This section will help you understand the tendinosis/tendinopathy injury. You might have more patience to wait for your injury to heal if you understand why it heals so slowly and what's happening at the cellular level. The numbers in brackets after some sentences on this page are references found on the References page.
Collagens are proteins that help strengthen the structure of tissues such as bones, tendons, cartilage, ligaments, vertebral disks, skin, and blood vessels. These tissues all contain collagen, but they have different proportions of different kinds of collagen (as well as various other constituents) and their structural characteristics vary.
The collagen in tendons and ligaments is arranged in bundles of parallel fibers, giving tendons and ligaments a rope-like structure. Some of the fibers in tendons and ligaments also run transverse to the parallel bundles, forming cross-links that add strength to the structure. The collagen in cartilage is arranged in a mesh with a large amount of gel-like substance between the collagen fibers, making the structure of cartilage more like a sponge. The characteristics of collagen-containing tissues also vary with position within the structure; for example, tendons and ligaments are different at the point of insertion to the bone than they are in the middle of the tendon or ligament.
Researchers have identified 19 kinds of collagen and given them names with Roman numerals. The main collagens found in connective tissue are Types I, II, and III; these collagens form fibers that give tensile strength to tissues. Tendons, ligaments, skin, and bone have mostly Type I collagen, and cartilage has mostly Type II collagen.
Tendons and ligaments also contain proteoglycans, elastin, and fibroblast cells. The collagen, elastin, and proteoglycans form the extracellular matrix. The fibroblast cells are embedded in the matrix and in fact synthesize and secrete the matrix collagen, elastin, and proteoglycans.
The proteoglycans are protein/polysaccharide complexes that trap water and affect the viscoelastic properties of the tissue, helping the tissue resist compressive forces. Proteoglycans consist of a protein core with attached glycosaminoglycans (GAGs). Cartilage contains a high percent of a mixture of proteoglycans and water that provides a gel-like cushioning for joints. Tendons contain less proteoglycans and water than cartilage. The proteoglycan/water component of tendon, ligament, and cartilage is called the "ground substance."
The elastin fibers, which can stretch and return to their original form, are interwoven with the collagen fibers to add elasticity and prevent tearing. The elastin fibers form a network throughout the tissue, but they only represent 1-2% of the dry weight of tendon. Collagen represents 65-80% of the dry weight of tendon and is by far the most abundant component of tendon.
When new tendon tissue is being formed, the fibroblasts are actively creating new collagen. When the tissue is mature, the fibroblasts become less active and are called fibrocytes. The fibrocytes don't actively create new tissue unless they are called on to repair damage or do remodeling of the old tissue. Fibroblasts tend to look thicker, rounder, and larger than fibrocytes, which tend to look thinner and more linear. Fibrocytes found in tendons are called tenocytes. (Likewise, fibrocytes found in cartilage are called chondrocytes and fibrocytes found in bone are called osteocytes.)
A typical collagen molecule consists of three subunits called alpha chains. For example, each molecule of Type I collagen has two alpha1 chains and one alpha2 chain. Each molecule of Type III collagen has three alpha1 chains. Since it is composed of three alpha chains, the collagen molecule is called a tripeptide. The alpha chains are composed of combinations of amino acids, which are the basic building blocks of proteins. The most abundant amino acids in collagen are glycine, proline, and lysine.
Type I, II, and III collagens are made in several steps. First, the fibroblast cell joins three alpha chains to make procollagen according to the instructions in the genes. Then, the procollagen is released from the cell membrane. The fibroblast cells secrete enzymes that remove extra sequences at the ends of the procollagen to make tropocollagen. Then the tropocollagen assembles into collagen fibrils, which then assemble into collagen fibers.
The collagen fibers in tendons are arranged in primary, secondary, and tertiary bundles within a sheath called the epitenon that surrounds the exterior surface of the tendon. To see a schematic diagram of this tendon structure, see Figure 1 in Histopathology of Common Tendinopathies by Khan et al (full pdf text of article at link).
