyocytes (CMs) were the only type of cell that proved infectable by SARS-CoV-2, from amongst the cell types tested (cardiomyocytes, cardiac fibroblasts, endothelial cells, and stem cells). This Example describes experiments for elucidating the mechanism of viral entry into CMs by using exogenous inhibition of CM factors.
Cells pretreated with an ACE2 blocking antibody, cathepsin inhibitor E-64-D, or serine protease inhibitor aprotinin were able to significantly reduce the detection of viral transcripts in infected CMs (
Taken altogether, these results strongly indicate that the SARS-CoV-2 virus employs the ACE2 receptor to bind to iPS-CMs and is able to utilize a cathepsin-L (CTSL)-dependent endolysosomal route, but not a cathepsin-B (CSTB)-dependent endolysosomal route, to infection without TMPRSS2/serine protease-mediated activation at the cellular membrane.
Based on the ability of SARS-CoV-2 to robustly infect and propagate through CMs, the inventors examined whether priming the innate immune response could effectively combat SARS-CoV-2 infection. CMs were primed with IFNα, IFNβ, IFNγ, or IFNλ, in addition to a combination of IFNs and a JAK/Stat inhibitor (ruxolitinib; ruxo) prior to infection. Only pre-exposure to IFNs was able to prevent infection, and this phenotype was reversed by JAK/Stat inhibition (
This Example describes experiments for evaluating the transcriptional response of cardiac cells exposed to SARS-CoV-2, and in particular to identify differences in the level of immune suppression or cytokine activation across different levels of viral load. The experiments involved RNA-sequencing of infected and mock-treated CFs, ECs, and iPSCs at a MOI of 0.006, or a range of MOIs (0.001, 0.01, and 0.1) for CMs.
Sequencing recovered a high proportion of SARS-CoV-2 transcripts in an MOI and cell-type dependent fashion (
However, the significant distance between infected and mock conditions indicates that viral infection impacted the variation in expression profiles at least as strongly as the differences in cell type. Individual samples within the low, middle, and high MOI conditions correlated poorly with the degree of transcriptional disruption observed, potentially due to natural stochasticity in the kinetics of infection.
Regrouping conditions by the level of transcriptional disruption allowed transcriptional trends to be deduced as a function of viral impact. Loading plots of the principal components indicated that the main axis of variation aligned along a CM, CF/EC spectrum with CM specific genes (MYH7, MYH6, TNNT2) at one pole (
Analysis of differential regulation of genes involved in inflammation and innate immunity for infected CFs, ECs, and CMs agree with the observed infectivity of CMs. Infected CFs and ECs have a depressed cytokine response compared to all three levels of disrupted CMs, which are enriched for genes involved in cytokine production and T-cell activation (OAS2, MX1, IFIT1, IL1B, IL6, TNF) (
Interestingly, the inventors noted that CMs at each MOI showed very clear dysregulation of genes involved in contractile machinery and proteasome homeostasis. All MOI conditions tested showed very clear dysregulation of genes involved in contractile machinery and proteasome homeostasis. In particular, sarcomeric structural proteins, myosin light chains, and proteasome kinases and chaperones were strongly downregulated, and most myosin heavy chains were significantly upregulated (
In light of observations that impairment of cardiac function can occur even in mild cases of COVID-19 (which were mimicked by low MOIs), these results illustrate that SARS-CoV-2 may have unique interactions with structural features of CMs that can potentially cause cardiac dysfunction. Deeper analyses of the individual genes driving the GO terms revealed significant downregulation of mitochondrial metabolism networks, decreased regulation of protein degradation, and loss of genes associated with sarcomere formation and maintenance.
Historical single-cell RNA-Seq data was first analyzed to determine the expression of putative viral entry host factors in CMs, ECs, and primary cardiac fibroblasts (see website at biorxiv.org/content/10.1101/2020.07.06.190504v1).
The primary SARS-CoV-2 receptor, ACE2, was detected at low levels in all cells, but ACE2 displayed greater than 10-fold higher expression in cardiomyocytes than in cardiac fibroblasts or endothelial cells, indicating that cardiomyocytes are more susceptible to infection than other cardiac cell types (
These data support the viability of SARS-CoV-2 infection of cardiac cells via an ACE2-endocytosis axis.
To validate expression of the ACE2 receptor in CMs, the inventors directly examined ACE2 transcript and protein expression. While ACE2 transcripts were undetected in iPSCs by qPCR, differentiated and purified CMs exhibited robust expression (
These results demonstrate that CMs are susceptible to SARS-CoV-2 infection.
As described in this Example, motivated by the discovery of disruptions to various structural and contractile genes in our transcriptomic data, the inventors performed high content imaging of CMs following SARS-CoV-2 infection.
