Brandon's Biochemistry Blog

BCM 441 Spring 2018

Rheumatoid Arthritis: The Other Form of Arthritis

Arthritis is a very common condition characterized by joint pain, stiffness, swelling, and decreased range of motion. Osteoarthritis is the most common form of arthritis, and rheumatoid arthritis is the second. Osteoarthritis comes with age, and occurs when wear and tear of the joints causes cartilage (the tissue on the ends of bones) to break down, resulting in bone on bone rubbing. On the other hand, rheumatoid arthritis is an autoimmune disorder, which results when the body’s immune system does not function properly and attacks its own tissues. It currently affects one percent of the population worldwide. In rheumatoid arthritis, the body perceives cells of the joint as foreign invaders and attacks them, resulting in inflammation and the breakdown of cartilage.

Rheumatoid arthritis is three times more common in women than men, and usually sets in between 40 and 60 years of age. The onset of rheumatoid arthritis usually occurs gradually, and begins in small joints of the hands and feet. Immune cells and chemicals that promote inflammation called cytokines can invade the lining of the joint, causing it to become inflamed and penetrate nearby cartilage and bone resulting in the joint to lose its shape and alignment. Joint cells that are promoting inflammation can enter the bloodstream and travel to other locations in the body. This is why rheumatoid arthritis can spread and affect not only joints, but also the skin, eyes, heart, lungs, and the digestive system.

The immune response is carried out by antibodies, which are proteins that attack foreign invaders. When antibodies mistakenly attack the body’s own cells, they are then called autoantibodies. Two common autoantibodies that spearhead rheumatoid arthritis are rheumatoid factor (RF) and anti-cyclic citrullinated peptide (ACCP) autoantibodies. Doctors will often take blood tests of patients and check for the presence of these autoantibodies when diagnosing rheumatoid arthritis.

Many research studies have been done to find out what went wrong with the immune system and why certain immune cells attack joints. There are many factors that can cause the autoimmune response of rheumatoid arthritis including genetic and environmental influences. Studies have shown that healthy cells in the joint can undergo chemical modifications that make them more susceptible to the immune response. Researchers have shown that smoking and certain infections can result in a specific type of chemical modification called citrullination. This process entails the chemical alteration of protein found in the joint, and the altered protein activates ACCP antibodies resulting in an autoimmune response. The detection of ACCP antibodies is a very conclusive way of diagnosing rheumatoid arthritis since other forms of autoantibodies can be found in other autoimmune disorders whereas ACCP antibodies are mostly only found in rheumatoid arthritis patients.

Some rheumatoid arthritis patients have been shown to have a slightly different T-cell structure. T-cells are crucial cells of the immune system which interact with foreign invaders and stimulate as well as tailor the immune response for that specific invader. The alteration of some T-cells found in rheumatoid arthritis patients enables the T-cell to more efficiently interact with the foreign invader, making an immune response more likely to occur. A larger immune response corresponds with a more aggressive case of rheumatoid arthritis.

Several genetic factors increase rheumatoid arthritis susceptibility, but the disease itself is not passed down through a gene. The combination of several genetic and environmental factors such as smoking is what can stimulate the onset of rheumatoid arthritis. The largest genetic risk factor for rheumatoid arthritis is a gene called HLA-DR. This gene stimulates the immune response by allowing T-cells to become more efficiently activated by the joint cells that have been modified by environmental risk factors.

The goal of rheumatoid arthritis treatment is to reduce pain, swelling, deformities, and maintain quality of life. This is possible to accomplish with disease-modifying antirheumatic drugs (DMARDs). These drugs inhibit cytokines from stimulating inflammation. Nonsteroidal anti-inflammatory drugs (NSAIDs) and corticosteroids can also reduce inflammation, but DMARDs are more specific for rheumatoid arthritis and yield better results. In very severe cases, joint replacement surgery may be an option if joint damage and symptoms cannot be controlled with medication and physical therapy.


For more detailed information about rheumatoid arthritis, please visit my theme pages.

An E3 ubiquitin ligase is essential for immune homeostasis

TRIM29, an E3 ubiquitin ligase as depicted in the above figure, tags STING for proteasome-dependent degradation to downregulate the antiviral cystolic DNA immune response.


