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Article SELECTION from Collection of Aviva Lev-Ari, PhD, RN Scientific Articles on PULSE on LinkedIn.com for Training Small Language Models (SLMs) in Domain-aware Content of Medical, Pharmaceutical, Life Sciences and Healthcare by 15 Subjects Matter
Article selection: Aviva Lev-Ari, PhD, RN
#1 – February 20, 2016
Contributions to Personalized and Precision Medicine & Genomic Research
Overview of Alzheimer’s Disease and Novel Treatments Targeting Beta-Amyloid Deposits
Reporter: Sharada Kittur, Research Assistant 1, Synthetic Biology in Drug Discovery
Alzheimer’s disease (AD) is a common type of dementia. People diagnosed with this disease suffer memory loss. Severe forms of the condition prevent the patients from responding to the environment. Alzheimer’s disease patients may also experience difficulty completing basic tasks, decreased or poor judgement as their executive function competence declines. Frequent changes in mood, personality, or behavior. AD is the 7th leading cause of death in the United States, and the 5th leading cause of death for adults aged 65 and over. Unlike cancer and heart disease, whose death rates are declining, the number of people struggling with Alzheimer’s disease is projected to increase in the coming years.
Currently, there are no cures for the disease. Many of the drugs on the market target only symptoms of the disease. The key mechanism of action (MOA) of AD drugs is inhibiting acetylcholinesterase. Acetylcholinesterase (AChE) is an enzyme that breaks down a neurotransmitter called acetylcholine (Ach), which is an important factor for memory functions. On average, Alzheimer’s disease patients have lower concentrations of acetylcholine. In order to treat this biomarker, scientists found molecules that can inhibit AChE, and reduce the breakdown of acetylcholine, thus improving the memory of patients with Alzheimer’s disease by enabling average levels of Ach. Some examples of AChE inhibitors currently on the market are
donepezil,
rivastigmine, and
galantamine.
One of the main causes of Alzheimer’s disease is believed to be the buildup of beta-amyloid plaques in the brain. Beta-amyloid is a toxic protein that is normally produced in small amounts in the brain. Then microglia, a type of macrophages in the nervous system, clear out the beta-amyloid deposits. In patients with Alzheimer’s disease, the microglia can’t clear away the beta-amyloid, and this obstructs neural function and attacks neurons. The cause of the microglia’s malfunction is still unknown, but it could be due to a gene called TREM2, that tells the microglia to clear the beta-amyloid proteins. When TREM2 doesn’t function properly, the microglia collects all of the beta-amyloid, but isn’t able to dispose of it. It then releases inflammatory chemicals, which increase the production of the amyloid precursor protein (APP). This also increases the production of β-secretase and γ-secretase, enzymes that form beta-amyloid by breaking down APP. This further exacerbates the problem.
On July 06, 2023, the Food and Drug Administration (FDA) fully approved Leqembi (lecanemab-irmb) to treat Alzheimer’s disease. Leqembi is a monoclonal antibody that specifically targets beta-amyloid proteins in the brain. It binds to the beta-amyloid proteins and clears them. This is very promising as in placebo-controlled clinical trials, it significantly decreased the beta-amyloid deposits in 18 months, and delayed cognitive decline by 5.3 months. It’s the first beta-amyloid targeting drug that was approved by the FDA as a Traditional Approval.
Leqembi is not a cure, however. It significantly slows down the mental function deterioration of the patients, but hasn’t been shown to fully maintain it at the current level over time. In addition, Leqembi has many side effects, such as headaches, and presents amyloid-related imaging abnormalities (ARIAs). ARIAs can cause swelling and bleeding in parts of the brain, but they should be temporary for most patients. Severe ARIAs only occur in a very small percentage of patients.
As researchers make progress in understanding the complex causes of Alzheimer’s disease, new treatments that are developed can help improve the lives of millions of people worldwide.
Wang, Shaoxun, et al. “Is Beta-Amyloid Accumulation a Cause or Consequence of Alzheimer’s Disease?” Journal of Alzheimer’s Parkinsonism & Dementia, U.S. National Library of Medicine, 17 Nov. 2016, www.ncbi.nlm.nih.gov/pmc/articles/PMC5555607/
Eight Subcellular Pathologies driving Chronic Metabolic Diseases – Methods for Mapping Bioelectronic Adjustable Measurements as potential new Therapeutics: Impact on Pharmaceuticals in Use
In this curation we wish to present two breaking through goals:
Goal 1:
Exposition of a new direction of research leading to a more comprehensive understanding of Metabolic Dysfunctional Diseases that are implicated in effecting the emergence of the two leading causes of human mortality in the World in 2023: (a) Cardiovascular Diseases, and (b) Cancer
Goal 2:
Development of Methods for Mapping Bioelectronic Adjustable Measurements as potential new Therapeutics for these eight subcellular causes of chronic metabolic diseases. It is anticipated that it will have a potential impact on the future of Pharmaceuticals to be used, a change from the present time current treatment protocols for Metabolic Dysfunctional Diseases.
