My retreat in an ocean of daily grind

Considering the longest lived members of my family, I have maximum of 30 years more to live. In three decades, I will be a pile of bones or a handful of ashes. I doubt that I have three decades to live since even now I am already feeling decrepit and tired despite my healthy diet, regular walks and normal weight.

The only direction in my life right now is to support my child through college. Therefore, the only purpose of my existence is to keep my salary coming for three years and seven months. It may sound sacrilegious to compare myself to a prisoner of war, but I just watched an episode of the British show Love Your Garden (available on YouTube) and the person, whom the new garden was dedicated to, was a World War II POW. He was enslaved by the Japanese for three years and seven months. He did survive the cruelty of the Japanese soldiers and lived a long and fruitful life. Many other POWs working along with him died.

I never dared to have major goals, inspirations, or a grand plan in life. It simply does not work to plan on a big scale, at least for me. I can plan my work lunches or my visit abroad to visit my family. This is the extent of the planning I have done. In general, I do prepare for the worst and hope for the best. Similar to our former POW, I do have my mental escapes in gardens and art. Another great escape are the books. However, these days, I am so busy at work that I need to do additional hours of work at home, rather than read for pleasure.

Yesterday, I finally allowed myself to get a few books from the library. It felt like an indulgence. Along with the books, I discovered that one of my favorite series of mystery books, the Agatha Raisin Mysteries by M.C. Beaton, have been made into British TV episodes and some are available on YouTube. It was a great pleasure to watch a strikingly beautiful Agatha solve murder cases on the background of a quirky and gorgeous British countryside. Not a mental-gymnastics time, but a few entertaining hours.

This weekend, I also tried a new cookie recipe that reminds me of some banana breakfast bars I have baked in the past. The recipe, Super Healthy Grab and Go Banana Breakfast Cookies, is available from https://thecookspyjamas.com/grab-and-go-breakfast-cookies/. I did a few changes in the amount of the ingredients and the prep.

Ingredients
4 very ripe, medium bananas (you can freeze whole bananas and use these for any baking recipes)
2 cups old fashioned oats
1/2 cup raw pumpkin seeds
1/2 cup shredded coconut (I found only sweetened in the supermarket)
1/2 cup raisins*
2 Tbsp chia seeds
1 teaspoon cinnamon
1 Tbsp vanilla extract
*the recipe called for currants, I used raisins

Instructions  
Combine the mashed bananas with the oats and chia seeds. Cover tight and keep overnight in the refrigerator. This allows for the oats and chia seeds to absorb the moisture from the bananas. In the morning, preheat the oven to 350°F. Add all other ingredients to the banana-oat mix. Distribute portions of 1/4 cup each on a cookie sheet lined with parchment paper. Press to thickness of half an inch. Bake for 20-25 minutes. The original recipe recommends that the cookies are kept for up to two days in an airtight container. Alternatively, these could be frozen. 

The result? The cookies were amazing! I will bake a double batch for Thanksgiving and probably Christmas! There is nothing better to indulge a bit your taste buds and know that the cookies are healthy. Thank you to Tania from The Cook's Pyjamas.

Have a great weekend! 

Determinants Of The Microbiome

Environmental effects are more important than genetic for determining the microbiome, strongly suggesting the malleability of the microbiome, which can influence human health.  Abstract:

Human gut microbiome composition is shaped by multiple factors but the relative contribution of host genetics remains elusive. Here we examine genotype and microbiome data from 1,046 healthy individuals with several distinct ancestral origins who share a relatively common environment, and demonstrate that the gut microbiome is not significantly associated with genetic ancestry, and that host genetics have a minor role in determining microbiome composition. We show that, by contrast, there are significant similarities in the compositions of the microbiomes of genetically unrelated individuals who share a household, and that over 20% of the inter-person microbiome variability is associated with factors related to diet, drugs and anthropometric measurements. We further demonstrate that microbiome data significantly improve the prediction accuracy for many human traits, such as glucose and obesity measures, compared to models that use only host genetic and environmental data. These results suggest that microbiome alterations aimed at improving clinical outcomes may be carried out across diverse genetic backgrounds.