Researchers have identified at least 30 collagen genes, and most of them encode procollagens. For example, the colIA1 gene encodes the alpha1 chain for Type I collagen, known as alpha1(I), and the colIA2 gene encodes the alpha2 chain for Type I collagen, known as alpha2(I). Defects in the collagen genes can cause the collagen to be constructed incorrectly (with abnormal quantity or quality), leading to weak tissue and various collagen diseases.
Normal tendons and ligaments consist mostly of Type I collagen, with smaller amounts of Type III collagen. When you develop tendinosis, some of your collagen is injured and breaks down. Your body tries to heal the tendon, but when you have chronic tendinosis your body doesn't repair the collagen properly.
Usually you can't see the tendinosis/tendinopathy injury from the outside of the body; swelling, heat, and redness are symptoms of an acute injury, not a chronic tendon injury. The tissue often looks different to the naked eye during surgery though, with regions of tendinosis/tendinopathy looking dull, slightly brown, and soft instead of white, glistening, and firm. Researchers have analyzed samples of tendons and ligaments under the microscope to discover the abnormalities that occur on a cellular scale in overuse injuries.
Research has shown that chronic overuse injuries such as tendinosis (including Achilles, rotator cuff, lateral and medial elbow, posterior tibial, digital flexor, and patellar), as well as carpal tunnel syndrome and even TMJ disorders are associated with a failed healing response in which the body's fibroblasts produce abnormal tendon and ligament collagen. [1,4,5,6,7,8,9,13,14,18,40,42] The composition and structure of the collagen is abnormal compared to uninjured tendon and ligament tissue. The following differences have been observed:
To see several interesting photographs of microscope slides, see the article "Cell-Matrix Response in Tendon Injury” by Leadbetter.  To see another photo of a microscope slide, see the article "Overuse Tendinosis, Not Tendinitis" from The Physician and Sport Medicine (full pdf text at link).  And a few more photos are available in the article Overuse Tendon Injuries: Where Does The Pain Come From? 
The above changes have all been observed in tendon samples taken from sites of tendinosis. Researchers have also taken tenocytes (the tendon cells that make new collagen) from sites of tendinosis and cultured them. The tenocytes cultured from tendinosis continue to produce abnormal collagen outside of the body; the tenocytes produced collagen with abnormally high Type III to Type I ratios (as compared to collagen produced by tenocytes cultured from normal tendon).  This observation is significant because it shows that the tenocytes have been altered and continue to produce abnormal collagen even when the repetitive motion is no longer present.
Tendons and ligaments are similar structures; tendons connect muscle to bone, and ligaments connect bone to bone. Ligaments, as well as tendons, can get chronic overuse injuries of failed healing. Ligaments with overuse injuries show the same kinds of abnormal appearance under the microscope as tendons with tendinosis. One study showed that cells from the flexor retinaculum ligament of carpal tunnel syndrome patients made collagen with an abnormally high Type III/Type I ratio just as has been observed with cells from tendons of patients with tendinosis.  The carpal tunnel study also found that the injured ligament cells made collagen with a higher than normal ratio of alpha2(I) to alpha1(I).
The tendinosis cycle begins when breakdown exceeds repair. Repetitive motion causes microinjuries that accumulate with time. Collagen breaks down and the tendon tries to repair itself, but the cells produce new collagen with an abnormal structure and composition.
The new collagen has an abnormally high Type III/Type I ratio. Experiments show that the excess Type III collagen at the expense of Type I collagen weakens the tendon, making it prone to further injury. Part of the problem is that the new collagen fibers are less organized into the normal parallel structure, making the tendon less able to withstand tensile stress along the direction of the tendon.
Therefore, tendinosis is a slow accumulation of little injuries that are not repaired properly and leave the tendon vulnerable to yet more injury. This failed healing process is the reason many people with tendinosis don't completely heal from it and can't go back to their previous level of activity. Once the tendinosis cycle starts, the tendon rarely heals back to its pre-injury state.