According to Dr. Robert Lustig, M.D, an American pediatric endocrinologist. He is Professor emeritus of Pediatrics in the Division of Endocrinology at the University of California, San Francisco, where he specialized in neuroendocrinology and childhood obesity, there are eight subcellular pathologies that drive chronic metabolic diseases.
These eight subcellular pathologies can’t be measured at present time.
In this curation we will attempt to explore methods of measurement for each of these eight pathologies by harnessing the promise of the emerging field known as Bioelectronics.
Unmeasurable eight subcellular pathologies that drive chronic metabolic diseases
Glycation
Oxidative Stress
Mitochondrial dysfunction [beta-oxidation Ac CoA malonyl fatty acid]
Insulin resistance/sensitive [more important than BMI], known as a driver to cancer development
Membrane instability
Inflammation in the gut [mucin layer and tight junctions]
Epigenetics/Methylation
Autophagy [AMPKbeta1 improvement in health span]
Diseases that are not Diseases: no drugs for them, only diet modification will help
Image source
Robert Lustig, M.D. on the Subcellular Processes That Belie Chronic Disease
These eight Subcellular Pathologies driving Chronic Metabolic Diseases are becoming our focus for exploration of the promise of Bioelectronics for two pursuits:
Will Bioelectronics be deemed helpful in measurement of each of the eight pathological processes that underlie and that drive the chronic metabolic syndrome(s) and disease(s)?
IF we will be able to suggest new measurements to currently unmeasurable health harming processes THEN we will attempt to conceptualize new therapeutic targets and new modalities for therapeutics delivery – WE ARE HOPEFUL
In the Bioelecronics domain we are inspired by the work of the following three research sources:
Michael Levin is an American developmental and synthetic biologist at Tufts University, where he is the Vannevar Bush Distinguished Professor. Levin is a director of the Allen Discovery Center at Tufts University and Tufts Center for Regenerative and Developmental Biology. Wikipedia
THE VOICE of Dr. Justin D. Pearlman, MD, PhD, FACC
PENDING
THE VOICE of Stephen J. Williams, PhD
Ten TakeAway Points of Dr. Lustig’s talk on role of diet on the incidence of Type II Diabetes
25% of US children have fatty liver
Type II diabetes can be manifested from fatty live with 151 million people worldwide affected moving up to 568 million in 7 years
A common myth is diabetes due to overweight condition driving the metabolic disease
There is a trend of ‘lean’ diabetes or diabetes in lean people, therefore body mass index not a reliable biomarker for risk for diabetes
Thirty percent of ‘obese’ people just have high subcutaneous fat. the visceral fat is more problematic
there are people who are ‘fat’ but insulin sensitive while have growth hormone receptor defects. Points to other issues related to metabolic state other than insulin and potentially the insulin like growth factors
At any BMI some patients are insulin sensitive while some resistant
Visceral fat accumulation may be more due to chronic stress condition
Fructose can decrease liver mitochondrial function
A methionine and choline deficient diet can lead to rapid NASH development
Neuroimmunology is a field that investigates the bi-directional communication between the nervous system (CNS and PNS) and the immune system. While these two physiological systems were traditionally thought to act independently and that the brain was a privileged site protected by the blood–brain barrier (BBB), researchers now appreciate the highly organized cross talk between the immune and nervous systems in health and disease. The CNS communicates with the immune system via hormonal and neural pathways. The hormonal pathway is predominantly via the HPA axis, which is the primary stress center in rodents, primates, and humans. The neural pathway is mediated via the sympathetic and parasympathetic (the vagus nerve) response. In turn, the immune system signals the CNS via cytokines released by activated immune cells in the periphery but also through activated microglia and astrocytes in the spinal cord and brain. The peripheral inflammation can lead to central proinflammatory milieu and ultimately to sickness behaviour defined as a set of behavioural changes that develop in individuals during the course of systemic inflammation (i.e., fever, lethargy, hyperalgesia). The peripheral inflammation can lead to central proinflammatory milieu and ultimately to sickness behaviour defined as a set of behavioural changes that develop in individuals during the course of systemic inflammation (i.e., fever, lethargy, hyperalgesia), Signals, originating from cellular and molecular elements of the immune system itself, constitute a level of autoregulation. There is also evidence of another more integrative level of regulation mediated by neuroendocrine signals
Pathological pain and the neuroimmune interface