You (including your microbiome) are what you eat.

Multiple Myeloma Treatment Options

Treatment options for relapsing/progressing multiple myeloma; abstract:

Despite enormous advances, management of multiple myeloma (MM) remains challenging. Multiple factors impact the decision to treat or which regimen to use at MM relapse/progression. Recent major randomized controlled trials (RCTs) showed widely varying progression-free survivals (PFS), ranging from a median of 4 months (MM-003) to 23.6 months (ASPIRE). Based on these RCTs, next-generation proteasome inhibitors (carfilzomib and ixazomib), next-generation immunomodulatory agent (pomalidomide), and monoclonal antibodies (elotuzumab and daratumumab) were approved for relapsed and refractory MM. Daratumumab, targeting CD38, has multiple mechanisms of action including modulation of the immunosuppressive bone marrow micro-environment. In addition to the remarkable single agent activity in refractory MM, daratumumab produced deep responses and superior PFS in MM when combined with lenalidomide/dexamethasone, or bortezomib/dexamethasone. Other anti-CD38 antibodies, such as isatuximab and MOR202, are undergoing assessment. Elotuzumab, targeting SLAMF7, yielded superior response rates and PFS when combined with lenalidomide/dexamethasone. New combinations of these next generation novel agents and/or antibodies are undergoing clinical trials. Venetoclax, an oral BH3 mimetic inhibiting BCL2, showed single agent activity in MM with t(11;14), and is being studied in combination with bortezomib/dexamethasone. Selinexor, an Exportin-1 inhibitor, yielded promising results in quad- or penta-refractory MM including patients resistant to daratumumab. Pembrolizumab, an anti-PD1 check-point inhibitor, is being tested in combination with lenalidomide/dexamethasone or pomalidomide/dexamethasone. Chimeric antigen receptor-T cells targeting B-cell maturation antigen have yielded deep responses in RRMM. Finally, salvage autologous stem cell transplantation (ASCT) remains an important treatment in MM relapsing/progressing after a first ASCT. Herein, the clinical trial data of these agents are summarized, cautious interpretation of RCTs highlighted, and algorithm for salvage treatment of relapse/refractory MM proposed.Leukemia advance online publication, 19 December 2017; doi:10.1038/leu.2017.329.

Immune Checkpoint Inhibitor Therapy Biomarkers

Immune checkpoints dampen the immune system’s ability to detect and fight cancer; thus, inhibits of such checkpoints, usually antibodies to checkpoint factors, have utility for immunotherapy against cancer.  Clinical success has been varied, and it would be helpful to identify biomarkers to ascertain what patients would most benefit by this therapeutic approach.  This study identifies some prospective markers that require more conformation.  Abstract:

Immune checkpoint blockers (ICB) have become pivotal therapies in the clinical armamentarium against metastatic melanoma (MMel). Given the frequency of immune related adverse events and increasing use of ICB, predictors of response to CTLA-4 and/or PD-1 blockade represent unmet clinical needs. Using a systems biology-based approach to an assessment of 779 paired blood and tumor markers in 37 stage III MMel patients, we analyzed association between blood immune parameters and the functional immune reactivity of tumor-infiltrating cells after ex vivo exposure to ICB. Based on this assay, we retrospectively observed, in eight cohorts enrolling 190 MMel patients treated with ipilimumab, that PD-L1 expression on peripheral T cells was prognostic on overall and progression-free survival. Moreover, detectable CD137 on circulating CD8+ T cells was associated with the disease-free status of resected stage III MMel patients after adjuvant ipilimumab + nivolumab (but not nivolumab alone). These biomarkers should be validated in prospective trials in MMel. The clinical management of metastatic melanoma requires predictors of the response to checkpoint blockade. Here, the authors use immunological assays to identify potential prognostic/predictive biomarkers in circulating blood cells and in tumor-infiltrating lymphocytes from patients with resected stage III melanoma.