It is commonly thought that the innate immune response is completely non-specific. However, relatively recent studies have shown that viral DNA is recognized by germline-encoded pattern recognition receptors (PRRs) on innate immune cells, which then trigger an immune response (Akira et al 2006). Viral DNA can be sensed by Toll-like receptors which are found on macrophages and dendritic cells (Takeda et al 2003). Activation of these receptors leads to downstream pathways that result in increased type I interferon-I (IFN-1) and pro-inflammatory cytokines (Li et al 2018). Pathogenic self-DNA that escaped from a cell’s nucleus or mitochondria can also result in increased IFN-1 (Takeda et al 2003). The recognition of such cytosolic DNA triggers the synthesis of cGAMP from cytosolic DNA sensor cyclic GMP-AMP synthase (cGAS), and then cGAMP binds directly to the stimulator of interferon genes (STING) (Ishikawa et al 2009). The STING protein can then phosphorylate interferon regulator factor 3 (IRF3), a transcription factor that enters the nucleus and promotes expression of interferon and cytokine genes (Li et al 2018).

Studies have shown that STING is the central signaling molecule in the innate immune response to cytosolic nucleic acids, which can indicate infection or cancer (Burdette et al 2013). Once activated, STING must have the ability to be deactivated to prevent chronic inflammation and inflammatory related disease. In a recent study presented by Li et al, TRIM29, an E3 ubiquitin ligase, has been shown to ubiquitinate STING and activate it for degradation and therefore downregulate the immune response (Li et al 2018). As studied in BCM441, ubiquitination is a critical process that enables misfolded proteins to be tagged for degradation. In this study, a key regulatory protein in the innate immune response to viral cytosolic DNA is shown to downregulate the immune response by being targeted for degradation by ubiquitination.

It has been previously reported that tripartite motif-containing protein 29 (TRIM29) is a key negative regulator of alveolar macrophages and downregulates the expression of type 1 interferons and pro-inflammatory cytokines in the lungs (Xing et al 2016). In order to explore the specific mechanism of TRIM29, Li et al first confirmed that TRIM29 mRNA levels in macrophages and dendritic cells were increased in the presence of cytosolic DNA from herpes simplex virus type 1 (Li et al 2018). The role of TRIM29 as a negative feedback inducer was then explored, and authors found that knocking down TRIM29 expression in macrophages led to significantly higher levels of interferons, cytokines, and interleukins (Li et al 2018). In fact, TRIM29 knockout mice infected with herpes simplex virus-1 (HSV-1) survived longer than WT mice infected with HSV-1, suggesting that TRIM29 knockout mice are more resistant to the virus due to heightened immune responses (Li et al 2018). TRIM29 knockout mice had higher levels of chemokines that recruit immune cells to the site of infection in addition to higher MX1 expression, an antiviral host protein that disrupts viral DNA and RNA replication (Li et al 2018). These experiments confirm that TRIM29 expression is necessary to suppress the immune system in response to pathogenic cytosolic DNA to prohibit a prolonged and exacerbated immune response.

After establishing TRIM29 as a negative regulator of the immune response to cytosolic DNA, the authors’ next goals were to determine which signaling pathway is affected, and where in the pathway TRIM29 exerts its effect. During antiviral immune responses, cytosolic DNA sensor cGAS synthesizes cGAMP which binds to STING, allowing it to phosphorylate transcription factor IRF3 to promote expression of inflammatory genes (Li et al 2018). Authors stimulated WT and TRIM29 knockout cells with increased STING ligand cGAMP and then infected the cells with HSV-60 (Li et al 2018). Authors detected increased amounts of phosphorylated IRF3 in TRIM29 knockout cells, suggesting that TRIM29 is downregulates the STING-IRF3 pathway (Li et al 2018). Reconstitution of TRIM29 in TRIM29 knockout cells abrogated the enhanced activation of the STING-IRF3 pathway (Li et al 2018).

Previous studies claim that STING is the central signaling molecule in response to pathogenic cytosolic DNA, and the authors’ observation of increased levels of IRF3 downstream of STING in TRIM29 deficient cells aligns with this assessment (Burdette et al 2013). Li et al hypothesized that TRIM29 exerts its negative feedback effect at the regulation point involving STING. Additional experiments determined that STING levels were indeed decreased in WT immune cells infected with HSV-60, while TRIM29 knockout cells did not have the ability to degrade STING (Li et al 2018). To investigate how TRIM29 reduces levels of STING, authors performed an immunoprecipitation experiment with an antibody to TRIM29, and determined that TRIM29 binds to STING (Li et al 2018). TRIM29 formed a complex with STING in cells infected with HSV-60, indicating that TRIM29 suppresses inflammation by directly interacting with STING (Li et al 2018).