The idea that pain and immunity might be associated beyond an acute response first arose from clinical observations in the 1970s that patients with chronic pain exhibited other symptoms, in addition to hyperalgesia, that parallel the classical systemic sickness response — including lethargy, depression and anxiety. The concomitance of sickness behaviors with chronic pain is therefore suggestive of underlying immune activity. Efforts to identify the origin and nature of the immune mediators involved soon followed, leading to the discovery that elevated peripheral levels of interleukin-1β (IL-1β) both induced hyperalgesia per se and mediated sickness-induced hyperalgesia1,2 . Although peripheral sensitization of pain fibers at local tissue sites of inflammation has a key role in heightening pain from those regions, these peripheral observations were soon extended with the discovery of a central nervous system (CNS) mechanism of action for IL-1β and other cytokines
Physiological pain processing
Pain (either nociceptive pain or inflammatory pain) is protective and adaptive, warning the individual to escape the pain-inducing stimulus and to protect the injured tissue site during healing. The basic scientific understanding of sensory processing and modulation has been dramatically improved by the development of pain assays that recreate some elements of clinical pain syndromes (BOX 1). Painful stimuli (for example, mechanical, thermal and chemical) are initially transduced into neuronal electrical activity and conducted from the peripheral stimulus site to the CNS along a series of well-characterized peripheral nociceptive sensory neurons (first-order primary afferent neurons). The nociceptive signal is then transmitted at central synapses through the release of a variety of neurotransmitters that have the potential to excite second-order nociceptive projection neurons in the spinal dorsal horn or hindbrain (FIG. 1). This process of nociception can occur through several mechanisms involving glutamate and neuropeptides (for example, substance P or calcitonin gene-related peptide (CGRP)). Glutamate activates postsynaptic glutamate AMPA (α-amino-3 -hydroxy-5-methyl-4-isoxazole proprionic acid) and kainate receptors on second-order nociceptive projection neurons. Interestingly, these receptor systems are not all engaged equally in response to different types of pain. Modification of the nociceptive signal can occur at the level of the spinal cord through activation of local GABAergic (that produce γ-aminobutyric acid) and glycinergic inhibitory interneurons.
10.3 Drugs that activate this novel stress response pathway, which they call the mitochondrial-to-cytosolic stress response, protected both nematodes and cultured human cells with Huntington´s disease from protein-folding damage.
Novartis uses a ‘dimmer switch’ medication to fine-tune gene therapy candidates
Reporter: Amandeep Kaur, BSc., MSc.
Using viral vectors, lipid nanoparticles, and other technologies, significant progress has been achieved in refining the delivery of gene treatments. However, modifications to the cargo itself are still needed to increase safety and efficacy by better controlling gene expression.
To that end, researchers at Children’s Hospital of Philadelphia (CHOP) have created a “dimmer switch” system that employs Novartis’ investigational Huntington’s disease medicine branaplam (LMI070) as a regulator to fine-tune the quantity of proteins generated from a gene therapy.
The investigational medicine branaplam was shown to fine-tune the expression of an erythropoietin gene therapy in mice by scientists from Children’s Hospital of Philadelphia and Novartis. (Novartis)
According to a new study published in Nature, the Xon system altered quantities of erythropoietin—which is used to treat anaemia associated with chronic renal disease—delivered to mice using viral vectors. The method has previously been licenced by Novartis, the maker of the Zolgensma gene therapy for spinal muscular atrophy.
The Xon system depends on a process known as “alternative splicing,” in which RNA is spliced to include or exclude specific exons of a gene, allowing the gene to code for multiple proteins. The team used branaplam, a small-molecule RNA-splicing modulator, for this platform. The medication was created to improve SMN2 gene splicing in order to cure spinal muscular atrophy. Novartis shifted its research to try the medication against Huntington’s disease after a trial failure.
A gene therapy’s payload remains dormant until oral branaplam is given, according to Xon. The medicine activates the expression of the therapy’s functional gene by causing it to splice in the desired way. Scientists from CHOP and the Novartis Institutes for BioMedical Research put the dimmer switch to the exam in an Epo gene therapy carried through adeno-associated viral vectors. The usage of branaplam increased mice Epo levels in the blood and hematocrit levels (the proportion of red blood cells to whole blood) by 60% to 70%, according to the researchers. The researchers fed the rodents branaplam again as their hematocrit decreased to baseline levels. The therapy reinduced Epo to levels similar to those seen in the initial studies, according to the researchers.
The researchers also demonstrated that the Xon system could be used to regulate progranulin expression, which is utilised to treat PGRN-deficient frontotemporal dementia and neuronal ceroid lipofuscinosis. The scientists emphasised that gene therapy requires a small treatment window to be both safe and effective.
