Biotech World

Saturday, April 29, 2017

Role of Berries in cancer prevention

Berries are loaded with antioxidants that can prevent cancer by mopping up the free radicals i.e. the oxygen molecules. Also all types of berries particularly strawberries and raspberries have high content of ellagic acid that can fight various types of cancers (skin, bladder, lung, esophagus and breast). Ellagic acid acts as an antioxidant, helps to deactivate specific carcinogens, slowing down the reproduction of cancer cells and it is also a potent anti-angiogenetic factor, which can slow the growth of blood vessels that feed new tumor cells. Another phytonutrient Quercetin that is found in abundance in strawberries, can induce apoptosis (programmed death of cancer cells). According to a recent study published in the Journal of Agriculture and Food Chemistry, Quercetin and whole strawberry extract inhibited the proliferation of human liver cancer cells, produced a dramatic increase in cell death (up to 80 percent) after 18 hours of treatment and retarded the proliferation of these cells prior to their death [1].

Blueberries contain a family of phenolic compounds called anthocyanosides (because of which these berries are blue), which are among the most potent antioxidants yet discovered [2]. Recent research found that black raspberry and strawberry extracts have the most effective apoptosis inducing effects. Recent studies from the College of Public Health at Ohio State University, Comprehensive Cancer Center in Columbus, Ohio, discovered that black raspberries prevent cervical cancer cell growth and tumor formation and also they inhibit inflammation and induce apoptosis in esophageal and colorectal cancer tissues [3]. The ellagic acid in strawberries can deactivate specific carcinogens and decrease the replication of cancer cells. Also The College of Pharmacy at the University of Rhode Island analyzed the Jamun berries (Indian blackberry) extract and found that it exhibited pro-apoptotic effects against breast cancer cells.

But it is very important to consume only organic berries because recent report from the U.S. Department of Agriculture found that a single sample of berries contained 13 different pesticides. Also a Pesticide Action Network analysis found 54 different pesticides among strawberry samples, including nine probable carcinogens, 24 suspected hormone disruptors, 11 neurotoxins and 12 reproductive toxins. Also the phytonutrient content of organic strawberries is higher than in conventionally grown strawberries, especially vitamin C. Compost as a soil supplement increases the level of antioxidant compounds in strawberries. A Swedish research found the most effective extracts at inhibiting cell proliferation contained 48 percent more ascorbate and five times more dehydroascorbate (Vitamin C is ascorbate plus dehydroascorbate.) The organic strawberries had more antioxidants and a higher ratio of ascorbate to dehydroascorbate. So adding a cup of cancer-fighting berries a day to diet may reduce many risk factors, and help battle certain types of cancers.

References:

https://www.wsj.com/articles/SB10001424052748703280904576246854013624530

Friday, March 31, 2017

Electronic nose

The electronic nose or nano nose is an artificial olfactory device that has a small array of flexible gold nanoparticle sensors that can accurately detect compounds in a breathing sample. Currently researchers tried to use this nano nose to detect various types of cancer such as ovarian, lung and brain cancer and got 82% accuracy. Disease detection by electronic nose is safer, simpler, more portable, inexpensive and less invasive diagnostic method than traditional methods such as imaging technique, biopsies etc. The nano nose comprises of a large number of flexible sensors that are based on molecularly modified gold nanoparticles (GNPs) [1]. These sensors are integrated into a dynamic cross-reactive diagnostic sensing array. Gold nanoparticles are highly sensitive in the detection of biomarkers at lower concentration levels and they are biocompatible. Each bending state of the flexible sensor gives unique nanoparticle spatial organization, altering the interaction between GNP ligands and volatile organic compounds (VOCs) that increases the amount of data obtainable from each sensor.

The individual dynamic flexible sensor of the nano nose could selectively detect ppb (parts per billion) level VOCs that are linked with cancers in exhaled breath. VOCs can be produced endogenously or exogenously and are used as biomarkers to detect diseases such as cancer in early stages fast and accurately. For example, lung cancer tissue emits some specific VOC biomarkers such as acetaldehyde, formaldehyde, undecane, isopropene, methanol, ethylbenzene and acetone that can be detected by sensors/chemiresistors coated with gold nanoparticles of a nano nose [2]. Breast cancer patients emit VOC biomarkers that includes derivatives of alkanes such as tridecane, hexanol, formaldehyde etc and bladder, and prostate cancer patients exhaled toluene, p-xylene, acetic acid etc. This electronic nose has a huge potential to detect and diagnose various types of diseases including cancer that can enhance the opportunities to save lives.