TRIM29 is an E3 ubiquitin ligase, and authors were fairly certain that TRIM29 ubiquitinates STING and marks it for degradation by the proteasome. To confirm this, authors introduced MG132, a proteasome inhibitor, into WT HSV-60 infected cells and rescued low levels of STING induced by TRIM29 (Li et al 2018). Authors then overexpressed ubiquitin with lysine residues in different locations, and discovered that K48 ubiquitin polyubiquitinates STING to mediate proteasome degradation. Lastly, authors further investigated the binding interaction of STING and TRIM29, and performed experiments with different truncated versions of TRIM29 to determine that TRIM29 interacts with STING through its C-terminal domain.

The authors were able to determine that TRIM29 binds and ubiquitinates STING to downregulate the inflammatory immune response and prevent excessive stimulation. This study provides unique information about one strategy of antiviral immune response, and can aid in vaccine development (Li et al 2018). The STING-IF3 pathway can be stimulated by both viral DNA and pathogenic host DNA that escaped into the cytosol. These findings can provide insight into strategies to prevent self-DNA triggered autoimmunity, and constitutive expression of TRIM29 is required for immune homeostasis (Li et al 2018).





Akira, Shizuo, Satoshi Uematsu, and Osamu Takeuchi. “Pathogen Recognition and Innate Immunity.” Cell 124, no. 4 (February 24, 2006): 783–801.

Burdette, Dara L., and Russell E. Vance. “STING and the Innate Immune Response to Nucleic Acids in the Cytosol.” Nature Immunology 14, no. 1 (January 2013): 19–26.

Ishikawa, Hiroki, Zhe Ma, and Glen N. Barber. “STING Regulates Intracellular DNA-Mediated, Type I Interferon-Dependent Innate Immunity.” Nature 461, no. 7265 (October 8, 2009): 788–92.

Li, Qijie, Liangbin Lin, Yanli Tong, Yantong Liu, Jun Mou, Xiaodong Wang, Xiuxuan Wang, et al. “TRIM29 Negatively Controls Antiviral Immune Response through Targeting STING for Degradation.” Cell Discovery 4, no. 1 (March 20, 2018): 13.

Takeda, Kiyoshi, Tsuneyasu Kaisho, and Shizuo Akira. “Toll-like Receptors.” Annual Review of Immunology 21, no. 1 (April 2003): 335–76.


Rheumatoid Arthritis

Rheumatoid arthritis (RA) is a systemic autoimmune disorder that affects 1% of the world’s population and is characterized by joint inflammation, swelling, pain, and loss of function (Trier et al, 2017). The immune system launches an attack on cells of synovial joints. Activated T-cells and macrophages rush to the joint and secrete cytokines that cause an inflammatory response (Begovich et al 2004). The increase in immune cells and cytokines causes synovial cells to proliferate, resulting in swelling of the synovial joint and eventually bone erosion and damage to the cartilage (Lefévre et al 2009). Rheumatoid arthritis usually starts in one joint and then spreads to other synovial joints throughout the body (Lefévre et al 2009). Research in the past couple of decades has led to a greater understanding of RA pathology and identification of key antibodies, antigens, and cytokines involved in RA progression. Better patient care has resulted due to more efficient drugs that target key players in RA that have been determined due to this research.

Many genetic and several environmental factors such as cigarette smoke and bacteria can trigger RA by modifying the patient’s antibodies and collagen found in synovial joints (Glant et al 2014). A major focus in RA research revolves around a modification of collagen and fibrinogen proteins called citrullination. Peptidylarginine deiminase enzymes catalyze the citrullination of collagen protein, the transformation of arginine residues into citrulline residues (Suzuki et al, 2003). Citrullinated proteins play a role in RA since they have been found to generate antibodies (Suzuke et al 2003). Many patients with RA have been found to have anti-citrullinated protein antibodies (ACPAs), which stimulate inflammatory responses and the synovial enlargement found in RA (Trier et al, 2018). After research labs have confirmed the presence of ACPAs in RA patients, research has shifted towards understanding the IgG antibodies that bind citrullinated proteins (Amara et al 2013), different haplotypes of peptidyl deiminase enzymes that may be more involved in RA pathogenesis (Suzuki et al 2003), and even improved detection of ACPAs to diagnose RA early on and achieve a better prognosis (Trier et al 2018).

Another high yield area of RA research shifts gears from studying the antigen to studying the activation and proliferation of B-cells and T-cells that work to create the RA associated inflammation. Research on T-cell regulation has ranged from kinase signaling pathways involving protein tyrosine phosphatase (Begovitch et al 2004) and MEK/ERK/MAP (Thiel et al 2007) to T-cell surface glycoprotein ligands that require binding its respective protein ligand to activate the T-cell (Berner et al 2000). These findings have led to drug discovery research that aims to block the interaction of the T-cell ligands to decrease the number of autoimmune collagen antibodies (Choi et al 2018). Other forms of treatment explored targeting the cytokines produced by activated T-cells such as interleukin-6 to suppress inflammation and joint destruction (Mihara et al 2001).