In a statement, Beverly Davidson, Ph.D., the study’s senior author,said, “The dose of a medicine can define how high you want expression to be, and then the system can automatically ‘dim down’ at a pace corresponding to the half-life of the protein.”
“We may imagine scenarios in which a medication is used only once, such as to control the expression of foreign proteins required for gene editing, or only on a limited basis. Because the splicing modulators we examined are administered orally, compliance to control protein expression from viral vectors including Xon-based cassettes should be high.”
In gene-modifying medicines, scientists have tried a variety of approaches to alter gene expression. For example, methyl groups were utilised as a switch to turn on or off expression of genes in the gene-editing system CRISPR by a team of researchers from the Massachusetts Institute of Technology and the University of California, San Francisco.
Auxolytic, a biotech company founded by Stanford University academics, has described how knocking down a gene called UMPS could render T-cell therapies ineffective by depriving T cells of the nutrition uridine. Xon could also be tailored to work with cancer CAR-T cell therapy, according to the CHOP-Novartis researchers. The dimmer switch could help prevent cell depletion by halting CAR expression, according to the researchers. According to the researchers, such a tuneable switch could help CRISPR-based treatments by providing “a short burst” of production of CRISPR effector proteins to prevent undesirable off-target editing.
Gene Therapy could be a Boon to Alzheimer’s disease (AD): A first-in-human clinical trial proposed
Reporter: Dr. Premalata Pati, Ph.D., Postdoc
A recent research work performed by the Researchers at the University of California San Diego School of Medicine has shared their first-in-human Phase I clinical trial to assess the safety and viability of gene therapy to deliver a key protein into the brains of persons with Alzheimer’s Disease (AD) or Mild Cognitive Impairment (MCI), a condition that often precedes full-blown dementia.
Mark Tuszynski, M.D., Ph.D., Professor of Neuroscience and Director of the Translational Neuroscience Institute at UC San Diego and team predicted that Gene therapy could be a boon to potential treatments for the disorders like AD and MCI.
The study provides an insight into the genetic source of these mental diseases.
The roots of mental disorders have remained an enigma for so many years. Alzheimer’s disease (AD) is an irreversible, progressive brain disorder that slowly destroys memory and thinking skills and, eventually, the ability to carry out the simplest tasks. AD is a neurodegenerative condition. A buildup of plaques and tangles in the brain, along with cell death, causes memory loss and cognitive decline. In most people with the disease, those with the late-onset type – symptoms first appear in their mid-60s. Alzheimer’s disease is the mostly appearing type of dementia in patients.
Despite decades of effort and billions of dollars of research investment, there are just mere two symptomatic treatments for AD. There is no cure or approved way to slow or stop the progression of the neurological disorder that afflicts more than 5 million Americans and is the sixth leading cause of death in the United States.
Prof. Tuszynski said gene therapy has been tested on multiple diseases and conditions, represents a different approach to a disease that requires new ways of thinking about the disease and new attempts at treatments.
The research team found that delivering the BDNF to the part of the brain that is affected earliest in Alzheimer’s disease; the entorhinal cortex and hippocampus – was able to protect from ongoing cell degeneration by reversing the loss of connections. “These trials were observed in aged rats, amyloid mice, and aged monkeys.”
The protein, calledBrain-Derived Neurotrophic Factor or BDNF, a family of growth factors found in the Brain and Central Nervous System that support the survival of existing neurons and promote growth and differentiation of new neurons and synapses. BDNF is especially important in brain regions susceptible to degeneration in AD. It is normally produced throughout life in the entorhinal cortex, an important memory center in the brain and one of the first places where the effects of AD typically appear in the form of short-term memory loss. Persons with AD have diminished levels of BDNF.
However, BDNF is a large molecule and cannot pass through the Blood-Brain Barrier. As a solution, researchers will use gene therapy in which a harmless Adeno-Associated Virus (AAV2) is modified to carry the BDNF gene and injected directly into targeted regions of the brain, where researchers hope it will prompt the production of therapeutic BDNF in nearby cells.
Precautions were taken precisely in injecting the patient to avoid exposure to surrounding degenerating neurons since freely circulating BDNF can cause adverse effects, such as seizures or epileptic conditions.
The recent research and study speculate a safe and feasible assessment of the AAV2-BDNF pathway in humans. A previous gene therapy trial from 2001 to 2012 using AAV2 and a different protein called Nerve Growth Factor (NGF) was carried out by Prof. Tuszynski and team where they observed immense growth, axonal sprouting, and activation of functional markers in the brains of participants.
He also shared that “The BDNF gene therapy trial in AD represents an advancement over the earlier NGF trial, BDNF is a more potent growth factor than NGF for neural circuits that degenerate in AD. Besides, new methods for delivering BDNF will more effectively deliver and distribute it into the entorhinal cortex and hippocampus.”
