Category Archives: Gene Medicine

When she isnt pursuing her favorite heart-pumping activities of running, swimming, or cycling, Sharlene M. Day, a presidential associate professor of cardiovascular medicine and director of Translational Research for the Penn Cardiovascular Institute, is focused on the heart in another way; trying to unlock and treat the mysteries of genetic heart disease.

As part of her research at the Day Lab, Day integrates translational and clinical science to understand the full spectrum of genetic heart disease evolution and progression, from gene mutations in heart muscle cells to ways of predicting negative outcomes in patients. Clinically, she sees patients with hypertrophic cardiomyopathy, a condition where the heart muscle becomes thick making it harder for blood to leave the heart, and other genetic heart conditions at the Penn Center for Inherited Cardiac Disease, such as inherited arrhythmias, high blood cholesterol, Marfan syndrome and familial amyloidosis. Her research program primarily focuses on these same conditions.

A physician scientist, Day completed her residency, followed by a cardiology fellowship, and a postdoctoral research fellowship at the University of Michigan before joining the faculty there, and spent 24 years there before coming to Penn. Day was recruited to Penn Medicine to lead initiatives in translational research within the Cardiovascular Institute and to grow the clinical and academic mission in the Penn Center for Inherited Cardiovascular Disease.

Very early on in my training, I became fascinated with the interplay between genetics and cardiac physiology that manifest in very unique observable cardiac traits and complicated disease trajectories including both heart failure and arrhythmias, also known as irregular heartbeats, says Day.

This story is by Sophie Kluthe. Read more at Penn Medicine News.

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Getting to the heart of genetic cardiovascular diseases | Penn Today - Penn Today

Northern Californias bay area, which includes San Francisco, San Mateo, Santa Clara, Napa, and Marin County, is home to some of the most well-established biopharma companies. The atmosphere is chill, the mood relaxed unless you happen to work for one of these scientific innovators where drive and determination are required to meet the mission.

The Biotech Bay region is home to 3,418 life sciences companies, and 96,574 employees making an average of $151,076. Focuses and technologies range from cell and gene therapy to precision medicine and polymer chemistry, targeting rare diseases along with more pervasive killers. And these seven companies just happen to have a wealth of job openings right now.

Gilead Sciences Inc.

Nestled in Foster City, a small hamlet in San Mateo County, Gilead Sciences is well-known for its achievements in viral diseases, most notably human immunodeficiency virus (HIV).

With a mission of developing novel therapeutics for life-threatening illnesses with unmet medical need, Gilead has an impressive list of FDA-approved medicines. These include Veklury, better known as the COVID-19 therapy, remdesivir, Biktarvy, a single tablet HIV regimen, and Yescarta, a chimeric antigen receptor T cell (CAR-T) drug acquired along with Kite Pharma in 2017.

In 2020, Gilead employed approximately 13,600 individuals. This was an increase of around 2000 (15.25%) from 2019, and the company is growing again.

For those passionate about global access to cancer medicines, Gilead is hiring a Director, Value & Access Strategy Oncology. The successful applicant will have at least 12 years of biopharma experience in market access-related activities bonus points if this is on a regional or country basis. For the more statistically-inclined, Gilead is looking for a Sr. Manager, Biostatistics Oncology.

With well over 300 positions available, opportunities abound to join this Biotech Bay leader.

BioMarin Pharmaceutical Inc.

Established in 1997, San Rafael-based BioMarin specializes in super-rare diseases. BioMarin is targeting cures for diseases like inherited metabolic disorder, Phenylketonuria (PKU), and the rapidly progressing pediatric brain disorder, late infantile neuronal ceroid lipofuscinosis type 2 (CLN2). The company also has a strong presence in hemophilia.

With six commercially approved drugs and a market cap of $15.4 billion, BioMarin was cited by Zacks Equity Research as one of four potential biotech takeover targets for 2021. Whether this will be the case, only time will tell, but BioMarin is getting even bigger, with nearly 200 open posts, including:

Associate Director, Global Brand Management - Strategy and Operations. Anyone wanting to make this strategic career move will need to have a minimum of 7 years of pharmaceutical/biotech industry experience.

Senior Associate - Regulatory Affairs. The successful candidate will possess superior decision-making and problem-solving skills and have a tendency to thrive in a cross-functional business environment. A degree in health or life sciences is required; Ph.D. preferred.

Category Manager, Single Use Technology. This job is for those passionate about supply chain operations, with 5-plus years of strategic procurement experience and 3-plus years in the biotech/life sciences industry. BioMarin would prefer someone with an MBA or MS, and a C.P.M.

Arcus Biosciences, Inc.

Founded in 2015, Arcus Biosciences is combining precision therapeutic strategies in an effort to defeat cancers that have thus far eluded medicine. Arcus has clearly been busy over the past six years, with 13 programs in clinical development and five more coming down the discovery pipeline. Targets include a wide range of cancers, including non-small cell lung cancer (NSCLC), metastatic castration-resistant prostate cancer, and colorectal cancer.

Those seeking a position within this unique biopharma company should check out some of the 90-plus jobs currently available. Here are just a couple:

Bioanalytical Scientist. Arcus is actively recruiting a scientist for its Drug Metabolism and Pharmacokinetics (DMPK) department. Interested candidates with a Ph.D. in pharmaceutical sciences or related disciplines should apply.

Principal Investigator/Clinical Biomarkers Translational Science. Arcus is seeking a candidate with expertise in the development, execution, and oversight of biomarker plans for oncology assets.

Associate Director, Clinical Supply. The winner of this position will play a role in all of Arcuss clinical development problems. The desired applicant will have 7-plus years of relevant experience and a Masters degree.

Global Blood Therapeutics

Global Blood Therapeutics (GBT) is comprised of nearly 400 people driven by the mission of delivering life-changing treatments for those with sickle cell disease (SCD) and other severe blood disorders. In late 2019, the FDA approved GBTs oxbryta (voxelotor) as the first treatment to directly inhibit sickle hemoglobin polymerization, the root cause of SCD. Other investigative medicines include a potential treatment to limit the frequency of vaso-occlusive crises (VOCs) and multiple other shots on goal for SCD.

Located on Oyster Point Boulevard in South San Francisco, GBT is looking for new talent to fill more than 80 positions, including:

Director, Clinical Operations. GBT is open to hiring the right person to work remotely from anywhere in the U.S. for this prime leadership position.

Associate Director, Pharmacovigilance Operations. Another remote opportunity for a vigilant leader with 10 or more years of pharmacovigilance experience in an operational and compliance position.

Nektar Therapeutics

San Francisco-based Nektar Therapeutics is focused on curing cancer and autoimmune disease using polymer chemistry, a unique approach to drug design that uses optimized pharmacology to create new molecular entities.

Nektar is leveraging this technology to develop five clinical-stage investigational drugs with partners Bristol Myers Squibb, Biogen, Eli Lilly & Co., and Vaccibody. The companys lead immuno-oncology candidate, bempegaldesleukin, is an IL-2 pathway agonist designed to stimulate the immune system to fight cancer. It is currently being tested in phase III for a number of indications in combination with BMSs OPDIVO. In February, Nektar inked a co-development deal with SFJ Pharmaceuticals to advance bempegaldesleukin in head and neck cancer.

