Exam 4 Flashcards
Primary immune deficiencies occur in several cell types, a deficiency in what cell type is the
most damaging and why?
T cell defects are more severe than B cells since T cells have multiple effects on target cells and are
essential for helping activate other immune.
main causes of SCID (severe combined
immunodeficiency)
1) Defective cytokine signaling. 2) Defects in purine metabolism (toxicity
death). 3) Rearrangement defects. 4) Signaling defects.
effects of SCID
The most extreme forms of combined immunodeficiencies
Stem from genetic defects leading to a lack of functional T cells
normally due to mutations in early T-cell development steps or upstream stem cells.
Infants with it have increased likelihood of viral and fungi infections and shortened lifespan
four main immunodeficiency mice described in the chapter
Nude mice, SCID mice, RAG knockout, RAG-g c knockout
Nude mice
have a vestigial thymus and no T cells. Can be used to study effects of transplantation
and cancers, drug testing, hybridoma implantation and antibody harvest.
SCID mice
are devoid of mature functional T and B cells. Can be “humanized” to study human immune system in mice. Over 30 immunodeficient SCID mouse models for disease research.
RAG knockout
have impairment of RAG1 or RAG 2 gene and are defective in VDJ recombination which results in no mature T or B cells. Often coupled with TCR or BCR transgene
RAG-gamma c knockout
mice have impairment of RAG1/2 gene and IL2 receptor g chain which results in
no mature T cells, B cells, and NK cells. Most common model for humanized mice.
What are the main causes of secondary immunodeficiencies?
The single most common cause of acquired immunodefiency is severe malnutrition. Other causes
include drug treatments, metabolic disease, age, and infectious agents such as HIV.
What is the structure of the HIV retrovirus?
HIV has two RNA genomes and reverse transcriptase (RT) enzyme that uses the RNA genome to form a cDNA copy that integrates into host cell chromosome, directing the rest of the viral replication cycle. HIV-1 is found in the U.S. and its close relative HIV-2 is found in Africa.
What is unique about the replication of HIV?
HIV retrovirus replicates through an RNA intermediate by making a DNA copy of its RNA genome (reverse transcription). Retrovirus particles contain a reverse transcription enzyme (RNA-dependent DNA polymerase) that catalyzes reverse transcription.
Outline the three main stages in the typical course of an HIV infection.
The precise course of HIV-1 infection and disease onset varies considerably in patents, but a general scheme with three phases can be outlined: 1) Acute phase. Spike in HIV levels in blood. Brought mostly under control by production of anti-HIV antibodies. 2) Asymptomatic phase. Lengthy, possibly years. Gradual decrease in CD4+ T cells and increase in viral load. 3) AIDS. Crash in CD4+ T cell numbers. High levels of HIV in blood. Fungal/opportunistic infections.
long-term non-progressors
individuals who are infected with HIV, but maintain a high CD4 count. Many of these patients have been HIV positive for 30 years without progressing to the point of needing to take medication in order not to develop AIDS. They have been the subject of a great deal of research, since an understanding of their ability to control HIV infection may lead to the development of immune therapies or a vaccine.
What stages in HIV replication cycle provide targets for therapeutic antiretroviral drugs?
HIV life cycle targets include chemokine receptor antagonists, fusion inhibition, reverse transcription inhibition, integrase inhibition, and protease inhibitors. High mutation rates make individual drugs less useful. Highly active antiretroviral therapy (HAART) is a multidrug cocktail that combines three or more drugs with different mechanisms. Unlikely mutations will sidestep all ndrugs. HAART can reduce viral loads below limits of detection, but not a cure.
How are countries working to prevent mother-to-child transmission of HIV?
The prescription of antiretroviral therapy for pregnant women and their babies has decreased transmission by more than 90% in the United States. The treatment is more difficult in sub-Saharan Africa and other less developed areas where many obstacles remain (higher rates of HIV infection, mothers not knowing of infection, poor access to health care, drug cost and availability). In these resource limited countries, a single dose of nevirapine at the onset of labor dramatically improves
the chances the baby will be born HIV free.
Why is it so difficult to make an HIV vaccine?