The research team hopes that the three-year-long trial will recruit 12 participants with either diagnosed AD or MCI to receive AAV2-BDNF treatment, with another 12 persons serving as comparative controls over that period.
The researchers have plans to build on recent successes of gene therapy in other diseases, including a breakthrough success in the treatment of congenital weakness in infants(spinal muscular atrophy) and blindness (Leber Hereditary Optic Neuropathy, a form of retinitis pigmentosa).”
Two brothers with MEPAN Syndrome: A Rare Genetic Disorder
Reporter: Amandeep Kaur
In the early 40s, a married couple named Danny and Nikki, had normal pregnancy and delivered their first child in October 2011. The couple was elated after the birth of Carson because they were uncertain about even conceiving a baby. Soon after birth, the parents started facing difficulty in feeding the newborn and had some wakeful nights, which they used to called “witching hours”. For initial six months, they were clueless that something was not correct with their infant. Shortly, they found issues in moving ability, sitting, and crawling with Carson. Their next half year went in visiting several behavioral specialists and pediatricians with no conclusion other than a suggestion that there is nothing to panic as children grow at different rates.
Later in early 2013, Caron was detected with cerebral palsy in a local regional center. The diagnosis was based on his disability to talk and delay in motor development. At the same time, Carson had his first MRI which showed no negative results. The parents convinced themselves that their child condition would be solved by therapies and thus started physical and occupational therapies. After two years, the couple gave birth to another boy child named Chase in 2013. Initially, there was nothing wrong with Chase as well. But after nine months, Chase was found to possess the same symptoms of delaying in motor development as his elder brother. It was expected that Chase may also be suffering from cerebral palsy. For around one year both boys went through enormous diagnostic tests starting from karyotyping, metabolic screen tests to diagnostic tests for Fragile X syndrome, lysosomal storage disorders, Friedreich ataxia and spinocerebellar ataxia. Gene panel tests for mitochondrial DNA and Oxidative phosphorylation (OXPHOS) deficiencies were also performed. No conclusion was drawn because each diagnostic test showed the negative results.
Over the years, the condition of boys was deteriorating as their movements became stiffer and ataxic, they were not able to crawl anymore. By the end of 2015, the boys had an MRI which showed some symmetric anomalies in their basal ganglia indicating a metabolic condition. The symptoms of Carson and Chase was not even explained by whole exome sequencing due to the absence of any positive result. The grievous journey of visits to neurologist, diagnostic tests and inconclusive results led the parents to rethink about anything happened erroneous due to them such as due to their lifestyle, insufficient intake of vitamins during pregnancy or exposure to toxic agents which left their sons in that situation.
During the diagnostic odyssey, Danny spent many restless and sleepless nights in searching PubMed for any recent cases with symptoms similar to his sons and eventually came across the NIH’s Undiagnosed Diseases Network (UDN), which gave a light of hope to the demoralized family. As soon as Danny discovered about the NIH’s Diseases Network, he gathered all the medical documents of both his sons and submitted the application. The submitted application in late 2015 got accepted a year later in December 2016 and they got their first appointment in early 2017 at the UDN site at Stanford. At Stanford, the boys had gone through whole-genome sequencing and some series of examinations which came back with inconclusive results. Finally, in February 2018, the family received some conclusive results which explained that the two boys suffer from MEPAN syndrome with pathogenic mutations in MECR gene.
MEPAN means Mitochondrial Enoyl CoA reductase Protein-Associated Neurodegeneration
MEPAN syndrome is a rare genetic neurological disorder
MEPAN syndrome is associated with symptoms of ataxia, optic atrophy and dystonia
The wild-type MECR gene encodes a mitochondrial protein which is involved in metabolic processes
The prevalence rate of MEPAN syndrome is 1 in 1 million
Currently, there are 17 patients of MEPAN syndrome worldwide
The symptoms of Carson and Chase of an early onset of motor development with no appropriate biomarkers and T-2 hyperintensity in the basal ganglia were matching with the seven known MEPAN patient at that time. The agonizing journey of five years concluded with diagnosis of rare genetic disorder.
Despite the advances in genetic testing and their low-cost, there are many families which still suffer and left undiagnostic for long years. To shorten the diagnostic journey of undiagnosed patients, the whole-exome and whole-genome sequencing can be used as a primary tool. There is need of more research to find appropriate treatments of genetic disorders and therapies to reduce the suffering of the patients and families. It is necessary to fill the gap between the researchers and clinicians to stimulate the development in diagnosis, treatment and drug development for rare genetic disorders.