With all of these programs, it is no wonder Nektar is sourcing new talent for more than 50 positions. Here are just a couple.

Clinical Trial Manager. If any (or all) of the above programs appeal, this role might be the right fit. The successful applicant will have eight years of pharmaceutical development experience, with at least two years overseeing trials.

Principal Medical Science Liaison (MSL)-Northeast. A remote opportunity for a creative, technical, and scientifically-minded individual hailing from the Northeast.

Sangamo Therapeutics, Inc.

This genomic medicine company touches on many of biotechs hottest areas including gene therapy, cell therapy, and in vivo genome editing. Sangamos diverse preclinical and clinical-stage pipeline is aimed at solving life-limiting diseases like Hemophilia A, Amyotrophic lateral sclerosis (ALS), Phenylketonuria (PKU), and Fabry disease.

In July 2020, Sangamo entered into a collaboration with Novartis to develop and commercialize gene regulation therapies for three neurodevelopment targets, including autism spectrum disorder. The agreement leverages Sangamos proprietary genome regulation technology, zinc finger protein transcription factors (ZFP-TFs), which aims to upregulate the expression of genes in these disorders.

Anyone wishing to participate in this mission should check out one of Sangamos available positions. A Research Associate III/IV job is one of many associate-level opportunities currently on the board. There are also openings for a few scientist-level positions, including a Research Scientist, Molecular Biology.

Sana Biotechnology

This cell and gene therapy hybrid is developing its cell engineering platform to deliver any payload to any cell in a specific, predictable and repeatable way. Sana is aiming this technology at a wide range of oncologic, genetic, CNS, and cardiovascular targets in a currently all preclinical pipeline.

Sana has been vocal about its culture of inclusion, diversity and equity (IDE), which leadership believes is paramount to its patient-centric culture. By tapping Head of Development Operations, Farah Anwar, as its IDE leader, Sana has ensured that a senior executive is privy to the people dynamics as well the medical ones.

Sana is currently looking to bring on board a Head of Facilities to spearhead its capital project master plan, a Principal Scientist, Genomics Core to advance this key technology, and a Cloud Systems Administrator to oversee the design.

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Biotech Bay is Rich With Opportunity in the Industry's Hottest Spaces - BioSpace

Kriya Therapeutics, based in Redwood City, Calif. and Research Triangle Park, NC,closedon a Series B financing worth $100 million.

Patient Square Capital led the round with participation from new investors Woodline Partners, CAM Capital, Hongkou, Alumni Ventures and others. Existing investors also took part, including QVT, Dexcel Pharma, Foresite Capital, Bluebird Ventures, Transhuman Capital, Narya Capital, Amplo and JDRF T1D Fund.

Kriya is one of BioSpaces NextGen Bio Class of 2021 life sciences startups to watch. In May 2020, it closed on an $80.5 million Series A financing. Its pipeline includes multiple AAV-based gene therapies for type 1 and type 2 diabetes, severe obesity, and other indications.

KT-A112 is a gene therapy to produce insulin and glucokinase for type 1 and 2 diabetes. KT-A522 is a gene therapy administered by salivary gland injection that carries the gene to produce a glucagon-like peptide 1 (GLP-1) receptor agonist for type 2 diabetes and severe obesity. And KT-A832 is a gene therapy that delivers the gene to produce modified insulin growth factor 1 (IGF-1) for type 1 diabetes.

In recent years, we have seen the promise of gene therapy become a reality for the treatment of a number of devastating diseases, said Shankar Ramaswamy, co-founder and chief executive officer of Kriya.

However, the field has been constrained by critical limitations in manufacturing technology, vector design capabilities and cost. Kriya was formed with the mission of revolutionizing how gene therapies are designed, developed and produced by fully integrating advanced manufacturing technologies, computational tools and development capabilities within a single company, Ramaswamy continued.

As part of the financing, Jim Momtazee, managing partner of Patient Square Capital, will join Kriyas board of directors.

We believe that gene therapy will have transformative impact on medicine over time, and companies that are able to integrate platform capabilities delivering better treatments, lower cost and broader applications of the technology are going to drive that innovation, Momtazee said. With that vision, we are incredibly excited to partner with the management team at Kriya to bring multiple important medicines to patients.

In August 2020, the companyannouncedit had secured a manufacturing facility in Research Triangle Park to support its pipeline production. The facility is 51,350 square feet and designed with a fully integrated process development lab, quality control and analytical development capability, pilot production suite, and current good manufacturing practice (cGMP) production infrastructure. It plans to manufacture its gene therapies at the site via its scalable suspension cell culture manufacturing process at up to a 2,000-liter bioreactor scale.

At the time, Britt Petty, Kriyas chief manufacturing officer, said, Manufacturing continues to be a critical bottleneck to the advancement of gene therapies for prevalent diseases. With the establishment of our cGMP manufacturing facility in North Carolina, we are preparing to have the capacity to support our pipeline of programs addressing large patient populations, from initial INDs through late-phase clinical studies. Moreover, we are investing in process innovation and scalable infrastructure with the goal of reducing the costs of goods of our therapies by orders of magnitude.

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Kriya Raised $100 Million in a Series B Round to Advance Gene Therapies - BioSpace

Introduction

Osteoporosis (OP) is a metabolic bone disorder characterized by low bone mass and micro-architectural deterioration of the bone tissue.1 OP increases the risk of bone fractures, which are associated with increased mortality and low quality of life.2 Postmenopausal OP and osteoporotic fractures are common, particularly among older women.3 As there are no signs or symptoms of OP other than bone fractures, risk assessment for OP is necessary to identify individuals at higher risks of future clinical events.4 A diagnosis of OP can be made based on low bone mineral density (BMD) measured by dual-energy X-ray absorptiometry.5 In a meta-analysis of genome-wide association studies, different BMD phenotypes were found to be associated with alpha-L-iduronidase (IDUA) gene polymorphisms.6

IDUA regulation has been demonstrated to affect bone formation. For instance, IDUA-deficient mice progressively developed a high bone mass phenotype with pathological lysosomal storage in cells of osteoblast lineage.7 Histomorphometric quantification further helped identify shortening of bone-forming units in these mice and a reduced quantity of osteoclasts per bone surface.7 In addition, an up-regulation of IDUA was observed in osteoporotic patients compared with healthy older adults.8 Within the IDUA protein, it is hypothesized that the phosphorylation site T366 is indirectly affected by IDUA rs6831280 (A361T) and phosphorylation sites T98 and S102 are affected by IDUA rs3755955 (R105Q).6 To this end, Wang et al recruited 328 OP patients, with or without osteoporotic fractures, to evaluate the association of IDUA gene polymorphisms with BMD and fractures in Chinese elderly patients with OP.9 They found that IDUA rs6831280 polymorphism was associated with BMDs at L2-L4 and total hip BMD.9 In this study, we aim to validate this finding in Chinese women with postmenopausal OP.