An HIV vaccine is hard because the virus mutates rapidly making it a moving target for the immune system and production of Ab is not good. There are many variants of the virus at any time. Good animal models are limited and there are dangers of testing attenuated vaccines.
characteristics of broadly neutralizing antibodies
appears to be the route for success with HIV. There are six sites in the HIV envelop that are “vulnerable”, meaning they are essential for membrane function
and are not mutated. To bind to these sites, broadly neutralizing antibodies must overcome the high levels of envelope glycosylation
Vaccine strategies are currently being examined that focus on finding the initial B cells that recognize these HIV epitopes and then designing a series of envelope protein boosts that could encourage the development of broadly neutralizing antibodies.
two main strategies broadly neutralizing antibodies use to penetrate the glycan barrier
1) 2/3 of the broadly neutralizing antibodies have extra-long heavy-chain CDR3 regions (15-
20 amino acids longer than standard antibodies).
2) Some broadly neutralizing antibodies have undergone extensive somatic hypermutation (up
to 30% of the nucleotides in the CDR3 regions are mutated)
How does an infant’s microbiome differ if it was born cesarean section?
The organisms associated with babies delivered vaginally look like those of the mother’s vagina, but babies born by cesarean section are originally colonized by organisms from the mother’s and the delivery nurses’ skins.
Describe the difference between animals
raised in standard versus “germ-free” environments.
Animals raised in the absence of
any sort of microbe are viable, but they develop abnormally. The heart, lungs, and livers are smaller, and the most noticeable
changes occur in the digestive tract. The cecum is dramatically enlarged, and the intestinal lining is altered. Germ-free animals require ~30% more calories to maintain their weight.
Why is our microbiome important for human nutrition?
Gut microbes enable us to use more nutrients by fermenting large molecules into smaller molecules that can be absorbed and used for energy by human cells. Gut microbes also produce nutrients that we couldn’t get otherwise, like vitamin B12 and vitamin
K.
How do commensal microbes help form a barrier between us and the outside world and aid in immunity?
Microbes form a barrier between us and the outside world by colonizing our skin and mucous membranes and preventing
disease-causing organisms from gaining a foothold by competing for nutrients and attachment sites. They also secrete
compounds that inhibit pathogens by altering the local environment or directly antagonizing pathogens. Germ-free animals are more susceptible to infectious diseases in part because the immune system is dependent on the normal microbiota for its
development. Microbes normally found in the gut educate the immune system to attack microbial invaders that may cause disease, while tolerating beneficial microbes.
What did Marshall and Warren discover about the role of H. pylori infection?
Marshall and Warren were awarded the Nobel Prize in 2005 for their discovery that H. pylori infection was a major cause of
chronic gastritis, peptic ulcers, and some types of stomach cancer. They overturned the conventional wisdom that ulcers were
caused by stress and no microbes could live in the stomach due to acid levels. This increased our understanding of chronic
infection, inflammation, and cancer. Treatment of H. pylori infection with antibiotics became the treatment for ulcers, and the incidence of stomach cancer fell.
What did René Dubos and Joshua Lederberg do to contribute to our understanding of the microbiome? What is the as “The Great Plate Count Anomaly” and how was it resolved?
Dubos initiated a shift in the microbiological paradigm to consider microorganism interactions with their environment and each
other. In contrast to the warlike germ theory model where microorganisms are the enemy, Dubos promoted viewing the human digestive tract an ecosystem, changing the conversation from “Us Against Them” to “We’re All in This Together”
. Joshua Lederberg later coined the term “microbiome”. The Great Plate Count Anomaly is where the number of bacteria in a sample counted directly under the microscope did not match the number of colonies that grew on agar plates. This was partially addressed by devising better methods to cultivate microbes. Finally, environmental microbiologists got past this issue by applying sensitive DNA-based technologies like sequencing to look directly at the genes. It was a culture-independent way to study complex
bacterial communities.
What main finding did the Human Microbiome project identify for determining a “healthy” microbiome?
There are many different microbiomes considered healthy. Individual genetic signatures of the microbiomes vary widely between individuals and metabolic function is more important than microbial composition; what they do is more important than what they are.
Despite
its distasteful smell, why is fecal microbiota transplantation of interest?