The family started a foundation named “MEPAN Foundation” (https://www.mepan. org) to reach out to the world to educate people about the mutation in MECR gene. By creating awareness among the communities, clinicians, and researchers worldwide, the patients having rare genetic disorder can come closer and share their information to improve their condition and quality of life.
Dysregulation of ncRNAs in association with Neurodegenerative Disorders
Curator: Amandeep Kaur
Research over the years has added evidences to the hypothesis of “RNA world” which explains the evolution of DNA and protein from a simple RNA molecule. Our understanding of RNA biology has dramatically changed over the last 50 years and rendered the scientists with the conclusion that apart from coding for protein synthesis, RNA also plays an important role in regulation of gene expression.
The universe of non-coding RNAs (ncRNAs) is transcending the margins of preconception and altered the traditional thought that the coding RNAs or messenger RNAs (mRNAs) are more prevalent in our cells. Research on the potential use of ncRNAs in therapeutic relevance increased greatly after the discovery of RNA interference (RNAi) and provided important insights into our further understanding of etiology of complex disorders.
Latest research on neurodegenerative disorders has shown the perturbed expression of ncRNAs which provides the functional association between neurodegeneration and ncRNAs dysfunction. Due to the diversity of functions and abundance of ncRNAs, they are classified into Housekeeping RNAs and Regulatory ncRNAs.
The best known classes of ncRNAs are the microRNAs (miRNAs) which are extensively studied and are of research focus. miRNAs are present in both intronic and exonic regions of matured RNA (mRNA) and are crucial for development of CNS. The reduction of Dicer-1, a miRNA biogenesis-related protein affects neural development and the elimination of Dicer in specifically dopaminergic neurons causes progressive degeneration of these neuronal cells in striatum of mice.
A new class of regulatory ncRNAs, tRNAs-derived fragments (tRFs) is superabundantly present in brain cells. tRFs are considered as risk factors in conditions of neural degeneration because of accumulation with aging. tRFs have heterogenous functions with regulation of gene expression at multiple layers including regulation of mRNA processing and translation, inducing the activity of silencing of target genes, controlling cell growth and differentiation processes.
The existence of long non-coding RNAs (lncRNAs) was comfirmed by the ENCODE project. Numerous studies reported that approximately 40% of lncRNAs are involved in gene expression, imprinting and pluripotency regulation in the CNS. lncRNA H19 is of paramount significance in neural viability and contribute in epilepsy condition by activating glial cells. Other lncRNAs are highly bountiful in neurons including Evf2 and MALAT1 which play important function in regulating neural differentiation and synapse formation and development of dendritic cells respectively.
Recently, a review article in Nature mentioned about the complex mechanisms of ncRNAs contributing to neurodegenerative conditions. The ncRNA-mediated mechanisms of regulation are as follows:
Epigenetic regulation: Various lncRNAs such as BDNF-AS, TUG1, MEG3, NEAT1 and TUNA are differentially expressed in brain tissue and act as epigenetic regulators.
RNAi: RNA interference includes post-transcriptional repression by small-interfering RNAs (siRNAs) and binding of miRNAs to target genes. In a wide spectrum of neurodegenerative diseases such as Alzheimer’s disease, Parkinson disease, Huntington’s disease, Amyotrophic lateral sclerosis, Fragile X syndrome, Frontotemporal dementia, and Spinocerebellar ataxia, have shown perturbed expression of miRNA.
Alternative splicing: Variation in splicing of transcripts of ncRNAs has shown adverse affects in neuropathology of degenerative diseases.
mRNA stability: The stability of mRNA may be affected by RNA-RNA duplex formation which leads to the degradation of sense mRNA or blocking the access to proteins involved in RNA turnover and modify the progression of neurodegenerative disorders.
Translational regulation: Numerous ncRNAs including BC200 directly control the translational process of transcripts of mRNAs and effect human brain of Alzheimer’s disease.
Molecular decoys: Non-coding RNAs (ncRNAs) dilute the expression of other RNAs by molecular trapping, also known as competing endogenous RNAs (ceRNAs) which hinder the normal functioning of RNAs. The ceRNAs proportion must be equivalent to the number of target miRNAs that can be sequestered by each ncRNAs in order to induce consequential de-repression of the target molecules.
The unknown functions of numerous annotated ncRNAs may explain the underlying complexity in neurodegenerative disorders. The profiling of ncRNAs of patients suffering from neurodevelopmental and neurodegenerative conditions are required to outline the changes in ncRNAs and their role in specific regions of brain and cells. Analysis of Large-scale gene expression and functional studies of ncRNAs may contribute to our understanding of these diseases and their remarkable connections. Therefore, targeting ncRNAs may provide effective therapeutic perspective for the treatment of neurodegenerative diseases.