Although rest is an essential part of the healing process for tendinosis, too much rest causes deconditioning of muscles and tendons. The weaker muscles and tendons leave the area more vulnerable to injury. Thus, the area becomes weaker on a large scale as well as on a cellular scale. This cycle of injury/rest/deconditioning/more injury can be difficult to break. Gradual, careful physical therapy exercises can help.
The source of pain from tendinosis/tendinopathy is controversial. At first, doctors labeled chronic tendon injuries as "tendinitis" and attributed the pain to inflammation. Later, researchers observed that inflammatory cells were rarely seen in microscope slides of chronic tendon injuries, so the terms tendinosis and tendinopathy became more popular because they do not imply an inflammatory process.
Recently, the inflammation question has come up again because signs of inflammatory cells have been seen at the cellular level as more researchers study tendinopathy/tendinosis. A blog post Tendons, Let’s Talk About Inflammation… on The Sports Physio blog summarizes the current thinking and links to some recent articles discussing the possible role of low level inflammation in tendinosis/tendinopathy. An article in the July 2014 American Journal of Sports Medicine discusses inflammatory cells seen in biopsies of chronic Achilles tendinopathy and an article in the March 2013 British Journal of Sports Medicine urges the medical community to acknowledge the existence of inflammatory cells in tendinopathy. Doctors are not saying that use of NSAIDS or cortisone is a cure or that their long-term use is a good idea, but researchers just don’t want to overlook any clues to the pathology of the injury, which is still not completely understood.
The pain from tendinosis probably comes partly from the physical injury itself (separation of collagen fibers and mechanical disruption of tissue) and partly from irritating biochemical substances that are produced as part of the injury process. The biochemical substances could irritate the pain receptors in the tendon and surrounding area. NSAIDs and cortisone injections might reduce the pain of tendinosis by reducing or blocking these biochemical substances and by interrupting any low level inflammation. See Overuse Tendon Injuries: Where Does The Pain Come From? 
Some people find that when the tendinosis in their wrists has an especially bad flare-up, they experience tingling or numbness in some fingers (carpal tunnel symptoms). The old explanation for the numbness was that severe flare-ups cause inflammation that presses on the nerves to the fingers and causes numbness. When the flare-up subsides, the numbness goes away. The newer theory is that the tendinosis injury causes thickening of the tendons in the wrists (partly from higher water content associated with the higher proteoglycan content), and this thickening can cause pressure on nerves to the fingers. In addition to thickening of the tendon, inflammation of the tendon sheath can also put pressure on nerves to the fingers.
The question of inflammation is likely to continue to be a hot topic.
Tendinosis/tendinopathy is a chronic degenerative tendon injury that is usually brought on by repetitive motion. The repetitive motion is often associated with activities in the workplace or with sports. Microinjuries gradually accumulate faster than they can heal until the area eventually becomes painful. The severity of the injury is influenced by many factors, including
People seem to vary in their susceptibility to tendinosis. Many people go through their entire lives without ever experiencing tendinosis. Some people experience mild tendon problems but recover. Others get chronic tendinosis from obvious overuse such as typing or sports. A few unlucky people get chronic tendon injuries in multiple places of the body, sometimes without obvious overuse. (Leadbetter refers to this propensity for tendinosis as mesenchymal syndrome. ) Even given the same ergonomics, different people have different levels of activity that constitute injury-producing overuse; the line between use and overuse varies with genetics.
Any genetic variant that causes tendons to be weaker or slower to heal could make people more susceptible to tendinosis. If we can understand the reasons for differences in susceptibility, we might find better treatments for tendinosis. For some studies on the genetic component, see Genetic risk factors for musculoskeletal soft tissue injuries, Tendon and ligament injuries: the genetic component, and related articles.
Some people carry a propensity for tendonisis to the extreme and develop soft tissue problems in so many places and with such severity that it prevents them from leading a normal life. If you fall into this category, you likely have something systemic going on that is affecting your whole body, rather than simply a number of individual injuries to multiple body parts. You should see doctors to rule out things like autoimmune diseases and fibromyalgia.