As distasteful as administering human feces to a patient might be, the clinical results have been astounding. C. diff,
fecal transplants have over 90% cure rates. The technique is being refined to be more precise, more convenient, and less pungent.
Untargeted interventions
Diets high in saturated or monounsaturated fat negatively
influenced the microbiota. Interventions with increased physical activity were linked with an increased capacity for breakdown of lactate, branched- chain amino acids, an
increased potential for synthesis of short- chain fatty acids that reduce inflammation.
targeted interventions
Targeting specific microbial- synthesized metabolites by delivering tailored drugs is an emerging frontier. Can use drug to block the microbial production of trimethylamine that can increase cardiovascular disease. Scientists are examining how to use Phage or CRISPR therapy to change the gut microbiome without undesired effects, but they represent intriguing means to alter microbiota communities.
Impact of diet on gut microbiota and host metabolism
A metabolically healthy microbiota is achieved by consuming a high-
fiber, low animal fat and low animal protein diet. The indigestible but fermentable polysaccharides are metabolized by the
microbiota of the large intestine and are fermented to produce an array of compounds, and to stimulate a thick intestinal mucus layer and strong barrier functions. Thus, a high-fiber, low animal fat and low animal protein diet provides optimal conditions for a healthy microbiome, which is protective against metabolic disease. Microbial dysbiosis is induced by a high animal fat and protein diet, sedentary life, smoking, alcohol intake and infrequent defecation may result in a leaky mucosa, intestinal and
systemic inflammation, and reduced production of SCFAs, leading to inflammation and less gut hormones secreted by L cells.
what is known about how microbial diversity affects obesity and what is not known
Following the discovery that a transferrable obesity- associated microbiota can induce weight gain in lean mice, subsequent epidemiological studies have shown differences in the gut microbiota of individuals with obesity and lean individuals.
what is known about how microbial diversity affects diabetes and what is not known
The microbiome in individuals with type 2 diabetes appears to be depleted in bacterial butyrate producers and to
exhibit an increase in species with a pro- inflammatory functional potential. Chronic inflammation can cause insulin resistance.
Describe the different purposes and findings of the 1st and 2nd phases of the NIH Human Microbiome Project.
Launched in 2007, the first phase of the program sought to determine whether there were common elements to ‘healthy’
microbiomes. One of the main findings of the HMP1 was that the metabolic function of the microbes was the best predictor of a
healthy microbiome. The second phase of the HMP, the Integrative HMP (iHMP), explored host–microbiome interplay in three specific disease populations over time (preterm birth, inflammatory bowel diseases, and prediabetes) to enable targeted therapy.
What three health conditions did the integrative human microbiome project focus on and what key finding did
they discover for each?
1) Preterm birth: Microbial signatures in the vaginal microbiome associated with full-term pregnancies differed from those with
PTB. Several taxa associated with pre-term birth were also associated with vitamin D deficiency.
2) Inflammatory bowel
disease: Compiled a gut microbiome-inflammation “dysbiosis score” and a network of interacting microbes and metabolites involved in these complex diseases.
3) Prediabetes: Establishing “baseline” measurements for early detection of numerous potential diseases (e.g. T2D, metabolic disease, cardiovascular disease, hematological or oncological conditions etc).
how does malignant transformation of cells occur?
DNA alterations can induce malignant transformation. Transformation can be induced by: Chemical substances
(e.g. formaldehyde, DDT, pesticides), physical agents (e.g. asbestos), ionizing radiation, and certain infectious agents (integrate into genome and disrupt chromosomal DNA). Results in cells being less dependent on survival factors required by most cells, are no longer anchorage dependent, and grow in a density independent fashion.
what are the three main genes associated with cancer control cell proliferation and survival
Normal tissues maintain homeostasis through a tightly regulated process of cell proliferation balanced by cell death. The genes involved in these homeostatic processes work by producing proteins that encourage or discourage cell proliferation and survival.