Lesson 7 of Cell Signaling 7 Motility: Tubulin and Tutorial Quizes for #TUBiol3373
Author: Stephen J. Williams, Ph.D.
This lesson (lesson 7) will discuss the last type of cytoskeletal structure: microtubules and tubulin. In addition I want to go over the last quiz answers and also introduce some new poll quizes.
I had given the lecture 7 over Canvas and each of you can download and go over the lecture but I will highlight a few slides in the lecture.
Let’s first review:
Remember that microtubules are the largest of the three cytoskeletal structures:
This is very important to understand as the microtubules, as shown later, shuttle organelles and cellular structures like synaptic vesicles, as well as forming the centrisome and spindle fibers of mitosis.
Now remember the quiz question from last time
Remember that actin monomers (the G actin binds ATP) while tubulin, the protein which makes up the microtubules binds GTP {although it is a little more complex than that as the following diagram shows}
See how the growth at the plus end is dependent on tubulin heterodimer GTP while when GDP is only bound to tubulin (both forms) you get a destabilization of the plus end and removal of tubulin dimers (catastrophe) if there is no source of tubulin GTP dimers (alpha tubulin GTP with beta tubulin GTP).
Also remember that like actin microfilaments you can have treadmilling (the plus end continues growing while minus end undergoes catasrophe). The VIDEO below describes these processes:
Certain SNPs and mutants of tubulin are found and can result in drastic phenotypic changes in microtubule stability and structure. Below is an article where a mutation in tubulin can result in microtubule catastrophe or destabilization of microtubule structures.
From: A mutation uncouples the tubulin conformational and GTPase cycles, revealing allosteric control of microtubuledynamics;, E.A. Geyer et al..; elife 2015;4:e10113
Abstract
Microtubule dynamic instability depends on the GTPase activity of the polymerizing αβ-tubulin subunits, which cycle through at least three distinct conformations as they move into and out of microtubules. How this conformational cycle contributes to microtubule growing, shrinking, and switching remains unknown. Here, we report that a buried mutation in αβ-tubulin yields microtubules with dramatically reduced shrinking rate and catastrophe frequency. The mutation causes these effects by suppressing a conformational change that normally occurs in response to GTP hydrolysis in the lattice, without detectably changing the conformation of unpolymerized αβ-tubulin. Thus, the mutation weakens the coupling between the conformational and GTPase cycles of αβ-tubulin. By showing that the mutation predominantly affects post-GTPase conformational and dynamic properties of microtubules, our data reveal that the strength of the allosteric response to GDP in the lattice dictates the frequency of catastrophe and the severity of rapid shrinking.
Remember the term allosterism: change in the affinity for binding of a ligand or substrate that is caused by the binding of another ligand away from the active site (for example like 2,3 DPG effect on oxygen binding to hemoglobin
Cellular transport of organelles and vesicles: a function of microtubules
Now the above figure (figure 9 in your Powerpoint) shows the movement of organelles and vesicles in two different types of cells along microtubules.
Note the magenta arrow which goes from the nucleus toward the plus end of the microtubule (at cell membrane) is referred to as anterograde transport and is movement away from center of cell to the periphery. Retrograde transport is movement of organelles and vesicles from periphery of cell to the center of the cell.
Note that kinesin is involved in anterograde transport while dyenin is involved in retrograde transport
Also refer to the Wiki page which shows a nice cartoon of this walking down a microtubule on the right hand side of the page
Defective cilia can lead to a host of diseases and conditions in the human body, from rare, inherited bone malformations to blindness, male infertility, kidney disease and obesity. It is known that these tiny cell organelles become deformed and cause these diseases because of a problem related to their assembly, which requires the translocation of vast quantities of the vital cell protein tubulin. What they didn’t know was how tubulin and another cell organelle known as flagella fit into the process.
Now, a new study from University of Georgia shows the mechanism behind tubulin transport and its assembly into cilia, including the first video imagery of the process. The study was published in the Journal of Cell Biology.
Cilia are found throughout the body, so defects in cilia formation affect cells that line airways, brain ventricles or the reproductive track. One of the main causes of male infertility is the cilia won’t function properly.
The team used total internal reflection fluorescence microscopy to analyze moving protein particles inside the cilia of Chlamydomonas reinhardtii, a green alga widely used as a model for cilia analysis.
The team exploited the natural behaviour of the organism, which is to attach by its cilia to a smooth surface, such as a microscope glass cover. This positions the cilia within the 200-nanometer reach of the total internal reflection fluorescence microscope allowing for the imaging of individual proteins as they move inside the cilia. A video explaining the process was published along with the study.