Optimal protein and calcium intake, vitamin D supply, and inhibition of smoking and drinking, together with regular weight-bearing physical exercise, are the corner stones for OP and/or osteoporotic fracture prevention.2 Several drugs are licensed to reduce fracture risk by slowing down bone resorption (eg, bisphosphonates and denosumab) or by stimulating bone formation (eg, teriparatide).1 Zoledronic acid (ZA) is an intravenous, highly potent aminobisphosphonate used in patients with primary or secondary OP or low bone mass.10 Its high affinity and long half-life in bones and long duration of action allow for a once-yearly administration.10 Therefore, we intended to explore the role of these two polymorphisms of IDUA gene in OP susceptibility and the therapeutic effect of intravenous ZA administration in Chinese postmenopausal women.

From April 2014 to August 2017, three hospitals (Jintan Hospital Affiliated to Jiangsu University, the Affiliated Changzhou No. 2 Peoples Hospital of Nanjing Medical University, and the Second Affiliated Hospital of Jiaxing University) continuously recruited 660 Chinese postmenopausal women (>1 year since menopause), including 357 OP patients and 303 healthy controls. BMD was measured by trained technicians at the lumbar spine (L2L4) and femoral neck via dual-energy X-ray absorptiometry (Lunar Radiation Corp., Madison, WI, USA). The daily inter-rater variation coefficient was within normal operational standards and in vivo variation coefficient was lower than 1.5%. Based on the definition by the World Health Organization (WHO), the presence of OP was characterized by a BMD T-score of less than 2.5 either at the femoral neck or lumbar spine. Those who had undergone oophorectomy or those who exhibited premature ovarian failure, thyroid disease, rheumatoid arthritis, hypercortisolism, calcium intake disorders, gastrointestinal, and/or renal diseases; those under the age of 40 years; and those who had a history of abnormal bone metabolism or use of medication interfering with bone metabolism were excluded from the investigation.

The annual treatment cost for ZA is equivalent to other oral anti-OP drugs; furthermore, it is easy to use and has good compliance and high bioavailability. Therefore, the OP patients were recommended to use ZA after a kidney function test (creatinine clearance rate 35 mL/min). Each enrolled OP patient received intravenous ZA once a year for 3 years. Intravenous ZA was administered at a dose of 5 mg per 100 mL of 0.9% saline solution with a standardized duration of 30 to 40 min. Patients received 500 mL of intravenous saline before/after ZA infusion. Daily supplementation with calcium (500 mg) and vitamin D (400 IU) was strongly recommended. However, 9 OP patients with severe cognitive impairment, bisphosphonate-related osteonecrosis of the jaw, allergy, and previous ZA contraindications were excluded during treatment. In all, 70 OP patients did not complete the entire treatment process. We finally performed data analysis on 278 OP patients and 303 healthy controls. The response to ZA treatment was evaluated based on the trend of BMD in the lumbar spine. An increase in lumbar spine BMD exceeding 0.05 g/cm2 was indicative of effective treatment, and any results otherwise were suggestive of ineffective treatment. Accordingly, the OP patients were divided into responders and non-responder groups with respect to ZA treatment. Individuals in the control group did not have a previous history of OP and/or fractures and were age matched to the participants with OP. All participants were of Chinese Han ethnicity and were genetically unrelated. Daily physical activity, menstrual history, and family history concerning the incidence of fractures were obtained from all participants. Data regarding calcium and vitamin D intake were also collected through a structured questionnaire. Body mass index (BMI) was calculated as weight in kilograms divided by the square of the height in meters. Written informed consent was obtained from all participants in the study before enrollment. Confidentiality of personal and medical data was conducted in accordance with the Helsinki declaration. The Clinical Ethics Committee of the aforementioned three hospitals [Jintan Hospital Affiliated to Jiangsu University (ID: KY-2014-010), the Affiliated Changzhou No. 2 Peoples Hospital of Nanjing Medical University (ID: [2017] KY008-01), and the Second Affiliated Hospital of Jiaxing University (ID: JXEY-2015SW68)] approved this investigation.

Blood samples collected from each participant were used to genotype polymorphisms. Genomic DNA was isolated from peripheral leukocytes using the TIANamp Blood DNA kit (Qiagen, Hilden, Germany). We selected single nucleotide polymorphisms (SNPs) in the IDUA gene according to the following criteria: minor allele frequency >5% and significant association with BMD or BMD-related risk factors reported in previous studies.

IDUA gene polymorphisms were genotyped via polymerase chain reaction (PCR) and Sanger sequencing (Genesky Biotechnologies Inc., Shanghai, China). The primers used in this study were as follows: rs3755955: 5-CGCAGCATCAGAACCTGCTACT-3 (forward); 5-CGGGTGTTGTTGACCTGGAAG-3 (Reverse); rs6831280: 5-TCTGAAACTGTCCTGTTGACTCAG-3 (forward); 5-ATCAATGTTGAGCAATTGTCAG-3 (Reverse). Five percent of the samples were repeatedly genotyped to ensure the validity of the genotyping methods.

A chi-square test was used to evaluate the differences in categorical variables and percentages were used between two groups. The mean and SD of continuous variables were calculated and tested using Students t-test or an analysis of variance. Deviation from HardyWeinberg equilibrium (HWE) for IDUA gene polymorphisms was assessed among the control individuals using chi-square test. Logistic regression analysis was applied to calculate the odds ratios (ORs) and 95% confidence intervals (95% CI) for evaluating the association between IDUA gene polymorphisms and the risk of OP. A value of P < 0.05 was considered statistically significant. All data were analyzed using SPSS 22.0 software (SPSS Inc., Chicago, USA).

Baseline participant characteristics are shown in Table 1. The case group comprised 278 postmenopausal women with a mean age of 62.788.40 years and BMI of 24.39 kg/m2. Among all participants, most women (65.1%) did not have diabetes; however, the number of women with diabetes differed significantly between groups (P=0.016). There was a significant difference between vitamin D and calcium intake and lumbar spine/femoral neck BMD between participants with OP and healthy controls (P<0.001).

Table 1 Patient Demographics and Risk Factors in Osteoporosis

The genotype distribution information of the two SNPs in IDUA is provided in Table 2. The A allele frequencies of IDUA rs3755955 and rs6831280 polymorphisms were 19.4% and 27.2% among participants, with OP and 13.5% and 21.3% among healthy controls, respectively. The genotype distribution of these two polymorphisms was in agreement with HWE in the healthy control group.

Table 2 Genotype Frequencies of IDUA Gene Polymorphisms in Cases and Controls

Our study demonstrated that the AA genotype or A allele of IDUA rs3755955 polymorphism was associated with an increased risk of OP (AA vs GG: OR, 2.88; 95% CI, 1.087.64; P = 0.034; A vs G: OR, 1.54; 95% CI, 1.132.11; P = 0.007). Similarly, GA+AA genotype had a 1.53-fold higher risk of OP than the GG genotype. Furthermore, IDUA rs6831280 polymorphism conferred susceptibility to OP under the homozygous, dominant, and allelic models. These associations remained significant after adjusting for age, BMI, and diabetes mellitus. Additionally, IDUA rs6831280 polymorphism increased the risk of OP in the recessive model.