Research has focused on citrullinated antigens and the immune response cells, and another major research theme involves synovial fibroblasts, which are the cells responsible for the production of collagen. Studies about the involvement of synovial fibroblasts in RA pathology have concluded that synovial fibroblasts in RA patients can bind cartilage and degrade it with proteases, then spread to other joints in the body (Lefévre et al 2009). Drug discovery research that targets inflammation of synovial fibroblasts in RA patients still needs further attention due to cross talk between kinase signaling pathways that causes another inflammatory pathway to be stimulated when another is blocked, making synovial fibroblast inflammation difficult to drug (Jones et al 2018).

Rheumatoid arthritis has genetic underpinnings, and studies have been done to locate risk loci for RA. Genome wide association tests were conducted to identify various single nucleotide polymorphisms in genes involved in immune function, and researchers have presented a list of genes that are risk factors for RA (Stahl et al 2010). In addition, epigenetics has been determined to play a role in RA by up-regulating proinflammatory genes such as aurora kinases that recruit transcription factor NF-kB which promotes cytokine genes (Gland et al 2014).

Rheumatoid arthritis research has revolved around a few major themes. The genetic underpinnings of RA have been studied to determine genetic risk factors. Knowledge of the citrullinated antigens that trigger RA, the activation process of T-cells and B-cells, and kinase pathways involved in synovial fibroblast inflammation have greatly aided the development of drugs that target known cytokines and cells involved in RA pathogenesis. Knowledge of the types of antibodies involved in RA pathogenesis have also allowed for early detection and better patient outcomes (Trier et al 2018).





  1. Trier, Nicole Hartwig, Bettina Eide Holm, Julie Heiden, Ole Slot, Henning Locht, Hanne Lindegaard, Anders Svendsen, et al. “Antibodies to a Strain-Specific Citrullinated Epstein-Barr Virus Peptide Diagnoses Rheumatoid Arthritis.” Scientific Reports 8, no. 1 (February 27, 2018): 3684.


  1. Begovich, Ann B., Victoria E. H. Carlton, Lee A. Honigberg, Steven J. Schrodi, Anand P. Chokkalingam, Heather C. Alexander, Kristin G. Ardlie, et al. “A Missense Single-Nucleotide Polymorphism in a Gene Encoding a Protein Tyrosine Phosphatase (PTPN22) Is Associated with Rheumatoid Arthritis.” The American Journal of Human Genetics 75, no. 2 (August 1, 2004): 330–37.


  1. Lefèvre, Stephanie, Anette Knedla, Christoph Tennie, Andreas Kampmann, Christina Wunrau, Robert Dinser, Adelheid Korb, et al. “Synovial Fibroblasts Spread Rheumatoid Arthritis to Unaffected Joints.” Nature Medicine 15, no. 12 (December 2009): 1414–20.


  1. Suzuki, Akari, Ryo Yamada, Xiaotian Chang, Shinya Tokuhiro, Tetsuji Sawada, Masakatsu Suzuki, Miyuki Nagasaki, et al. “Functional Haplotypes of PADI4, Encoding Citrullinating Enzyme Peptidylarginine Deiminase 4, Are Associated with Rheumatoid Arthritis.” Nature Genetics 34, no. 4 (August 2003): 395–402.


  1. Glant, Tibor T., Katalin Mikecz, and Tibor A. Rauch. “Epigenetics in the Pathogenesis of Rheumatoid Arthritis.” BMC Medicine 12 (February 26, 2014): 35.


  1. Amara, Khaled, Johanna Steen, Fiona Murray, Henner Morbach, Blanca M. Fernandez-Rodriguez, Vijay Joshua, Marianne Engström, et al. “Monoclonal IgG Antibodies Generated from Joint-Derived B Cells of RA Patients Have a Strong Bias toward Citrullinated Autoantigen Recognition.” Journal of Experimental Medicine 210, no. 3 (March 11, 2013): 445–55.


  1. Thiel, Melissa J., Caralee J. Schaefer, Mark E. Lesch, James L. Mobley, David T. Dudley, Haile Tecle, Stephen D. Barrett, Denis J. Schrier, and Craig M. Flory. “Central Role of the MEK/ERK MAP Kinase Pathway in a Mouse Model of Rheumatoid Arthritis: Potential Proinflammatory Mechanisms.” Arthritis & Rheumatism 56, no. 10 (October 1, 2007): 3347–57.