Tubulin is transported by this process called intraflagellar transport, or IFT. Though it has long been suspected in the field and there was indirect evidence to support the theory, this is the first time it has been shown directly, through live imaging, that IFT does function as a tubulin pump. The team observed that about 400,000 tubulin dimers need to be transported within 60 minutes to assemble a single cilium. Being able to see tubulin moving into cilia allowed for first insights into how this transport is regulated to make sure cilia will have the correct size.
The new findings are expected to have wide implications for a variety of diseases and conditions related to cilia defects in the body. The team state that they are on the very basic side of this research. But because more and more diseases are being connected to cilia-related conditions, including obesity and even diabetes, the number of people working on cilia has greatly expanded over the last few years.
So here are the answer to last weeks polls
Actin filaments are the SMALLEST of the cytoskeletal structures. As shown in this lecture it is tubulin that binds GTP. Actin binds ATP.
ARP2/3 or actin related proteins 2 and 3 are nucleating proteins that assist in initiating growth of branched chain micofiliment networks. Formins are associated with unbranched actin formations.
The answer is GAPs or GTPase activating proteins. Remember RAS in active state when GTP is bound and when you hydrolyze the GTP to GDP Ras is inactive state
4. Okay so I did a type here but the best answer was acetylcholinesterase (AchE) degrading acetylcholine. Acetylcholinesterase degrades the neurotransmitter acetylcholine into choline and acetate not as I accidentally put into acetylCoA. The freed choline can then be taken back up into the presynaptic neuron and then, with a new acetyl group (with Coenzyme A) will form acetylcholine.
Synthesis of the neurotransmitter acetylcholine
The neuromuscular junction
Thanks to all who took the quiz. Remember it is for your benefit.
Parkinson’s Disease (PD), characterized by both motor and non-motor system pathology, is a common neurodegenerative disorder affecting about 1% of the population over age 60. Its prevalence presents an increasing social burden as the population ages. Since its introduction in the 1960’s, dopamine (DA)-replacement therapy (e.g., L-DOPA) has remained the gold standard treatment. While improving PD patients’ quality of life, the effects of treatment fade with disease progression and prolonged usage of these medications often (>80%) results in side effects including dyskinesias and motor fluctuations. Since the selective degeneration of A9 mDA neurons (mDANs) in the substantia nigra (SN) is a key pathological feature of the disease and is directly associated with the cardinal motor symptoms, dopaminergic cell transplantation has been proposed as a therapeutic strategy.
Researchers showed that mammalian fibroblasts can be converted into embryonic stem cell (ESC)-like induced pluripotent stem cells (iPSCs) by introducing four transcription factors i.e., Oct4, Sox2, Klf4, and c-Myc. This was then accomplished with human somatic cells, reprogramming them into human iPSCs (hiPSCs), offering the possibility of generating patient-specific stem cells. There are several major barriers to implementation of hiPSC-based cell therapy for PD. First, probably due to the limited understanding of the reprogramming process, wide variability exists between the differentiation potential of individual hiPSC lines. Second, the safety of hiPSC-based cell therapy has yet to be fully established. In particular, since any hiPSCs that remain undifferentiated or bear sub-clonal tumorigenic mutations have neoplastic potential, it is critical to eliminate completely such cells from a therapeutic product.
In the present study the researchers established human induced pluripotent stem cell (hiPSC)-based autologous cell therapy. Researchers reported a platform of core techniques for the production of mDA progenitors as a safe and effective therapeutic product. First, by combining metabolism-regulating microRNAs with reprogramming factors, a method was developed to more efficiently generate clinical grade iPSCs, as evidenced by genomic integrity and unbiased pluripotent potential. Second, a “spotting”-based in vitro differentiation methodology was established to generate functional and healthy mDA cells in a scalable manner. Third, a chemical method was developed that safely eliminates undifferentiated cells from the final product. Dopaminergic cells thus produced can express high levels of characteristic mDA markers, produce and secrete dopamine, and exhibit electrophysiological features typical of mDA cells. Transplantation of these cells into rodent models of PD robustly restored motor dysfunction and reinnervated host brain, while showing no evidence of tumor formation or redistribution of the implanted cells.
Together these results supported the promise of these techniques to provide clinically applicable personalized autologous cell therapy for PD. It was recognized by researchers that this methodology is likely to be more costly in dollars and manpower than techniques using off-the-shelf methods and allogenic cell lines. Nevertheless, the cost for autologous cell therapy may be expected to decrease steadily with technological refinement and automation. Given the significant advantages inherent in a cell source free of ethical concerns and with the potential to obviate the need for immunosuppression, with its attendant costs and dangers, it was proposed that this platform is suitable for the successful implementation of human personalized autologous cell therapy for PD.
2012pharmaceutical
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