We further investigated the association of IDUA gene polymorphisms with the demographic (ie, age and BMI) and clinical data (ie, diabetes and lumbar spine/femoral neck BMD) (Table 3). For rs3755955, the age of the AA genotype carrier was found to be significantly younger than that of the GA/GG genotype carriers. In addition, IDUA rs3755955 polymorphism was significantly associated with lumbar spine BMD, with the AA genotype having the lowest BMD. Furthermore, the femoral neck BMD of the AA genotype carrier in rs3755955 polymorphism was significantly lower than that of GA/GG genotype carriers. However, no significant association with clinical parameters was found for rs6831280 polymorphism.

Table 3 The Biochemical Measurements of the Study Population

We recorded baseline characteristics of responders (61.5% of participants) and non-responders to ZA treatment (Table 4). The mean age and BMI of responders and non-responders were not significantly different (all P > 0.05). Similarly, among responders, there was no significant difference between participants with OP and healthy controls with regard to vitamin D and calcium intake, diabetes status, and lumbar spine/femoral neck BMD.

Table 4 Clinical Characteristics of Patients Treated with Aclasta

Furthermore, this study investigated the effect of these two polymorphisms on the therapeutic effect of intravenous ZA (Table 5). There was no significant difference in the genotypic distribution of rs3755955 polymorphism between responders and non-responders to ZA treatment. However, the incidence of the A allele, GA+AA genotype, or AA genotype of IDUA rs6831280 polymorphism was higher in responders than in non-responders (A vs G: OR, 0.50; 95% CI, 0.330.75; P = 0.001). The findings remained significant after adjusting for age, BMI, and diabetes mellitus. This indicated that ZA treatment was more effective in individuals with the A allele.

Table 5 The Distribution of Genotype Frequencies of IDUA Gene Polymorphisms in Responders and Non-Responders

In this study, we found that IDUA rs3755955/rs6831280 polymorphisms increased the risk of OP in a population of Chinese women. Furthermore, IDUA rs3755955 polymorphism in women with OP was associated with a younger age and lower lumbar spine BMD. Finally, IDUA rs6831280 polymorphism caused differences in individual sensitivity to ZA treatment for OP.

Protein phosphorylation is the most basic, universal, and most important mechanism for regulating and controlling protein vitality and function.11 Protein phosphorylation occurs mainly in two amino acids: serine (including threonine), and tyrosine.11 Gene polymorphisms that create, alter, or destroy phosphorylation sites have been recognized as functional variants for human diseases, such as prostate cancer (TP53 rs1042522)12 and tuberculosis (TLR2 rs5743708).13 Niu et al found that IDUA phosphorylation-related SNPs rs3755955 and rs6831280 exert indirect effects on nearby phosphorylation sites, which could affect the risk of OP.6

Wang et al recruited 172 OP patients with low-traumatic fractures and 156 OP patients without fracture to investigate the relationship of two SNPs (rs3755955 and rs6831280) with BMD and fractures.9 They found that BMDs at lumbar spine L2L4 and total hip among subjects with the GA genotype of rs6831280 polymorphism were lower than those among subjects with the GG or AA genotype carriers.9 IDUA rs6831280, and not rs3755955, polymorphism is a genetic risk factor for osteoporotic fractures.9 Our results revealed that IDUA rs3755955 and rs6831280 polymorphisms increased the susceptibility of postmenopausal women to OP. Individuals with the AA genotype of rs3755955 polymorphism had the lowest lumbar spine BMD compared with GA or GG genotype. Notably, this study focused on the association of IDUA gene polymorphisms with OP, but not with fractures. Furthermore, our study demonstrated that IDUA rs3755955 polymorphism is associated with BMD at lumbar spine, instead of rs6831280 polymorphism reported by Wang et al.9 This inconsistency may be attributed to geographical differences (Northern and Southern), dietary differences, and population heterogeneity. A single infusion of intravenous ZA decreases bone turnover and improves BMD after 12 months in postmenopausal women with OP10 and significantly reduces the risk of vertebral, hip, and other fractures.14 Since IDUA rs3755955 and rs6831280 polymorphisms were associated with lumbar spine BMD, our study evaluated the effect of these SNPs on the sensitivity to ZA. There was no significant difference between responders and non-responders to ZA treatment in the allelic and genotypic distribution of the rs3755955 polymorphism. However, we could not rule out the possibility of false-positive results because of a small sample size. Nevertheless, the A allele frequency of rs6831280 polymorphism in participants with OP was significantly higher than that in healthy controls. Therefore, mutant genotypes were more sensitive to ZA, and the increased treatment effect was significant. To the best of our knowledge, this study is the first to evaluate the association between IDUA gene polymorphisms and ZA treatment, and may serve to guide further studies in this field.

Several potential limitations of our study merit careful consideration. First, the sample size was relatively small, which could have produced false-positive or false-negative results. Second, this study only genotyped two SNPs of the IDUA gene and the coverage of this gene was incomplete. Third, we did not include many risk factors for OP (eg, smoking and history of personal fractures) into consideration because of the limited data availability. Finally, these results should be validated in other populations in China and in other countries.

In conclusion, our group identified a significant association between IDUA gene polymorphisms and OP. Further studies with larger sample sizes in other races and ethnicities are urgently warranted to identify the genetic profile of individuals with OP.

The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.

This study was supported by the National Natural Science Foundation of China (81702179), Funding from Young Talent Development Plan of Changzhou Health Commission (CZQM2020059), Science and Technology Plan Project of Changzhou (CJ20190002), and Zhejiang Medicine and Health Technology Plan (2020KY313).

No potential conflict of interest was reported by the authors.

1. Eastell R, ONeill TW, Hofbauer LC, et al. Postmenopausal osteoporosis. Nat Rev Dis Primers. 2016;2:16069. doi:10.1038/nrdp.2016.69

2. Rizzoli R. Postmenopausal osteoporosis: assessment and management. Best Pract Res Clin Endocrinol Metab. 2018;32(5):739757. doi:10.1016/j.beem.2018.09.005

3. Black DM, Rosen CJ, Solomon CG. Postmenopausal osteoporosis. N Engl J Med. 2016;374(18):1797. doi:10.1056/NEJMx160008

4. Watts NB. Postmenopausal osteoporosis: a clinical review. J Womens Health (Larchmt). 2018;27(9):10931096. doi:10.1089/jwh.2017.6706

5. Baccaro LF, Conde DM, Costa-Paiva L, Pinto-Neto AM. The epidemiology and management of postmenopausal osteoporosis: a viewpoint from Brazil. Clin Interv Aging. 2015;10:583591. doi:10.2147/CIA.S54614

6. Niu T, Liu N, Yu X, et al. Identification of IDUA and WNT16 phosphorylation-related non-synonymous polymorphisms for bone mineral density in meta-analyses of genome-wide association studies. J Bone Miner Res. 2016;31(2):358368. doi:10.1002/jbmr.2687

7. Kuehn SC, Koehne T, Cornils K, et al. Impaired bone remodeling and its correction by combination therapy in a mouse model of mucopolysaccharidosis-I. Hum Mol Genet. 2015;24(24):70757086. doi:10.1093/hmg/ddv407

8. Zhou Z, Gao M, Liu Q, Tao MD. Comprehensive transcriptome analysis of mesenchymal stem cells in elderly patients with osteoporosis. Aging Clin Exp Res. 2015;27(5):595601. doi:10.1007/s40520-015-0346-z