References:

1. https://phys.org/news/2015-09-sniffing-cancer-electronic-nose-sensors.html

2.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4645969/

Monday, February 20, 2017

KRAS - the protooncogene

KRAS gene is Kirsten ras oncogene homolog of mammalian ras gene family and encodes K-Ras protein which regulates cell division and proliferation. Cytogenetically this gene is located in the short arm of chromosome 12 (12p12.1), encoded by 189 amino acids [1]. KRAS protein (also called p21) is a member of RAS/MAPK signalling pathway (for cellular signal transduction) and acts as molecular switch which is turned on by GTP (for cell growth and differentiation) and turned off by GDP molecules. KRAS gene is activated by guanine nucleotide exchange factor (GEF) and inactivated by GTPase activating proteins (GAP) [2]. KRAS is the most frequently mutated oncogene and somatic mutation in this gene results in various types of cancer such as lung, colon and pancreatic.

Around 15 - 25% lung adenocarcinoma/non small cell lung cancer (NSCLC) is related with KRAS mutation (missense mutation that introduces an amino acid substitution most frequently at codons 12, 13 and less frequently codon 61) which affects the KRAS signalling pathways (MAP kinase pathway, AKT/MTOR pathway etc.). The unregulated signalling of RAS through these pathways results in increased cell proliferation, decreased apoptosis, disrupted cellular metabolism and increased angiogenesis that leads to tumor cell proliferation [3]. Currently there is no targeted therapy for the NSCLC patients with KRAS mutation except some promising drug agents such as mitogen activated enzyme kinase inhibitors/MEKi (Trametinib and Selumetinib in combination with chemotherapy), CDK/Cyclin dependent kinase inhibitors (Palbociclib, Abemaciclib) in clinical trial.

Pancreatic ductal adenocarcinoma (PDAC) is the predominant form of pancreatic cancer which develops via acinar-ductal metaplasia and pancreatic intraepithelial neoplasia (PIN/PanIN), IPMN (intraductal papillary mucinous neoplasia) and AFLs (atypical flat lesions). 90% of PDAC is driven by mutationally (point mutation at codon G12) active KRAS oncogene/oncogenic KRAS signalling which results in intrinsic GTPase activity that block the KRAS and GAP interaction. Oncogenic KRAS signalling involves Raf/Mek/Erk pathway and P13K/Pdk1/Akt pathway and signalling in pancreas generates a fibro-inflammatory microenvironment which promotes neoplastic progression by paracrine stimulation. Also oncogenic KRAS drives metabolic reprogramming in tumor cells by aerobic glycolysis (by increasing glycolytic enzyme expression). Until now there is no cure for PDAC and average life expectancy is less than 5 years.

Around 30% to 50% colorectal cancer (CRC) is associated with KRAS mutation/point substitution (the most frequent is glycine for aspartate) mutation in codon 12, 13, 61, 146 and 154. KRAS gene is an important member of EGFR signalling cascade and involved in intracellular signal transduction [4]. EGFR is a transmembrane receptor tyrosine kinase that is overexpressed in 25% to 75% colorectal tumor/cancer. CRC carcinogenesis involves 3 pathways including chromosomal instability pathway/CIN (defects in chromosomal segregation and telomere stability), microsatellite (short tandem repeats/STRs) instability pathway/MSI (loss of DNA mismatch repair which is most common in CRC) and serrated pathway (progression of serrated polyps)/CpG island methylator phenotype pathway [5]. CIN pathway (also known as adenoma-carcinoma sequence) is the most common one (70%) which involves activation of KRAS proto-oncogene and inactivation of tumor suppressor genes such as APC (that normally blocks transition from G1 to S phase in cell cycle), p53 (that is involved in cell cycle control). CIN also results in aneuploid karyotype, loss of heterozygosity at tumor suppressor gene loci and chromosomal rearrangements [6]. Cetuximab and panitumumab are anti EGFR monoclonal antibodies which are engineered to block the EGFR signalling pathway at the extracellular domain of EGFR receptor. These are currently FDA approved CRC drugs but KRAS mutated patients showed no response to these drugs.