  1. Berner, Beate, Gabriele Wolf, Klaus M. Hummel, Gerhard A. Müller, and Monika A. Reuss-Borst. “Increased Expression of CD40 Ligand (CD154) on CD4+ T Cells as a Marker of Disease Activity in Rheumatoid Arthritis.” Annals of the Rheumatic Diseases 59, no. 3 (March 1, 2000): 190–95.


  1. Choi, Eun Wha, Kyo Won Lee, Hyojun Park, Hwajung Kim, Jong Hyun Lee, Ji Woo Song, Jehoon Yang, et al. “Therapeutic Effects of Anti-CD154 Antibody in Cynomolgus Monkeys with Advanced Rheumatoid Arthritis.” Scientific Reports 8, no. 1 (February 1, 2018): 2135.


  1. Mihara, Masahiko, Masao Kotoh, Norihiro Nishimoto, Yasuhiro Oda, Eiji Kumagai, Nobuhiro Takagi, Kunihiko Tsunemi, et al. “Humanized Antibody to Human Interleukin-6 Receptor Inhibits the Development of Collagen Arthritis in Cynomolgus Monkeys.” Clinical Immunology 98, no. 3 (March 1, 2001): 319–26.


  1. Jones, Douglas S., Anne P. Jenney, Brian A. Joughin, Peter K. Sorger, and Douglas A. Lauffenburger. “Inflammatory but Not Mitogenic Contexts Prime Synovial Fibroblasts for Compensatory Signaling Responses to P38 Inhibition.” Signal. 11, no. 520 (March 6, 2018): eaal1601.


  1. Stahl, Eli A., Soumya Raychaudhuri, Elaine F. Remmers, Gang Xie, Stephen Eyre, Brian P. Thomson, Yonghong Li, et al. “Genome-Wide Association Study Meta-Analysis Identifies Seven New Rheumatoid Arthritis Risk Loci.” Nature Genetics 42, no. 6 (June 2010): 508–14.




Biochemistry enables one to navigate through the biological hierarchy with ease and have a greater understanding of not just how, but why cells, tissues, and organs carry out their specific roles. The key benefit to having this greater understanding is to have the ability to troubleshoot when things go wrong. Knowing biochemistry is essential to pinpointing the etiology of diseases and finding a cure.

Rheumatoid arthritis (RA) is a less typical form of arthritis characterized by pain, swelling, and stiffness in the joints, and is most common in the hands. Rheumatoid arthritis occurs when the immune system attacks the linings of joints. However, research has not yet shown a definitive cause of this autoimmune disorder.

Influenza has been unusually bad this year and the amount of hospitalizations due to influenza are the highest the CDC has seen since they began recording data. Influenza is a contagious respiratory infection that infects the nose, throat, and lungs, and can lead to more severe cases such as pneumonia. This contagious illness is caused by various virus strains, and most influenza cases this year are due to the H3N2 strain.

A rare form of dementia known as Creutzfeldt-Jakob disease occurs in elderly patients and causes failing memory, behavioral changes, lack of coordination, weakness of extremities, and 90 percent die within one year of diagnosis. This rare disease is caused by a prion, which leads to a mass of insoluble proteins that penetrate the brain and cause loss of neuronal cell function.






N-3 PUFA rich diets reduce risk of developing symptoms of clinical depression: Eat your n-3 PUFAs, and depressive symptoms may only be “super fish oil”

Paper: N-3 PUFA diet enrichment prevents amyloid beta-induced depressive-like phenotype


As studied in BCM 441, polyunsaturated fats (PUFAs) are a main component of neuronal cell membranes, and n-3 and n-6 PUFAs can be released from membranes to play roles in signal transduction either directly or by being converted to various mediators. N-3 PUFAs such as docosahexaenoic acid (DHA) are prevalent in the brain and can modulate synaptic plasticity, carry out neuroprotective roles, and exhibit anti-inflammatory effects while n-6 PUFAs such as arachidonic acid induce inflammation (Luchtman et al., 2016). Due to the cognitive enhancing effects of n-3 PUFAs, these fatty acids are crucial for proper brain development and function, and n-3 PUFA deficient diets have even been linked to symptoms of clinical depression (Colangelo et al,. 2009). In a recent study by Morgese et al. titled, “N-3 PUFA diet enrichment prevents amyloid beta-induced depressive-like phenotype,” lifelong n-3 PUFA rich diets have been shown to demonstrate a preventative role against depression caused by beta-amyloid protein (Morgese et al,. 2017).