9. Wang Q, Tang C, Jia J, Zhang G, Liu Z. Associations of IDUA and PTCH1 with bone mineral density, bone turnover markers, and fractures in Chinese elderly patients with osteoporosis. Dis Markers. 2019;2019:9503762. doi:10.1155/2019/9503762

10. Dhillon S. Zoledronic acid (Reclast((R)), Aclasta((R))): a review in osteoporosis. Drugs. 2016;76(17):16831697. doi:10.1007/s40265-016-0662-4

11. Humphrey SJ, James DE, Mann M. Protein phosphorylation: a major switch mechanism for metabolic regulation. Trends Endocrinol Metab. 2015;26(12):676687. doi:10.1016/j.tem.2015.09.013

12. Fan S, Hao ZY, Zhang M, Liang CZ. Association between the rs1042522 polymorphism in TP53 and prostate cancer risk: an updated meta-analysis. Chronic Dis Transl Med. 2017;3(2):95104. doi:10.1016/j.cdtm.2017.04.001

13. Cubillos-Angulo JM, Arriaga MB, Silva EC, et al. Polymorphisms in TLR4 and TNFA and risk of mycobacterium tuberculosis infection and development of active disease in contacts of tuberculosis cases in Brazil: a prospective cohort study. Clin Infect Dis. 2019;69(6):10271035. doi:10.1093/cid/ciy1001

14. Black DM, Delmas PD, Eastell R, et al. Once-yearly zoledronic acid for treatment of postmenopausal osteoporosis. N Engl J Med. 2007;356(18):18091822. doi:10.1056/NEJMoa067312

Link:
IDUA Gene Variants and Response to Zoledronic Acid Treatment in Chines | PGPM - Dove Medical Press

British-born cardiologist Dr Euan Angus Ashley, 49, is one of the pioneers in the application of gene sequencing in medicine and part of an international network of specialists working tirelessly to make the long-held dream of genetic-based medicines an everyday reality.

Based in California, where he serves as Professor of Medicine and Genetics at Stanford University as well as the Head of Stanford Center for Undiagnosed Diseases, and the founding director of the Center for Inherited Cardiovascular Disease as well as Stanfords Clinical Genomics Program, Dr Ashley has just published new popular science book The Genome Odyssey, which reveals how our understanding of the human genome is now revolutionizing medicine, unlocking the secrets of mystery diseases and leading to powerful new treatments for our most intractable illnesses.

In this exclusive interview, Dr Ashley discusses his fascinating new book, explains why we are currently in a golden age of genomic medicine, and reveals just how fundamentally the rise of genetic healthcare will transform society for the better.

Q. How can our genetics cause illnesses? To what extent would you say that diseases and morbidity ultimately have bad genes to blame?

A. Essentially, all diseases have a genetic component. For some diseases they can be almost entirely explained by one letter change in the genome, for others its half nature and half nurture, and for some others still, a pathogen (like a virus) or the immune system is more to blame than the human genome, which plays a smaller role. Even for those diseases, though, genetic sequencing can help us understand the pathogen or the changes in our immune cells.

Q. As you make clear in your new book, The Genome Odyssey, we are on the cusp of a new era of genetic-based medicine. Why should we be excited about this?

A. We are finally understanding diseases that have remained mysterious for hundreds of years. And that understanding now allows us to develop medicines that can very precisely target those diseases. We sometimes call this precision medicine. Devastating illnesses that affect millions of people around the world like sickle cell disease or haemophilia could in the near future be, essentially, cured. This is not business as usual. This is a revolution.

Q. You say that we will all benefit from genetic medicine in the future. Does this mean that the costs of genetic sequencing and treatments have come down significantly in recent years?

A. Its hard to think of an example where a technology has become as accessible so quickly as is the case with genome sequencing. People often talk about how fast computers advance in their computing power but genome sequencing has advanced much faster. Its like being able to buy a Ferrari for a penny!

Q. What has been your role in the development of genetic-based medicine?

A. Back in 2009 I walked into a colleagues office and he showed me his genome. He was the fifth person in the world to have his genome sequenced. After he started showing me his genome I recognized a few of the genes in which he had variations, and which were known to be associated with hypertrophic cardiomyopathy, an inherited cause of sudden death. I started asking him about his family medical history to see if there were cases of sudden, unexplained deaths. It turned out his family had quite a lot of these incidents, including his cousins son who had died suddenly aged 19 years. Long story short, shortly after, he became the first patient in the world to walk into a doctors office with his genome. And rather terrifyingly at the time, that doctor was me!

Q. The Genome Odyssey provides a fascinating survey of genetic medicine. What motivated you to write it?

A. I love stories. I live in awe of my patients and what they go through living from one day to the next with these challenging diseases. I wanted to tell the stories of these brave individuals in the hope that it would give others strength and inspiration.I am also fascinated by stories of scientists and innovators who break boundaries to push technologies to the limits. I love the fact I get to live among these amazing scientists here in Silicon Valley. I try to emulate them and make discoveries to help humanity.I hoped in the book to weave the very human stories of the patients and families affected by disease together with the stories of the scientists who make those breakthroughs possible. I explain some science along the way but always try to keep it light and anchor each chapter with a remarkable story from a patient so we can understand how those scientific breakthroughs come to affect real people.

Q. In your book you compare doctors involved with genomic medicine as akin to fictional detective Sherlock Holmes. Can you explain the similarity?

A. Solving medical mysteries is exactly like solving crimes. In fact, not many people realize that Sherlock Holmes creator, Arthur Conan Doyle, was himself a physician (an ophthalmologist) and that he based the character of Holmes on a Scottish surgeon with an uncanny eye for detail. In medical or criminal mysteries, you have to survey the scene, interrogate the witnesses, come up with hypotheses, and then test them. What TV shows like House, M.D. and CSI: Crime Scene Investigation have illustrated is that the application of technology to these mysteries raises the odds of solving the case. The genome is a big part of that.

Q. Towards the close of your book you project forward to future applications of genetic medicine. One of these involves identifying and harnessing the genetic powers of superhumans. What do you mean by the term superhuman, and how do you think learning about their genetic codes will help make us all healthier?

A. It turns out that if you study large populations of humans (who are willing to share their health and genetic data) you find out a lot about disease. One of the unusual things you can detect is that some people are remarkably resilient to disease. I discuss a few examples in the book, such as an Olympic athlete, a woman with extremely low cholesterol, and a young boy who didnt feel pain. These genetic superheroes can, in effect, teach us how to make everyone else just a bit more super. And its now a big focus for pharmaceutical companies. More than that, it appears to be paying off. New drugs developed following on from this genomic revolution are coming to market and showing major benefits. In fact, it would be reasonable to say that no drug will likely be developed in the future without someone asking if there is human genetic evidence that it will work. This is a big change from how we used to develop drugs, where we would often test a number of theories in small animals like mice before we ever got near humans.

Q. You mention in your book that the UK is leading the way in the field of genomic medical research. Can you explain more?