References:

Tuesday, January 31, 2017

Apolipoproteins

Apolipoproteins are plasma lipoproteins that consist of a core of triglycerides and cholesterol esters and plays an important role in lipid transport & distribution in various cells and tissues and lipid metabolism (functions as cofactors for enzymes). They also maintain the structural integrity of lipoprotein complex and facilitate the lipoprotein uptake by acting as ligands for specific cell surface receptors. Apolipoproteins are of different types and has different roles which are as follows:

1. Apolipoprotein A (ApoA): ApoA is the major protein component (70%) of HDL (high density lipoprotein) the "good cholesterol" which promotes cholesterol efflux from tissues to the liver for excretion and plays an important role in reverse cholesterol transport. These lipoproteins also function as a cofactor for lecithin cholesterolacyltransferase LCAT (enzyme responsible for plasma cholesterol esters formation and in HDL catabolism) [1]. ApoA concentrations are inversely linked to coronary artery disease (CAT)/cardiovascular disease (CVD).

2. Apolipoprotein B (ApoB): ApoB is the main protein component of LDL (low density lipoprotein) the "bad cholesterol", VLDL (very low density lipoprotein), IDL (intermediate density lipoprotein) and chylomicrons (a type of lipoprotein which carries fat and cholesterol to blood and also helps to absorb vit A and vit E). ApoB are mainly of 2 types: ApoB100 which produced in liver and ApoB48 which is produced in intestine [2]. ApoB100 is an important lipoprotein that is involved in atherosclerosis (chronic inflammation in arterial wall of heart mainly results from lipid metabolism disorder) and cardiovascular disease (CAD). Increased serum ApoB concentration is an important coronary heart disease (where arteries that supply blood to the cardiac muscles become narrowed due to the deposition of cholesterol, fatty cellular waste products in the inner lining of coronary artery) risk factor because ApoB is a major component of all atherogenic particles (LDL, VLDL and IDL) [3]. However several studies found that ApoA1 and ApoB ratio is more accurate predictor of heart attack /acute myocardial infarction risk than ApoB alone. ApoB is also essential for the binding of LDL particles to the LDL receptor for cellular uptake and degradation of LDL particles. Mutation in ApoB gene results in abetalipoproteinaemia (a rare autosomal recessive disorder that affects the fat and fat soluble vitamin absorption in the body and is caused by mutation in microsomal triglyceride transfer protein/MTTP gene) and hypercholesterolaemia (an autosomal dominant disorder caused by a mutation in ApoB100 gene) [4].

3. Apolipoprotein C (ApoC): ApoC is a low molecular weight apolipoprotein which includes Apo C1, Apo CII and Apo CIII. Apo CII is activator of lipoprotein lipase in capillaries and hydrolyzes the triglyceride component of chylomicrons and VLDL. ApoC III inhibits lipoprotein lipase and hepatic lipase and prevent the hepatic uptake of chylomicrons and VLDL [5].

4. Apolipoprotein E (ApoE): This is arginine rich glycoprotein found in plasma lipoproteins and is involved in recognition, regulation and uptake of lipoproteins from plasma. ApoE is also involved in catabolism and metabolism of cholesterol and in receptor recognition of IDLs and chylomicrons remnant by the liver. ApoE4 is linked to atherosclerosis, Alzheimer's disease and impaired cognitive function.

References:

Thursday, January 12, 2017

Genetics of sickle cell

Sickle cell disease (SCD) is an autosomal (could affect both male and female) recessive inherited disorder that is caused by genetic mutation in the β hemoglobin (as hemoglobin has 2 subunits: 2 α chains and 2 β chains) gene found on chromosome 11. Hemoglobin transports oxygen from lungs to other parts of the body such as liver, muscle etc. So mutation in hemoglobin (HbB) gene leads to the formation of sickle shaped abnormal hemoglobin S (HbS) or sickle hemoglobin that results in sickle cell disease or sickle cell anemia. Red blood cells with normal hemoglobin (HbA) can smoothly move through the blood vessels but HbS containing blood cells cannot move normally and become stiff, harder, less flexible and pile up and block the flow of blood through vessels. This blockage results in damaging of vital tissue and organs (vasoocclusion) such as lungs, spleen, kidney and liver and causes related pain. Also the sickle or crescent shaped red blood cells polymerize at reduced oxygen tension and die prematurely that results in hemolytic anemia or sickle cell anemia [1].

SCD is a monogenic disorder that results from the missense mutation that substitutes thymine for adenine in the 6th codon of the β chain gene (GAG to GTG) that causes coding of glutamic acid by valine at 6th amino acid position (Glu6val) of the β chain of hemoglobin [2]. Other types of SCD such as sickle hemoglobin C disease (HbSC) and sickle β thalassemia (HbS β) result from coinheritance of HbS with other abnormal β hemoglobin chain variants. SCD is recessive genetic disease i.e. 2 genes for the HbS must be inherited from the parents in order to get the disease. If the person has just one copy of the mutated gene and one normal gene then they are sickle cell trait (who are mostly normal but usually carrier of the SCD) but if the individual has 2 copies of mutated gene (Hb S) that results in SCD. When both parents are sickle cell trait then their child has 25% chance to have two defective genes and suffer from SCD, 50% chance to have one defective gene and develop sickle cell trait and 25 % chance to inherit two normal genes and being unaffected by the gene mutation and diseases [3].