CDK8 Inhibitors And Cancer

CDK8 seems to have dual functions with respect to cancer, and investigating these roles, for potential therapeutic applications, will require CDK8 inhibitors.  This is how basic science intersects with the development of future therapies.  Abstract:

Cyclin-dependent kinase 8 (CDK8) plays a vital role in regulating transcription either through its association with the Mediator complex or by phosphorylating transcription factors. Myriads of genetic and biochemical studies have established CDK8 as a key oncogenic driver in many cancers. Specifically, CDK8-mediated activation of oncogenic Wnt-β-catenin signaling, transcription of estrogen-inducible genes, and suppression of super enhancer-associated genes contributes to oncogenesis in colorectal, breast, and hematological malignancies, respectively. However, while most research supports the role of CDK8 as an oncogene, other work has raised the possibility of its contrary function. The diverse biological functions of CDK8 and its seemingly context-specific roles in different types of cancers have spurred a great amount of interest and perhaps an even greater amount of controversy in the development of CDK8 inhibitors as potential cancer therapeutic agents. Herein, we review the latest landscape of CDK8 biology and its involvement in carcinogenesis. We dissect current efforts in discovering CDK8 inhibitors and attempt to provide an outlook at the future of CDK8-targeted cancer therapies.

More On CRISPR

Using new methodologies to optimize the CRISPR system.  Abstract:

CRISPR-Cas systems offer versatile technologies for genome engineering, yet their implementation has been outpaced by ongoing discoveries of new Cas nucleases and anti-CRISPR proteins. Here, we present the use of E. coli cell-free transcription-translation (TXTL) systems to vastly improve the speed and scalability of CRISPR characterization and validation. TXTL can express active CRISPR machinery from added plasmids and linear DNA, and TXTL can output quantitative dynamics of DNA cleavage and gene repression-all without protein purification or live cells. We used TXTL to measure the dynamics of DNA cleavage and gene repression for single- and multi-effector CRISPR nucleases, predict gene repression strength in E. coli, determine the specificities of 24 diverse anti-CRISPR proteins, and develop a fast and scalable screen for protospacer-adjacent motifs that was successfully applied to five uncharacterized Cpf1 nucleases. These examples underscore how TXTL can facilitate the characterization and application of CRISPR technologies across their many uses.

Liver Cancer, Males Vs. Females, And ZebraFish

At left, adult female zebrafish. By Azul (Own work) [Copyrighted free use], via Wikimedia Commons

Liver cancer is more prevalent in men. There may be both biological and lifestyle reasons for this. To study possible biological mechanism, a zebrafish model was used. Abstract:

Hepatocellular carcinoma (HCC) is more prevalent in men than women, but the reason for this gender disparity is not well understood. To investigate whether zebrafish could be used to study the gender disparity of HCC, we compared the difference of liver tumorigenesis between female and male fish during early tumorigenesis and long-term tumor progression in our previously established inducible and reversible HCC model - the krasV12 transgenic zebrafish. We found that male fish developed HCC faster than females. The male tumors were more severe from the initiation stage, characteristic of higher proliferation, activation of WNT/β-catenin pathway and loss of cell adhesion. During long-term tumor progression, the male tumors developed into more advanced multi-nodular tumors, whereas the female tumors remain uniform and homogenous. Moreover, regression of male tumors required longer time. We further investigated the role of sex hormones in krasV12 transgenic fish. Estrogen treatment showed tumor suppressing effect during early tumorigenesis through inhibiting cell proliferation, whereas androgen accelerated tumor growth by promoting cell proliferation. Overall, our study presented the zebrafish as a useful animal model for study of gender disparity of HCC.

Obviously, humans are not zebrafish and it is not certain that the possible hormonal mechanism identified in the fish applies to humans, but it is a possible avenue for study.