Deposition of amyloid beta-peptide plaques (Aß) in the brain is thought by many to be the driving force behind Alzheimer’s disease (AD), which influences other AD-associated pathologies such as neurofibrillary tangles of tau protein and neuroinflammation (Hardy et al,. 2002). Increased Aß levels have also been found in depressed patients, which helps support the theory that depression in elderly patients is common in the first stages of AD and can indicate the onset of AD (Colaianna et al,. 2010). Authors have previously found that injection of Aß in rat cerebrospinal fluid induces depression, marked by low serotonin (5-HT) and neuronal growth factor levels (Colainna et al,. 2010). Due to the neuroproctective roles of n-3 PUFAs, Morgese et al. 2017 hypothesized that n-3 PUFA deficiency may predispose individuals to depression by increasing Aß levels and altering neurotransmission (Morgese et al,. 2017). The authors were the first to evaluate how lifelong n-3 PUFA rich or n-3 PUFA poor diet influenced depressive symptoms induced by Aß administration.

Authors first analyzed the role of lifelong PUFA diets by examining depressive-like phenotypes in rats that were fed a lifelong n-3 PUFA rich diet, n-6 rich PUFA diet, or balanced n-6/n-3 PUFA diet, and then injected with Aß peptides. Depressive-like phenotypes were detected by a forced swimming test (FST), a widely used test in which mice are placed in cylinders filled with water. Mice make immediate attempts to escape, and then give up and become immobile. The immobility time is measured and positively correlated with a state of depression. N-3 PUFA fed rats displayed shorter immobility times and longer swimming times than n-6 PUFA fed or balanced n-6/n-3 PUFA diets. Thus, the authors concluded that n-3 PUFA fed diets prevented Aß-induced depressive like behavior.

To validate and further explain the Aß-induced depression phenotypes detected by the FST, authors obtained neurochemical data by quantifying biological markers of depression. Biological markers were detected in n-3 PUFA fed mice, n-6 PUFA fed mice, and balanced n-6/n-3 PUFA fed mice after being injected with Aß peptides. The authors found higher levels of serotonin (5-HT) in n-3 PUFA fed mice than the other two groups, aligning with the FST result that lifelong n-3 PUFA enriched diets prevent Aß-induced depression. Serotonin deficiency is associated with depression, and this deficiency can be caused by tryptophan’s metabolism into kynurenine (KYN) instead of serotonin due to the cortisol-induced stimulation of the liver enzyme tryptophan 2,3 dioxygenase (Oxenkrug et al,. 2013). Authors measured levels of KYN, and found higher levels of KYN in n-6 PUFA and n-6/n-3 PUFA fed mice, suggesting that this tryptophan metabolism shunt is the cause of reduced serotonin levels in n-3 PUFA deficient diets.

To further investigate PUFA diet on central nervous system function, the authors measured levels of neurotrophins in n-3, n-6 PUFA and n-6/n-3 balanced diets after Aß injection. Neurotrophins are growth factor proteins that regulate neural survival, development, plasticity, and function (Huang et al,. 2009). Two families of neurotrophins are nerve growth factors (NGF) and brain-derived neurotrophic factors (BDNF), and DHA levels are positively correlated with these neurotrophins (Huang et al,. 2009). Morgese et al. have previously found that Aß injection negatively regulates neurotrophin regulation in the prefrontal cortex (PFC) of mice. This result was consistent with n-6 and n-6/n-3 PUFA fed mice since decreased NGF mRNA and BDNF mRNA levels were observed in these groups. However, a lifelong enriched n-3 PUFA diet actually resulted in increased NGF mRNA levels after Aß was administered, while BDNF mRNA levels did not decrease in n-3 PUFA fed mice after injection of Aß. The authors also measured NGF and BDNF protein levels to verify the mRNA quantification results and observed similar patterns. These findings suggest that n-3 PUFA enriched diets prevent Aß-induced depression by safeguarding neurotrophin levels essential for proper brain function.

This is a unique study that examines protective effects of lifelong n-3 PUFA diets in specific regard to Aß-induced depression, which is often a prodromal symptom of AD in elderly patients. N-3 PUFA rich diets prevent Aß-induced depression by maintaining levels of serotonin and increasing production of neurotrophins. These findings support a diet supplemented with n-3 PUFAs as an effective method of warding off depression and other Aß-related symptoms. The complete molecular mechanism underlying the protective effects of n-3 PUFAs needs to be further addressed. In particular, methods of shifting Aß towards the fibril form as opposed to the soluble form needs to be studied since soluble Aß is the most detrimental form (Morgese et al,. 2017). It has previously been shown that n-3 PUFAs in the membrane can cause Aß to favor the lipid bilayer, thus removing it from its soluble form in the cell (Vitiello et al,. 2013). N-3 PUFAs are crucial for proper central nervous system function as discussed in BCM 441, and are rich in flaxseed oil, salmon fat, spinach, walnuts, and soybeans.