This list gives some of the possible explanations researchers have suggested for the abnormal collagen production associated with chronic overuse injuries. These four factors (the poor healing capacity of tendon, genetic variants in collagen, long-term exposure to growth factors, and abnormal levels of proteolytic enzymes) are just some of the possible reasons that have been suggested for the failed healing of collagen in tendinosis, but more research is needed to fully understand the tendinosis injury.
Tendons and ligaments don't heal well, even when the injury does not become chronic. The strength of tendons and ligaments remains as much as 30% lower than normal even months or years following an acute injury.[7,8] Repair of acute injuries usually begins with the deposition of more Type III collagen than Type I, and the site gradually returns to a more normal composition and structure with time. The site can have an abnormally high Type III/Type I collagen ratio even after a year, and this abnormal collagen composition contributes to the weakness of the tissue.[7,8] Possibly, some people with chronic injuries just never get past the initial phases of healing.
A team at the University of Glasgow is researching a possible way to correct the imbalance in Types I and III collagen in tendinopathy. They discovered that a microRNA called miR-29a can up-regulate the production of type I collagen relative to type III to restore collagen to pre-injury levels. Trials have been done in cultured cells and in mice, and horses will be next. One of their papers can be found here.
Another possible explanation for the abnormal collagen associated with chronic overuse injuries is that the fibroblasts could be damaged by long-term exposure to growth factors. The repetitive motion causes tissue breakdown, which stimulates growth factors to make repairs; if more injury is done before the repairs are complete, the tissue is continually exposed to growth factors for long periods of time. The repetitive motion itself could even stimulate production of growth factors. Some researchers suggest that this long exposure to growth factors could make the cells produce abnormal collagen and that this cell behavior can become permanent even after the exposure to growth factors stops.
In the previously mentioned study of carpal tunnel syndrome, cells were cultured from the wrist ligaments of injured patients and uninjured control patients. The cells were exposed to four different growth factors, including transforming growth factor beta (TGF-beta). The cells from injured patients produced abnormally high amounts of Type III collagen and low amounts of Type I collagen when exposed to the growth factors, as compared to cells from the control patients.
The authors conclude that the cells in the injured patients had been altered by the injury so that the response to growth factors was different. They hypothesize that one explanation for this change in response to growth factors is the long exposure to growth factors while the injury was accumulating. Their study demonstrates that using growth factors to try to treat chronic overuse injuries is a tricky proposition because the growth factors could have different effects on the injured cells than you might expect based on their effects on healthy cells.
Growth factors have the potential to help tendons and ligaments heal, but sometimes they might actually hinder the process. We need more research to sort out the effects of various growth factors and to investigate whether they can be used as treatments to promote collagen healing in tendinosis. One complication for this research is that growth factors can have completely different effects on cells in the body than on cells in the petri dish. Another complication is that many studies look at acute surgically-induced injuries rather than chronic overuse injuries, and the effects of growth factors could be very different in these two cases.
Another possibility is that some people with chronic overuse injuries could have genetic differences that make their tendons and ligaments weaker and make them heal with abnormal collagen. Quite possibly, more than one genetic variant exists that causes tendons and ligaments to be prone to overuse injuries.
Many genetic collagen defects have already been discovered; some cause fairly rare collagen diseases, but some cause more common problems like osteoporosis, osteoarthritis, and vertebral disk herniations. A colIA1 defect has been discovered to cause some cases of osteoporosis; the colIA1 defect causes weaker Type I collagen in the bones because of an abnormally high alpha1(I) to alpha2(I) ratio.[10,12] A defect in Type II collagen has been associated with osteoarthritis. A colIXA2 defect is associated with an increased susceptibility to vertebral disk herniations (Type IX collagen is found in small amounts in vertebral disks).
The following list summarizes several observed collagen abnormalities that could contribute to the failed healing response of chronic overuse injuries. Perhaps we will soon discover the causes for these abnormalities.