A. The UK is, indeed, at the forefront of genomic research globally. In fact, the genetic technology that has been responsible for the genome revolution came together in Cambridge! And a new disruptive sequencing technology is being developed in Oxford. But the UK is also at the forefront of population genetic studies. Without doubt the most influential genetic population study in the world today is the UK Biobank. Literally thousands of papers have been written as a result of the 500,000 UK citizens being willing to share their health and genetic data. I discuss a few examples in the book of insights that have come from the UK biobank research. But those insights are just the beginning. Also in the application of genome sequencing to medical care, Genomics England is one of the worlds most successful endeavourshaving sequenced more than 100,000 individuals with rare disease to try to find answers. Finally, the UK is not resting on its laurels, launching soon a new program called Our Future Health which aims to recruit five million Britons into the largest study of preventive genomics anywhere in the world. Our Future Health is focused on incorporating knowledge of your genome to help you better direct lifestyle and preventive efforts to avoid disease.

Q. You also discuss the development of gene therapy in providing new treatments for such conditions as haemophilia. What are the current challenges in changing genes or gene expression itself within the human body and how will these be overcome?

A. The history of genetic therapy has been long and winding, and many lessons have been learned along the path to the current golden age of genetic therapywith many successes building on the lessons of the last 30 years. The challenges that remain now are to broaden the impact of therapies beyond the organs and organ systems that are easiest to deliver therapies to (the liver, the eye, and cells outside of the body like from our bone marrow). Getting gene therapies to the heart or the brain is much harder than to the liver or eye so we have to work towards new delivery systems using fat particles or inactivated viruses that can help us approach those conditions.

Q. Just how far do you think genetic-based testing and treatment will change the face of medicine in the coming decades?

A. I think genetic testing and treatment will touch every aspect of health and medicine. There isnt a disease without a genetic component. And as we understand that better we will be able to integrate that with knowledge of our environment (it is often said that your postcode might be more important than your genetic code in predicting your future health, but in reality they are inseparable and each provides insight into how best to avoid or treat disease).

Q. The Genome Odyssey is packed with fascinating stories and information on the cutting edge of medical science, but what for you is the most interesting element of the book?

A. Well, the obvious answer is the stunning advances in genome sequencing, the computing that makes analysis of this data possible, and the patients it impacts. But the less obvious answer is that, at various times during writing, I became obsessed with other smaller things, many of which made it into the book in some form like Sherlock Holmes (I read all the books) or Homers Odyssey (that is a looong book) but many of which did not (or if they did, they live in the endnotes). For example, I got deeply obsessed with sentences that only contain the word Buffalo (little known fact: the word can be a verb, noun, and adjective). Related, the origin of Buffalo chicken wings was fascinating to me. Also, the origin of the Human Genome Project and things like the fact that two of the people drawing blood for the original volunteers were identical twins. I love these kinds of trivial and sometimes tangential observations.

Q. What first led you into becoming a doctor, and why did you choose to specialise in both cardiology and rare diseases?

A. For as long as I can remember I have always wanted to be a doctor. My dad was a GP in Glasgow and my mum a midwife, and they used to take me on their house calls when I was little. I was also always fascinated by the heart. I just loved the fact that it moved with rhythm and its movement made sounds like music. Genetics was somehow also in my destiny after my biology teacher gave me a copy of The Selfish Gene by Richard Dawkins when I was in secondary school (he also told my parents I was a buffoon who would never amount to muchchallenge accepted). But it was my nerdy nature and the fact I loved to program computers that really sealed my fate. As genetics became a specialty where you needed large computers to understand the big data, I was drawn to that like a magnet. And Silicon Valley was the place it all seemed to be coming together. So today, I am lucky enough to get to do all this with amazing colleagues in a beautiful and sunny part of the world.

Q. What is the most satisfying part of your vocation?

A. My patients. I live for my patients. And I live in awe of my patients and what they go through. We get to stand next to them for a while as they go through lifes ups and downs but we should never forget that as we move on the next patient they are still there living through the challenges of their disease. So for me everything starts and ends with the patients. But I also love the scientific process. I love the excitement of a new idea. The frisson of the unknown. The anticipation of what might be. I also love the energy of teams. I feed off that energy and try to reflect it back.

Q. Being a doctor must take up most of your time but, in those rare moments that it doesnt, how do you like to unwind?

A. Well, for many years I spent as much time playing saxophone in various jazz bands as I did learning medicine. I still love jazz and play now with my kids (my daughter plays saxophone and my youngest son just started drums). I also love sport and am on a quest to finally understand American sports (whereas football and rugby are engraved in my soul). Im also known for my love of single malt and I enjoy imparting a little piece of Scotland to my California friends who are always eager to learn.

Q. What has been your proudest medical achievement to date, and what are you and your team currently working on?

A. I think seeing what our community around the world has been able to do with genome sequencing technology is very fulfilling. I am proud to have been a small part of that. We are currently working on how to make genome sequencing faster, cheaper, more accurate and, most importantly, more available to everyone who could benefit. But we also want to cure the diseases that cause heart failure and sudden death. Too many people still die unnecessarily, devastating the families left behind. We understand those diseases better now thanks to genome sequencing but the journey towards curing those diseases is just beginning.

The Genome Odyssey: Medical Mysteries and the Incredible Quest to Solve Them (St. Martins Press) by Dr Euan Angus Ashley is out now on Amazon in hardcover, eBook, and audiobook formats, priced 22.99, 9.49, and 20.47 respectively. For more information visit http://www.genomebook.info.

The rest is here:
Charting The Genetic Medicine Revolution: An Interview With Author Of The Genome Odyssey, Dr Euan Angus Ashley - The London Economic

CAMBRIDGE, Mass.--(BUSINESS WIRE)--Foundation Medicine, Inc. today announced that it has received approval from the U.S. Food and Drug Administration (FDA) for FoundationOneLiquid CDx to be used as a companion diagnostic to aid in identifying patients with MET exon 14 skipping (METex14) in metastatic non-small cell lung cancer (NSCLC) for whom treatment with TABRECTA (capmatinib) may be appropriate. TABRECTA is the first therapy approved by the FDA for adult patients with metastatic NSCLC whose tumors have an alteration that leads to METex14. FoundationOne Liquid CDx analyzes the largest genomic region of any FDA-approved comprehensive liquid biopsy test and was approved by the FDA in August 2020 to report genomic alteration results for patients with any solid tumor.

NSCLC accounts for approximately 85% of lung cancer diagnoses,[1] 3 to 4% of which are associated with METex14.[2] Today's approval adds to the number of therapies for which both of Foundation Medicines FDA-approved comprehensive genomic tests are listed as companion diagnostics. FoundationOneCDx, Foundation Medicines tissue test, was approved as a companion diagnostic for TABRECTA in May 2020.

For lung cancer patients with METex14, having the option of a non-invasive liquid biopsy expands access to this first-of-its kind therapy and helps meet a critical patient need, said Brian Alexander, M.D., M.P.H., chief executive officer at Foundation Medicine. This approval, coupled with last years simultaneous therapy and companion diagnostic approval for TABRECTA and our tissue test, FoundationOne CDx, is an important advancement and demonstrates the value of having multiple highly-validated comprehensive genomic testing options for physicians to consider for the individual needs of each patient.

Using a simple blood sample, FoundationOne Liquid CDx analyzes over 300 cancer-related genes for genomic alterations. The test is now approved as a companion diagnostic for nine targeted therapies across four cancer types. TABRECTA is the second therapy for which both of Foundation Medicines FDA-approved tests, FoundationOne CDx and FoundationOne Liquid CDx, are listed as companion diagnostics.