  1. Luchtman, Dirk W., and Cai Song. “Cognitive Enhancement by Omega-3 Fatty Acids from Child-Hood to Old Age: Findings from Animal and Clinical Studies.” Neuropharmacology, Cognitive Enhancers: molecules, mechanisms and minds, 64 (January 1, 2013): 550–65.


  1. Colangelo, Laura A., Ka He, Mary A. Whooley, Martha L. Daviglus, and Kiang Liu. “Higher Dietary Intake of Long-Chain ω-3 Polyunsaturated Fatty Acids Is Inversely Associated with Depressive Symptoms in Women.” Nutrition 25, no. 10 (October 1, 2009): 1011–19.


  1. Morgese, M. G., S. Schiavone, E. Mhillaj, M. Bove, P. Tucci, and L. Trabace. “N-3 PUFA Diet Enrichment Prevents Amyloid Beta-Induced Depressive-like Phenotype.” Pharmacological Research, December 5, 2017.


  1. Hardy, John, and Dennis J. Selkoe. “The Amyloid Hypothesis of Alzheimer’s Disease: Progress and Problems on the Road to Therapeutics.” Science 297, no. 5580 (July 19, 2002): 353–56.


  1. Colaianna, M, P Tucci, M Zotti, Mg Morgese, S Schiavone, S Govoni, V Cuomo, and L Trabace. “Soluble Βamyloid1-42: A Critical Player in Producing Behavioural and Biochemical Changes Evoking Depressive-Related State?” British Journal of Pharmacology 159, no. 8 (April 1, 2010): 1704–15.


  1. Oxenkrug, Gregory. “Serotonin-Kynurenine Hypothesis of Depression: Historical Overview and Recent Developments.” Current Drug Targets 14, no. 5 (May 1, 2013): 514–21.


  1. Huang, Eric J, and Louis F Reichardt. “Neurotrophins: Roles in Neuronal Development and Function.” Annual Review of Neuroscience 24 (2001): 677–736.


  1. Vitiello, Giuseppe, Sara Di Marino, Anna Maria D’Ursi, and Gerardino D’Errico. “Omega-3 Fatty Acids Regulate the Interaction of the Alzheimer’s Aβ(25–35) Peptide with Lipid Membranes.” Langmuir 29, no. 46 (November 19, 2013): 14239–45.

Lymphangiogenesis is promoted by epigenetic modifications

Acetyl CoA is an infamous metabolic player that links many biochemical pathways. It can be formed by the pyruvate dehydrogenase complex after glycolysis and by the process of fatty acid oxidation (FAO). Acetyl CoA also has many metabolic roles such as entry into the citric acid cycle, serving as a precursor for lipid synthesis, and its acetyl group can be used by histone acetyltransferases (HATs) to regulate gene expression. FAO is the cell’s way of creating more acetyl CoA to create energy when the cell requires it, and researchers recently found higher rates of FAO in lymphatic endothelial cells (LEC) than other human endothelial cell types when investigating metabolism in lymphatic development (Wong et al,. 2016).

In order for fatty acids to be metabolized into acetyl CoA, they must enter the mitochondria via the carnitine shuttle. The outer mitochondrial membrane is the site of carnitine palmitoyltransferase I (CPT1), which catalyzes the transformation of fatty acyl CoA to fatty acyl carnitine. Fatty acyl carnitine then enters the mitochondria by traveling through a transporter in the inner mitochondrial membrane, and then it is converted back to fatty acyl CoA by carnitine palmitoyltransferase II (CPTII). The fatty acyl CoA can then undergo a series of oxidations, resulting in the two-carbon product, acetyl CoA, each round.

Lymphatic vessels are formed through lymphangiogenesis, and the vessels are composed of LECs that differentiated from venous endothelial cells (VEC). Proper cell differentiation is required for the lymphatic system to successfully carry out its roles in the body such as absorbing excess fluid to redirect to the circulatory system and aid in mounting immune responses. The significant amount of FAO occurring in LEC was linked to increased expression of the CPT1A isoform of CPT1 in LECs (Wong et al,.).  Thus, Wong et al. hypothesized that CPT1A promotes lymphangiogenesis.