Due to its shape and increased stickiness sickle cells/sickle RBCs adhere to endothelium and express a bunch of adhesion molecules such as CD36, CD18, ICAM 4 (intercellular cell adhesion molecule), P selectin etc. which causes increased microvascular transit times and vaso occlusion. Sickle RBC survives for only 10-20 days (where normal RBCs survives for 90-120 days) and then hemolysis occurs intravascularly that results in releasing of plasma free hemoglobin (PFH) and arginase to plasma [4]. These cause endothelial injury including proinflammatory stress, scavenging NO (nitric oxide) and degradation of arginine (substrate for NO synthesis) which results in low level of NO production and development of pulmonary artery hypertension and severe acute chest syndrome (which is the major cause of mortality for SCD patients). As vaso occlusion damages the spleen of people with SCD they have very low level of immunity (because of low level of serum IgM molecule) and they have increased risk of certain types of bacterial infection such as Mycoplasma pneumoniae, E. coli, Staphylococcus aureus etc. Children with SCD have painful spleen enlargement due to large number of sickle cells which is known as ‘splenic sequestration’ and they also have dactylitis (pain and swelling in hand and feet) [5].

Hemoglobin electrophoresis/cellulose acetate electrophoresis, isoelectric focusing (higher resolution), HPLC (High performance liquid chromatography) are the procedures for diagnosis of SCD. Treatment of SCD includes regular blood transfusion, antibiotics, gene therapy/gene editing, bone marrow transplantation from healthy genetically compatible sibling donor, and hematopoietic stem cell transplantation in severe cases. A new drug called Hydroxycarbamide/hydroxyurea (brand name Droxia which is FDA approved) which is basically an antitumor drug is currently used for SCD [6]. This drug stimulates fetal hemoglobin (that is found only in newborns) production which helps to prevent the sickling of red blood cells and cause improved red cell survival and reduction of white blood cell, reticulocyte and platelet counts. But this drug has significant toxicity including myelosuppression so patients treated with this drug should be monitored closely with routine CBCs and reticulocyte count. Recently Global Blood Therapeutics from South San Francisco developed a pill named gbt440 which can prevent the sickling of red blood cells [7].

References:

Friday, December 16, 2016

Vitamin D and longevity

The main function of vitamin D is to maintain the calcium and phosphorus levels in blood. However recent research found that it also has a huge impact on longevity. New studies found that vitamin D enhances lifespan and promotes protein homeostasis via stress response and cellular detoxification genes skn-1, ire-1 and xbp-1. The circulatory form of vitamin D is 25 hydroxyvitamin D [25(OH)D3]/calcidiol which utilizes longevity genes to increase lifespan and blocks the accumulation of toxic insoluble proteins (e.g. human β amyloids) that are associated with various age-related diseases such as Parkinson's, Alzheimer's, cognitive impairment, diabetes, heart disease, autoimmune disorders, and even cancer. Recent research (on C. elegans) from Buck institute of biological research discovered that vitamin D could increase lifespan by 33% and slow down the aging related protein misfolding because human age-related diseases are very often connected with vitamin D deficiency [1].

Vitamin D (Vitamin D3 or cholecalciferol and Vitamin D2 or ergocalciferol) is a fat soluble hormone that is produced naturally in the body from 7-dehydro-cholesterol by either ultraviolet light of sun (at the wavelength of 290 to 315 nm) or dietary intake [2]. Then it is transported to the liver/hepatocytes (where it is stored) by vitamin D binding protein (DBP) and hydroxylized by the enzyme 25 hydroxylase to form the 25 (OH) D3 (the serum vitamin D). The active form of vitamin D is calcitriol which acts as a hormone that is controlled by parathyroid hormone (PTH). This calcitriol mediates its biological function by binding with vitamin D receptor (VDR) of white blood cells or T cells or B cells. But the most important function of calcitriol is controlling phosphorus magnesium and calcium homeostasis with the help of PTH to maintain normal levels of calcium, phosphorus and magnesium level in the blood. PTH stimulates calcitriol to increase the calcium absorption by the intestine and reabsorption by the kidneys and also stimulate the calcium release from the bone. Without calcitriol calcium absorption would be only 15% and phosphorus would be 60% but calcitriol increases calcium absorption by 30- 40% and phosphorus level by 80% and then deposits these mineral crystals onto the collagen fibres of the osteoid protein matrix. Vitamin D regulates synthesis of calbindine, a cell membrane protein that binds with calcium and help to opens the Ca 2+ channels and by this mechanism ⅓ of daily calcium is absorbed by body daily. Also calcitriol stimulates normal bone growth, bone remodelling, bone metabolism and mineralization process [3].