Additionally, as a laboratory professional service which has not been reviewed or approved by the FDA, the FoundationOne Liquid CDx report delivers information about the genomic signatures microsatellite instability (MSI) and blood tumor mutational burden (bTMB), as well as single gene alterations, including NTRK fusions, to help inform the use of other therapies including immunotherapies. Also, as a laboratory professional service, the report provides relevant clinical trial information and includes interpretive content developed in accordance with professional guidelines in oncology for patients with any solid tumor.

Foundation Medicines strategic collaboration with Novartis now includes four companion diagnostics for the Novartis portfolio of targeted oncology therapeutics.

About FoundationOne Liquid CDx

FoundationOne Liquid CDx is a qualitative next generation sequencing based in vitro diagnostic test for prescription use only that uses targeted high throughput hybridization-based capture technology to analyze 324 genes utilizing circulating cell-free DNA (cfDNA) isolated from plasma derived from anti-coagulated peripheral whole blood of advanced cancer patients. The test is FDA-approved to report short variants in over 300 genes and is a companion diagnostic to identify patients who may benefit from treatment with specific therapies (listed in Table 1 of the Intended Use) in accordance with the approved therapeutic product labeling. Additional genomic findings may be reported and are not prescriptive or conclusive for labeled use of any specific therapeutic product. Use of the test does not guarantee a patient will be matched to a treatment. A negative result does not rule out the presence of an alteration. Patients who are negative for companion diagnostic mutations should be reflexed to tumor tissue testing and genomic alteration status confirmed using an FDA-approved tumor tissue test, if feasible. For the complete label, including companion diagnostic indications and complete risk information, please visit http://www.F1LCDxLabel.com.

About Foundation Medicine

Foundation Medicine is a molecular information company dedicated to a transformation in cancer care in which treatment is informed by a deep understanding of the genomic changes that contribute to each patient's unique cancer. The company offers a full suite of comprehensive genomic profiling assays to identify the molecular alterations in a patients cancer and match them with relevant targeted therapies, immunotherapies and clinical trials. Foundation Medicines molecular information platform aims to improve day-to-day care for patients by serving the needs of clinicians, academic researchers and drug developers to help advance the science of molecular medicine in cancer. For more information, please visit http://www.FoundationMedicine.com or follow Foundation Medicine on Twitter (@FoundationATCG).

Foundation Medicine and FoundationOne are registered trademarks of Foundation Medicine, Inc.

TABRECTA is a trademark of Novartis.

Source: Foundation Medicine

Original post:
Foundation Medicine Expands Indication for FoundationOneLiquid CDx to be Used as a Companion Diagnostic for TABRECTA (capmatinib) - Business Wire

Introduction

Osteonecrosis of the femoral head (ONFH) is a disease in which the local death of osteocytes and bone marrow components is caused by venous congestion or impaired arterial blood supply or the femoral head rupture.1,2 ONFH usually occurs between 30 and 50 years old.1 It is reported that the risk factors of ONFH included corticosteroid use, trauma, alcohol consumption, coagulation abnormalities, hyperlipidemia, and smoking.1 Numerous epidemiological and multicenter studies have shown that most ONFH patients have a history of alcohol abuse. It has been reported that alcohol can destroy bone homeostasis by directly inhibiting the proliferation and differentiation of bone marrow mesenchymal stem cells (BMSCs).3 In particularly, alcohol significantly inhibited the proliferation and DNA synthesis of osteoprogenitor cells.4 Therefore, alcohol is a factor that cannot be ignored to cause osteonecrosis of the femoral head.5 At present, there are two main types of osteonecrosis: traumatic and non-traumatic.2 Alcohol-induced ONFH belongs to non-traumatic osteonecrosis.6 Epidemiological studies have reported that 2045% of ONFH patients are associated with alcohol consumption.1 Excessive drinking may lead to dyslipidemia, abnormal differentiation of BMSCs differentiation, and abnormal bone metabolism. In addition, alcohol has a significant dose effect on bone homeostasis.7 However, each individual have different susceptibility, which may be related to genetic predispositions.8 Some studied showed that MMP-8 and MMP-3 gene polymorphisms were related to the risk of alcohol-induced ONFH.9

RAB40C, also known as RARL/RASL8C, is located in 16p13.3. It is a member of the RAS oncogene family and encodes the protein RAB40C. The RAB family of small GTPases was regards as the cellular regulators of vesicular transport,10 and RAB proteins were the key regulators of eukaryotic biofilm transport in all eukaryotes.11 Studies have found that RAB40C was directly regulated by let-7a and played an important regulatory role in the biological role of gastric tumorigenesis.12 Aberrant methylation in RAB40C may be related to the pathogenesis of prostate cancer.13 Our previous work has proved that RAB40C is a novel lipid droplet-related RAB protein,11 which is one of the RAB proteins regulating lipid droplets (LDs) homeostasis.14 Lipid metabolism disorder is considered as the main factor of the pathogenesis of alcohol-induced ONFH.15 Thus, the occurrence of alcohol-induced ONFH may be relevant to RAB40C gene.

In order to verify this hypothesis, this study aimed to search for the association between RAB40C single nucleotide polymorphisms (SNPs) and alcohol-induced ONFH susceptibility, so as to provide guidance for the potential treatment and prevention of the disease.

The ethical approval of this study is in line with the ethical principles of the Helsinki declaration on human medical research. Our study has been approved by the ethics committee of Hong Hui hospital in Xi an, China, and all participants have signed informed consent before participating in the study.

All subjects were the Chinese Han population and included 201 patients and 201 controls. Participants underwent routine physical examinations including internal medicine, surgery, and specialized facial examinations. The diagnostic criteria for alcohol-induced ONFH are based on the clinical manifestations of hip, lumbar, and knee pain and mobility limitations. We further diagnosed the disease by MRI analysis and X-ray examination, such as deformities of the femoral head, hip stenosis, protuberances, or collapsed cartilage fractures.16 The patients were diagnosed with ONFH after using plain radiographs in stage II, III, and IV of the Ficat Classification systems. Stage I is characterized by no radiological abnormalities. Only some joints are stiff and painful, usually with limited joint movement. The symptoms were relieved after rest, and no positive results were found on X-ray films. Occasionally, uniform or spotty osteoporotic areas could be seen. The second stage is characterized by bone reconstruction on X-ray film, with sparse bone and diffuse bone, but no change in the shape of femoral head or joint space. A plain or CT scan of the femoral head shows osteosclerosis, focal osteoporosis, or cystic changes. Stage III is characterized by continuous fracture of subchondral trabeculae with obvious cystic changes and sclerotic margin around it. The femoral head is flattened due to subchondral fracture, mainly in the load-bearing area. Stage IV is characterized by progressive enlargement of subchondral osteonecrosis, further compression and destruction of the femoral head and acetabulum, with narrowing of joint space and typical changes of osteoarthritis.16 The enrolled patients had a history of drinking pure alcohol > 400 mL (320g/week, any alcoholic beverage) per week for six months or more. The inclusion criteria of the control group were as follows: (1) healthy, excluding asymptomatic ONFH (stage I) subjects; (2) age and BMI-matched Han Population in the control group; (3) no recent infection; (4) no other medical history; (5) no history of alcohol abuse.