1) oncogenes, 2) tumor supressor genes, 3) apoptosis genes
oncogene
genes that encourage growth and proliferation
tumor suppressor genes
genes that inhibit cell proliferation or mediate cell repair
apoptosis genes
genes that control programmed cell death
what are the main hallmarks of cancer that are shared by all cancers?
centered around cell fate determination, genome maintenance, and cell survival
1) sustaining proliferative signaling
2) evading growth suppression
3) activating invasion and metastasis
4) enabling replicative immorality
5) inducing angiogenesis
6) resisting cell death
tumor specific antigens
antigens that are unique to tumor cells, and may result from incorporated viral genes or mutations in tumor cells that generate altered proteins (new Ag)
tumor associated antigens (TAAs)
normal cellular proteins with unique expression patterns. not unique to the cancer itself, and they may be normal proteins that are expressed only during specific developmental stages
what are the three E’s of cancer immunoediting?
1) elimination = attacking and removing the cells that can be targeted
2) equilibrium = state of balance between destruction/survival of best cells
3) escape = most aggressive, least immunogenic cells thrive and spread
does the immune system protect against or promote tumor growth?
Immunoediting protects against and promotes tumor growth. Immunodeficient mice are more prone to develop
tumors. Tumors induced in immunodeficient mice that are transferred to wild type recipients are much more
likely to be rejected, suggesting that the immune system plays a Darwinian role in sculpting the tumor cells. Anti-tumor immune responses remove most tumors, but also selects for toughest cancer cells.
What immune response elements promote cancer survival?
Leukocyte infiltration is important for removing tumors, however, chronic inflammation and tumor enhancing
antibodies correlate negatively with survival. Immunosuppressive cells (MDSCs, M2 macrophages, and TREG
cells and they respective immunosuppressive cytokines) foster tumor survival and evasion.
How does the innate immune system play an important role in eradicating cancer cells?
Several innate cells and process aid in the recognition and removal of cancerous cells including NK cells, M1 macrophages, and maybe eosinophils along with cytokines produced by these cells such as IFN-g, TNF-a, and IL-5 respectively. NK cells and M1 macrophages have Fc receptors that can bind to tumor specific antibodies
and initiate ADCC.
What are the main three strategies described in the book that tumor cells use to evade immune recognition and activation?
1) Reduced MHC expression in tumor cells. = Tumor cells that have mutations in genes for MHC class I expression or antigen processing make poor CTL targets
2) Tumor cell subversion of apoptosis signals. = Up-regulation of anti-apoptotic mediators or down regulation of death receptors can lead to tumor cells that are resistant to programmed cell death.
3) Enhanced co-inhibitory and immunosuppressive tumor signals. = Tumors often block T cell co- stimulation or upregulate immuosuppresive signals to initiate anergy of tumor specific T cells
What is Coley’s toxin and how does it work?
In 1891 William Coley resolved tumor by injecting bacteria directly into patient. Regression of some patient tumors when injected with a mixture of bacterial toxins (called Coley’s toxins). Response most likely due to
effects of infection and/or immunostimulatory products like LPS.
Why do clinicians calculate an immunoscore when determining the best treatment options?
Cancer prognosis is evaluated using the TMN system, which measures tumor size, lymph node spread, and
metastasis and enables them to determine the cancer “stage” (I-IV). Immunoscores evaluate the spatial distribution of immune cell types within and surrounding a tumor and low scores correspond to an
immunosuppressed tumor microenvironment and higher rates of recurrence after treatment.
What are the five main types of immunotherapies that are currently available?
1) Monoclonal antibodies
2) Immune checkpoint blockade
3) Transferred T cells
4) Cancer Vaccine
5) Oncolytic viruses.
How can co-stimulatory signals be manipulated to improve cancer immunity?
Immune checkpoint therapy is having amazing success (won the 2018 Noble prize in medicine). mAb CTLA-4 blockade or mAb impairment of PD-L1 immune regulatory molecules. Frequently used in the
clinics and has saved many lives already.
What is a Chimeric Antigen Receptor (CAR) and how is it useful for immunotherapy?
A Chimeric Antigen Receptor (CAR) consists of an antibody-derived targeting domain fused with T-cell signaling domains that, when expressed by a T-cell, endows the T-cell with antigen specificity determined by the targeting domain of the CAR. CARs can potentially redirect the effector functions of
a T-cell towards any protein and nonprotein target expressed on the cell surface as long as an antibody or similar targeting domain is available.