Genetics will probably turn out to be an important piece of the tendinosis puzzle. Only one small study looked at the alpha2(I) to alpha1(I) ratio, so it might not be significant. Many studies of all kinds of overuse injuries have observed the abnormally high Type III/Type I ratio, so that observation is likely to be very significant.[1,6,9,13,14] Other collagen abnormalities might be discovered to be associated with overuse injuries as more research is done.
Proteolytic enzymes are substances that help break down proteins; they are used to break down old tissue in order to repair it and also to break down new proteins in the various stages of building new collagen fibers. For example, enzymes are needed to remove the extra sequences at the ends of procollagen to make tropocollagen that can then assemble into Type I, II, and III collagen fibers.
MMP-3, or stromelysin, is a proteolytic enzyme that is important in tissue remodeling. A study of Achilles tendinosis found that tendons with tendinosis had lower levels of MMP-3 mRNA than other tendons without tendinosis in the same patients. Even more interesting, the "normal" tendons of patients with tendinosis had lower MMP-3 mRNA than tendons of control patients who had no tendinosis anywhere. This study implies that differences exist not only between tendons with and without tendinosis, but also between people who are and are not prone to tendinosis. Maybe people who are prone to tendinosis start out with a lower rate of collagen turnover even before the injury cycle begins, possibly because of a down-regulation of proteolytic enzymes. This MMP-3 observation was made only in one small study, but it does show that another factor to consider in the failed healing of tendinosis is the level of proteolytic enzymes available for tendon repair.
Of course too high a level of proteolytic enzymes can also be a problem. You don't want the tissue to be broken down by the body so quickly that normal remodeling efforts can't keep up. Tendinosis already involves an injury rate that exceeds the rate of repair, so you want to encourage the repair process and slow the injury rate. You need enough proteolytic enzymes to enable repair of injured tissue, but not so much proteolytic enzymes that uninjured tissue is broken down. Normally the body maintains a balance between proteolytic enzymes and their inhibitors to achieve a balance between tissue breakdown and repair.
We have changed the name of the site from tendinosis.org to tendonpain.org because the information here covers both tendinosis and tendinopathy.
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University of Glasgow: Scientific breakthrough unlocks potential novel tendon therapy
”Tendinopathy is essentially the result of an imbalance between collagen type-1 and type-3 and we have discovered the molecular cause. This breakthrough has allowed us to find a way to alter the levels of collagen type-3 in tendons, with the ultimate aim to get patients with tendon injuries better quicker."
Biologic augmentation of rotator cuff repair with mesenchymal stem cells during arthroscopy improves healing and prevents further tears: a case-controlled study
“This study showed that significant improvement in healing outcomes could be achieved by the use of BMC (bone marrow concentrate) containing MSC (mesenchymal stem cells) as an adjunct therapy in standard of care rotator cuff repair. Furthermore, our study showed a substantial improvement in the level of tendon integrity present at the ten-year milestone between the MSC-treated group and the control patients.”
Treatment of Lateral Epicondylosis Using Allogeneic Adipose-Derived Mesenchymal Stem Cells: A Pilot Study
“This pilot study on the safety and efficacy of allo-MSC injection for treating chronic LE demonstrated that the intervention was safe and efficacious in improving pain, performance, and anatomical defects for more than a 52-week follow-up period. This is the first clinical study using allogeneic MSCs to treat chronic tendinopathy.”
Cell Therapy Ltd announces positive Phase II clinical trial results of Tendoncel ™, a first-in-class topical regenerative medicine for severe tendon injury
“Patients using the non-invasive Tendoncel ™ topical gel for 21 days experienced a clinically relevant and statistically significant improvement in their tendon injury. Reporting an average improvement of 70% on the DASH disability scale and 74% improvement on the PRTEE scale, Tendoncel’s results exceed those expected of injectable treatments and have the advantage of painless topical application.”
Mechanotherapy: how physical therapists’ prescription of exercise promotes tissue repair
“Mechanotransduction is the physiological process where cells sense and respond to mechanical loads. This paper reclaims the term “mechanotherapy” and presents the current scientific knowledge underpinning how load may be used therapeutically to stimulate tissue repair and remodelling in tendon, muscle, cartilage and bone.”