Levels of FAO were shown to respond to lymphangiogenic signals that promote VEC-to-LEC differentiation. The authors overexpressed PROX1 in vitro, a transcription factor, and this resulted in an increase in CPT1A mRNA and FAO levels that was similar to those observed in LECs (Wong et al,.). Similarly, silencing PROX1 resulted in lower levels of FAO and CPT1A (Wong et al,.). Levels of FAO and CPT1A were then linked to LEC differentiation when CPT1A knockdown mice displayed reduced LEC proliferation marked by low levels of VEGFR3, which results in lymphatic defects (Wong et al,.). PROX1 induces CPT1A expression which increases FAO, and the resulting acetyl CoA molecules can help deoxyribonucleotide synthesis, but this is not directly linked to LEC differentiation. The authors then hypothesized that acetyl CoA could play an epigenetic role that increases the expression of lymphangiogenic genes (Wong et al,.).

Co-immunoprecipitation experiments showed that a well-known histone acetyltransferase, p300, interacts with PROX1 (Wong et al,.). This histone acetyltransferase was found to acetylate histone H3 at lysine 9, loosening the interaction between DNA and the histone, allowing PROX1 to bind the promotor sequence and stimulate lymphangiogenic gene expression (Wong et al,.). Acetyl CoA levels were also shown to depend on histone acetylation by p300 (Wong et al,.). Lymphangiogensis is dependent on this epigenetic modification, and when acetyl CoA is absent, the authors have demonstrated that supplementing with acetate can restore lymphangiogenesis by serving as an acetyl donor that p300 can use to stimulate lymphangiogenic gene expression (Wong et al,.). The findings of Wong et al,. can be translated in the clinic, and further studies of the many fates of acetyl CoA should be conducted. The importance of acetyl CoA cannot be emphasized enough, and its many fates are still being discovered. These pathways need to be elucidated to understand healthy physiology in addition to disease pathology.



Wong, B.W., Wang, X., Zecchin, A., Thienpont, B., Cornelissen, I., Kalucka, J., Garcia-Caballero, M., Missiaen, R., Huang, H., Bruning, U., et al. (2016). Nature.



Why biochemistry?

Biology cannot be understood without understanding the organ systems. The organ systems cannot be understood without understanding the structure and function of each organ and the tissues that compose them. The tissues cannot be understood without understanding cellular function, and what happens inside the cell cannot be understood without biochemistry. Everything comes back to biochemistry, and in my view, biochemistry is the central science.

Biochemistry is more than just memorizing a sequence of chemical events in the body. Many pathways and reactions should be present in a biochemist’s everyday knowledge, but pathways can be referenced when needed. To study biochemistry is to understand how these chemical reactions are so intricately related and depend on each other to sustain life. Energy is harnessed for cellular work through complex chemical pathways, and these pathways are heavily regulated and dependent on the current state of the organism. Glycolysis, the Krebs cycle, and the electron transport chain are the central focus of energy production, and the energy is used to perform further biochemical work which consists of what seems like an endless amount of other chemical processes that can be studied. It is the job of a biochemist to make sense of the endless amount of chemical activity in the body by linking the pathways together to understand the effect on the organism.

At the root of any biology process lies biochemistry. Biochemistry must be studied to understand genetics, gene regulation, metabolism, and many processes that maintain homeostasis such as glycolysis and gluconeogenesis, glycogenesis and glycogenolysis, insulin and glucagon effects, bone production and resorption; the list goes on and on. Biochemistry is used to understand these processes, and knowledge of many other fields is essential to understand biochemistry. It is the central science because it brings these other fields together. Organic chemistry is needed to understand the chemical and physical properties of molecules and how atoms rearrange to form products through bond breaking and bond forming events. Biology is needed to understand the context of the reactions and where they take place as well as the effect. Physical chemistry and thermodynamics are needed to understand why some reactions proceed while others don’t in addition to the kinetic versus thermodynamic product.

I chose biochemistry as my major because I want to go beyond a typical understanding of biological processes. I want to interrogate concepts and weave them together to understand how they are all related. With biochemistry, I can get to the root cause of how and why things take place in the body. I feel more comfortable being able to understand biological phenomena at all levels of the biological hierarchy from the organ right down to the molecular processes in the cell. I aspire to be a physician, and having this kind of knowledge is essential to be able to troubleshoot problems and come up with efficient treatments. I want to be link a patient’s symptoms to the biological cause and trace it all the way back to its core; biochemistry. To take this even further, I want to be able to refer to scientific literature and understand the experiments and results to seek out relevant findings and apply them in a patient centered way. Biochemistry will enable me to link fragile bones to an imbalance between calcitonin versus parathyroid hormone and the bone forming osteoblasts versus bone resorbing osteoclasts. Knowing the fine details of bone chemistry and hormones will enable me to understand the cause, and biochemistry will also allow me to understand pharmacology and prescribe the right medication to provide an effective treatment plan. In medical school, I will study different organ systems and learn the specifics of each one, but they will all be seemingly linked by the central science: biochemistry.


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