Epigenetics And Stomach (Gastric) Cancer

The importance of epigenetic changes is underscored by its relationship to progression to gastric cancer, observed in a 10-year study.  Abstract;

Intestinal metaplasia (IM) is a pre-malignant condition of the gastric mucosa associated with increased gastric cancer (GC) risk. We performed (epi)genomic profiling of 138 IMs from 148 cancer-free patients, recruited through a 10-year prospective study. Compared with GCs, IMs exhibit low mutational burdens, recurrent mutations in certain tumor suppressors (FBXW7) but not others (TP53, ARID1A), chromosome 8q amplification, and shortened telomeres. Sequencing identified more IM patients with active Helicobacter pylori infection compared with histopathology (11%-27%). Several IMs exhibited hypermethylation at DNA methylation valleys; however, IMs generally lack intragenic hypomethylation signatures of advanced malignancy. IM patients with shortened telomeres and chromosomal alterations were associated with subsequent dysplasia or GC; conversely patients exhibiting normal-like epigenomic patterns were associated with regression.

Potential Parkinson’s Therapeutic Agent

See this.  Abstract:

Activation of microglia by classical inflammatory mediators can convert astrocytes into a neurotoxic A1 phenotype in a variety of neurological diseases1,2. Development of agents that could inhibit the formation of A1 reactive astrocytes could be used to treat these diseases for which there are no disease-modifying therapies. Glucagon-like peptide-1 receptor (GLP1R) agonists have been indicated as potential neuroprotective agents for neurologic disorders such as Alzheimer's disease and Parkinson's disease3-13. The mechanisms by which GLP1R agonists are neuroprotective are not known. Here we show that a potent, brain-penetrant long-acting GLP1R agonist, NLY01, protects against the loss of dopaminergic neurons and behavioral deficits in the α-synuclein preformed fibril (α-syn PFF) mouse model of sporadic Parkinson's disease14,15. NLY01 also prolongs the life and reduces the behavioral deficits and neuropathological abnormalities in the human A53T α-synuclein (hA53T) transgenic mouse model of α-synucleinopathy-induced neurodegeneration 16 . We found that NLY01 is a potent GLP1R agonist with favorable properties that is neuroprotective through the direct prevention of microglial-mediated conversion of astrocytes to an A1 neurotoxic phenotype. In light of its favorable properties, NLY01 should be evaluated in the treatment of Parkinson's disease and related neurologic disorders characterized by microglial activation.

Screening For Factors Influencing Neurodegenerative Diseases

Screening for factors influencing neurodegenerative diseases, such as amyotrophic lateral sclerosis and frontotemporal dementia, shows the importance of modifiers of an important mechanism of those diseases: hexanucleotide-repeat expansions in the C9ORF72 gene that result in toxic dipeptide-repeat proteins that aggregate – abnormal protein aggregation being a key feature of many nervous system-related diseases. This may have implications for treatment.  Abstract:

Hexanucleotide-repeat expansions in the C9ORF72 gene are the most common cause of amyotrophic lateral sclerosis and frontotemporal dementia (c9ALS/FTD). The nucleotide-repeat expansions are translated into dipeptide-repeat (DPR) proteins, which are aggregation prone and may contribute to neurodegeneration. We used the CRISPR-Cas9 system to perform genome-wide gene-knockout screens for suppressors and enhancers of C9ORF72 DPR toxicity in human cells. We validated hits by performing secondary CRISPR-Cas9 screens in primary mouse neurons. We uncovered potent modifiers of DPR toxicity whose gene products function in nucleocytoplasmic transport, the endoplasmic reticulum (ER), proteasome, RNA-processing pathways, and chromatin modification. One modifier, TMX2, modulated the ER-stress signature elicited by C9ORF72 DPRs in neurons and improved survival of human induced motor neurons from patients with C9ORF72 ALS. Together, our results demonstrate the promise of CRISPR-Cas9 screens in defining mechanisms of neurodegenerative diseases.