Epidemiological studies showed that increased level of vitamin D intake either by sunlight or from supplements could reduce all causes of mortality in general population. After the age of 62-65 years there is a decline of intestinal calcium absorption rate due to decreased production of gastric acid and lower level of vitamin D/reduced numbers of intestinal VDRs that results in a lower amount of intra luminal ionized calcium, progressive loss of bone mass (that results in osteoporosis), changes of duodenal mucosa, increased level of PTH (secondary hyperparathyroidism), progressive decline of renal functions (due to reduced efficiency of renal 1 α hydroxylase enzyme). Children, elders (because of reduction of 7-dehydro-cholesterol only 25% of vitamin D3 is synthesized in a 70 years old) and people with darker skin (because most of the UVB rays are absorbed by melanin) are at high risk of vitamin D deficiency. According to NIH 15 mins of direct exposure to sunlight twice a week without sunscreen (because it reduces vitamin D synthesis) is sufficient to maintain optimum serum vitamin D level [4]. Several studies found that daily intake of 600-1000 IU vitamin D can protect skeleton, improve muscle functions, prevent rickets and other vitamin D related disorders in children and increase longevity. Recent studies on human LTL (leukocyte telomere length) found that people with high blood calcidiol level had low C reactive protein and longer LTL that results in 5 years of aging difference which means vitamin D could prolong lifespan by 5 years.

References:

Wednesday, November 30, 2016

Piezo - the mechanosensor

Piezo proteins (piezo1 and piezo2) are evolutionarily conserved transmembrane proteins (24-40 domains) which are involved in mechanotransduction in mammalian cells and function as mechanosensor. Piezo proteins are 2500-2800 amino acids long and are identified as mechanically activated ion channels(MA) / mechanosensitive channels that are encoded by FAM 38 genes. Piezo proteins mediate mechanosensory transduction i.e. conversion of mechanical forces into biological signals which is a very important physiologic process for all types of mammalian cells. This mechanotransduction regulates vital processes in mammals including embryonic development, blood pressure regulation, various sensations such as touch, hearing, pain, proprioception, urine flow regulation, cell migration, proliferation and elongation, bladder distension, vascular tone regulation, sensation of shear stress etc. All organisms have mechanosensitive channels which are directly gated by forces to convert mechanical stimuli into electrical signals in mechanosensory transduction. The 3 important mechanical sensory modalities are touch, hearing and proprioception that are mediated by mechanosensory channels. These channels open very rapidly with short latency (<5 milliseconds) and directly gated by forces [1].

Piezo1 is expressed with high levels in erythrocytes, endothelial cells and periodontal ligament cells in skin, lung, bladder, and kidney. Piezo2 is mostly expressed in sensory trigeminal ganglia (TG) and dorsal root ganglia (DRG), Merkel cells (epidermal mechanoreceptor involved in touch), lung and bladder. Piezo 1 acts as an endothelial sensor of blood flow, promotes endothelial cell organization, regulates erythrocyte volume, maintains structural integrity of red cells, detects urothelial extension during bladder distension, regulates stretch activated calcium pathway and also acts as an osmoreceptor in erythrocytes [2]. Piezo2 is involved in mechanosensation (such as light, touch and noxious stimuli) and somatosensation through cutaneous mechanoreceptor.

Mutation in human piezo protein results in various disorders including hereditary xerocytosis (a dominant disorder of erythrocyte dehydration results from missense mutation in piezo1) and different types of neuromuscular disorders such as distal arthrogryposis type 5 (another dominant disorder characterized by skeletal muscle contractures and restrictive lung disease), Gordon syndrome (piezo 2 mutation) etc. A new study from Scripps research institute suggests that Piezo1 could help to design better pain medication and future therapies for blood disorders and hypertension because piezo proteins can control the sensation of touch / sense force by detecting tension in the cell membrane [3].

References:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3018681/

http://www.jbc.org/content/early/2014/10/10/jbc.R114.612697.full.pdf

http://www.sci-news.com/biology/piezo-protein-senses-touch-04364.html