A number of abnormal structural features were immediately observed in many of the infected CMs that were not seen in parallel mock samples. Widespread myofibrillar disruption throughout the cytoplasm was the most common feature observed, which manifested as a unique pattern of very specific and periodic cleavage of myofibrils into individual sarcomeric units of identical size but without any alignment (
Since transcriptomic profiling data indicated viral infection altered the proteasome system (
Altogether, these results indicate that the observed fragmentation of the sarcomere is dependent on SARS-CoV-2 infection of neighboring CMs. Reducing productive infection of CMs by means of IFN-β pre-treatment or E64D treatment did not reduce the incidence of myofibrillar disruption. However, ACE2 blocking did reduce the incident of myofibrillar disruption, potentially indicating an immediate response to viral exposure to the cell surface.
Co-staining SARS-CoV-2-exposed CMs with cTnT and the Z-disk marker α-actinin 2 revealed the myofibrillar fragments observed upon SARS-CoV-2 exposure consisted of two cTnT-positive bands flanking a single α-actinin 2 band, indicating cleavage at the M-line or a separation of thick and thin filaments (
In addition, the inventors observed that CMs with intact or moderately disrupted myofibrils often appeared to lack nuclear DNA staining (
Based on the in vitro findings, the inventors sought to identify whether similar features were contributing to COVID-19 myocardial damage in vivo. The sarcomere fragmentation observed in COVID-19 patients appears to present some extreme features even compared to in vitro system.
Patient specimens were obtained from four COVID-19 positive patients—one diagnosed with viral myocarditis. Compared to healthy myocardial tissue (
The tissues from the COVID-19 myocarditis case exhibited signs of edema with increased spacing between adjacent cardiomyocytes (
In COVID-19 infected patients that were not diagnosed with myocarditis (
The results described herein demonstrate that the in vitro phenotypes are able to predict previously unobserved disruptions in myocardium. Therefore, the in vitro methods described herein can be used to dissect the mechanisms of COVID-19 cardiovascular injury and identify agents that reduce or inhibit such injury.
All patents and publications referenced or mentioned herein are indicative of the levels of skill of those skilled in the art to which the invention pertains, and each such referenced patent or publication is hereby specifically incorporated by reference to the same extent as if it had been incorporated by reference in its entirety individually or set forth herein in its entirety. Applicants reserve the right to physically incorporate into this specification any and all materials and information from any such cited patents or publications.
The following statements are intended to describe and summarize various embodiments of the invention according to the foregoing description in the specification.
The specific methods and compositions described herein are representative of preferred embodiments and are exemplary and not intended as limitations on the scope of the invention. Other objects, aspects, and embodiments will occur to those skilled in the art upon consideration of this specification and are encompassed within the spirit of the invention as defined by the scope of the claims. It will be readily apparent to one skilled in the art that varying substitutions and modifications may be made to the invention disclosed herein without departing from the scope and spirit of the invention. The invention illustratively described herein suitably may be practiced in the absence of any element or elements, or limitation or limitations, which is not specifically disclosed herein as essential. The methods and processes illustratively described herein suitably may be practiced in differing orders of steps, and the methods and processes are not necessarily restricted to the orders of steps indicated herein or in the claims.
The terms and expressions that have been employed are used as terms of description and not of limitation, and there is no intent in the use of such terms and expressions to exclude any equivalent of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the invention as claimed. Thus, it will be understood that although the present invention has been specifically disclosed by preferred embodiments and optional features, modification and variation of the concepts herein disclosed may be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this invention as defined by the appended claims and statements of the invention. Under no circumstances may the patent be interpreted to be limited to the specific examples or embodiments or methods specifically disclosed herein. Under no circumstances may the patent be interpreted to be limited by any statement made by any Examiner or any other official or employee of the Patent and Trademark Office unless such statement is specifically and without qualification or reservation expressly adopted in a responsive writing by Applicants.
This application is a U.S. National Stage Filing under 35 U.S.C. 371 from International Patent Application Serial No. PCT/US2021/047255, filed Aug. 24, 2021, published on Mar. 3, 2022 as WO2022/046706 which application claims benefit of priority to the filing date of U.S. Provisional Application Ser. No. 63/069,361, filed Aug. 24, 2020, the contents of which are specifically incorporated herein by reference in their entireties.
This invention was made with government support under ES032673 and RO1-HL135358 awarded by the National Institutes of Health, and under ERC 1648035 awarded by the National Science Foundation. The government has certain rights in the invention.
Filing Document | Filing Date | Country | Kind |
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PCT/US21/47255 | 8/24/2021 | WO |
Number | Date | Country | |
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63069361 | Aug 2020 | US |