Protein And Fat Free mass in Female Resistance Training

In a group of female athletes undergoing resistance training, a high protein diet improved fat free mass gain but was not required for gains in strength.  This is an interesting finding that may or may not be generally applicable to all resistance trainers.  It can make sense if one presumes maximal hypertrophy requires significant extra protein, but that the neural and muscular adaptions required for strength do not.  However, more study is required to determine how applicable this is for, e.g., the advance trainee, including men.  Abstract:

Aspiring female physique athletes are often encouraged to ingest relatively high levels of dietary protein in conjunction with their resistance-training programs. However, there is little to no research investigating higher vs. lower protein intakes in this population. This study examined the influence of a high vs. low protein diet in conjunction with an 8-week resistance training program in this population. Seventeen females (21.2±2.1 years; 165.1±5.1 cm; 61±6.1 kg) were randomly assigned to a high protein diet (HP: 2.5g/kg/day; n=8) or a low protein diet (LP: 0.9g/kg/day, n=9) and were assessed for body composition and maximal strength prior to and after the 8-week protein intake and exercise intervention. Fat-free mass (FFM) increased significantly more in the HP group as compared to the LP group (p=0.009), going from 47.1 ± 4.5kg to 49.2 ± 5.4kg (+2.1kg) and from 48.1 ± 2.7kg to 48.7 ± 2 (+0.6kg) in the HP and LP groups, respectively. Fat mass significantly decreased over time in the HP group (14.1 ± 3.6kg to 13.0 ± 3.3kg; p<0.01) but no change was observed in the LP group (13.2 ± 3.7kg to 12.5 ± 3.0kg). While maximal strength significantly increased in both groups, there were no differences in strength improvements between the two groups. In aspiring female physique athletes, a higher protein diet is superior to a lower protein diet in terms of increasing FFM in conjunction with a resistance training program.

HCMV And Cancer

By Transferred from en.wikipedia to Commons.This media comes from the Centers for Disease Control and Prevention's Public Health Image Library (PHIL), with identification number #958.Note: Not all PHIL images are public domain; be sure to check copyright status and credit authors and content providers.English | Slovenščina | +/−, Public Domain, https://commons.wikimedia.org/w/index.php?curid=1880647

Human cytomegalovirus (HCMV) is common lifelong infection agent that usually remains latent after the initial infection and can become reactivated later in life. HCMV infection can promote the growth and metastatic potential of colorectal cancer cells.  Therefore, HCMV may contribute to the human cancer burden.  Abstract:

Increasing evidence suggests a link between persistent human cytomegalovirus (HCMV) infection and cancer. Although the role of HCMV in cancer is still elusive, recent studies revealed the presence of HCMV nucleic acids and proteins in different cancer types such as glioblastoma, colorectal, breast, and prostate cancers, and neuroblastoma. Although HCMV may not be directly associated with the neoplastic transformation, the presence of HCMV DNA in the tumorous tissue has been associated with altered clinical outcomes in cancer patients. However, the mechanisms involved in the association between colorectal cancer (CRC) and HCMV are unclear. In this study, we investigated the influence of HCMV infection on CRC or their derived cells. Proliferation and migration assays revealed a high infection efficiency in CRC-derived HT29 and SW480 'stem‑like' cells. After 24, 48 and 72 h of HCMV infection, both HT29 and SW480 parental and stem‑like cells showed a significant increase in cell proliferation and viability (p<0.0001). Moreover, HCMV infection promoted cell migration. These results demonstrate a significant phenotypic alteration in the CRC cell line upon HCMV infection. Using epithelial to mesenchymal transition (EMT) assays, we demonstrated that the EMT markers and driver genes were upregulated during the virus infection. The WNT signaling pathway, which is associated with the proliferation and migration of CRC cells, was upregulated (6-fold) in HCMV-infected cells as compared to the non‑infected cells at day 7 from infection.