In 1000 genome project (http://www.internationalgenome.org/), we selected RAB40C candidate SNP sites with allele frequency (MAF) over 5%. Three SNPs (rs4984677, rs62030917 and rs2269556) in RAB40C were finally identified in the case - control study. We isolated the genomic DNA from the whole blood sample using the Goldmag-mini Purification Kit (GoldMag Co. Ltd, Xian, China), and DNA concentration was measured using the NanoDrop 2000 (Thermo Scientific, Waltham, MA). Multiplexed SNP Mass EXTEND assay was designed by Agena MassARRAY Assay Design 4.0 software, and SNP genotyping was performed by Agena MassARRAY RS1000 (Agena, San Diego, CA, USA) according to the standard scheme.17 We also used Agena Typer 4.0 software to analyze and manage our data.18

We used Microsoft Excel (Microsoft, Redmond, WA) and SPSS Statistics (version 17.0, SPSS, Chicago, IL) to analyze the collected data. All the pvalues in the study were two - tailed, and p < 0.05 was statistically significant. The chi-square test was used to evaluate the deviation of Hardy-Weinberg equilibrium (HWE). Pearson Chi - square test or Fishers accurate test were also used to compare the allele frequency and genotype frequency of alcohol-induced ONFH patients with that of the control group. The association between polymorphisms in the RAB40C gene and the risk of alcohol-induced ONFH was calculated on the basis of logistic regression analysis. Four models (co-dominant, dominant, recessive, and log-additive) were established using PLINK version 1.07 software to assess the association between each sites and the alcohol-induced ONFH risk. The pairwise linkage disequilibrium (LD), haplotype construction, and genetic association of polymorphism loci were assessed using the Haploview software package (version 4.2).

This study contained 201 alcohol-induced ONFH patients with an average age of 42.68 12.875 years old and 201 healthy controls with an average age of 42.87 13.270 years old. The independent sample t test showed that no significant difference was between the case group and the control group. In the case group, there were 54 cases in stage I and II, 147 cases in stage III and IV. Moreover, 44 cases with unilateral lesions and 157 cases with bilateral lesions. The information of BMI, alcohol and tobacco use in both cases and controls were shown in the Table 1. Supplementary Table S1 listed the plasma lipoprotein and lipid levels between patients and controls, and the results of the table indicated that there was a significant difference in PLT levels between the two groups.

Table 1 Comparison of Clinical Data in Case and Control Groups

Supplementary Table S2 showed the primers were used for this study. We have successfully genotyped three SNPs of RAB40C gene, and the genotype frequency distribution of all SNPs in the control groups did not deviate from the HWE (p > 0.05). Table 2 showed the basic information of chromosome position, role, MAF (Minor allele frequency) of cases and controls and HWE p-value of the three SNPs located in RAB40C gene. In these three SNPs, the minor allele G of rs62030917 was significantly associated with an increased alcohol-induced ONFH risk (OR = 1.47, 95% CI = 1.072.02, p = 0.017).

Table 2 Basic Information of the Three SNPs in This Study

Then, we used four genetic models (co-dominant, dominant, recessive, and log-additive models) to analyze the relationship between three SNPs and alcohol-induced ONFH risk (Table 3). The result indicated that carriers with G/A-G/G genotype in rs62030917 were more likely to have alcohol-induced ONFH risk compared with AA homozygous carriers (adjusted OR = 1.52, 95% CI=1.022.26, p = 0.039) in the dominant model. In the log-additive model, rs62030917 also increased the risk of alcohol-induced ONFH (adjusted OR = 1.42, 95% CI=1.051.93, p = 0.025).

Table 3 Association Analysis Between SNPs and Alcohol-Induced ONFH Risk

In addition, we also analyzed the association between these loci and the risk of alcoholic osteonecrosis by age stratification and hip lesions stratification (Table 4). Our results suggested that rs62030917 increased the risk of alcohol-induced ONFH among people 42 years old shown in the allele model (OR = 1.62, 95% CI = 1.042.54, p = 0.033), the co-dominant model (OR = 2.99, 95% CI = 1.088.30, p = 0.035), the recessive model (OR = 2.77, 95% CI = 1.037.47, p = 0.044) and the log-additive model (OR = 1.53, 95% CI = 1.002.33, p = 0.048). In patients with unilateral lesions vs controls, rs62030917 conveyed a increasing risk of alcohol-induced ONFH in the allele model (OR = 2.01, 95% CI = 1.233.29, p = 0.005), the co-dominant model (OR = 2.20, 95% CI = 1.084.45, p = 0.036; OR = 3.20, 95% CI = 1.089.48, p = 0.029), the dominant model (OR = 2.37, 95% CI = 1.224.61, p = 0.011) and the log-additive model (OR = 1.90, 95% CI = 1.183.08, p = 0.009). Likewise, rs2269556 also increased the risk of alcohol-induced ONFH (patients with unilateral lesions vs controls) in the allele model (OR = 1.70, 95% CI = 1.072.71, p = 0.023), the co-dominant model (OR = 2.83, 95% CI = 1.137.10, p = 0.027) and the log-additive model (OR = 1.68, 95% CI = 1.062.67, p = 0.028).

Table 4 Correlation Analysis of Rs62030917, Rs2269556 and Alcohol-Induced ONFH After Stratificated by Age and Hip Lesions in Different Genetic Models

Linkage disequilibrium (LD) blocks composed of rs62030917 and rs2269556 were found in unilateral lesions (Figure 1) and older than 42 years old groups (Figure 2), respectively. However, there are no statistically significant correlation between the risk of alcohol-induced ONFH and haplotype. Comparative analysis of plasma lipoprotein and lipid levels (TC, TG, HDL-C, LDL-C and PLT) in carrier with different genotypes of rs4984677, rs62030917 and rs2269556 was shown in Table 5. The results showed that carriers of AA, GA and GG genotypes in rs2269556 had LDL-C levels of 2.55 0.71 mmol/L, 2.78 0.83 mmol/L and 2.95 1.08 mmol/L, respectively, which were significantly different (p = 0.047). Among them, carriers of GG genotype had the highest LDL-C levels.

Table 5 Comparative Analysis of Plasma Lipoprotein and Lipid Levels in Carrier with Different Genotypes of Rs4984677, Rs62030917 and Rs2269556

Figure 1 In patients with unilateral lesions, LD plots containing three SNPs from RAB40C.

Figure 2 In patients older than 42 years old, LD plots containing three SNPs from RAB40C.

The pathogenesis of non-traumatic osteonecrosis is vascular injury, osteocyte death, or defective bone repair.19,20 Long term excessive drinking can lead to dyslipidemia and then induce ONFH.21,22 In recent years, people began to pay attention to the relationship between hereditary susceptibility and alcohol-induced ONFH.2325 Our study on the relationship RAB40C gene polymorphisms and alcohol-induced ONFH is the novel study.

The coding region of RAB40C contains 281 amino acids, which is longer than most small GTPases because it contains a unique SOCS box domain between the conserved GTPase domain and the pre-acylated C-terminal. Special SOCS box domain interacted with the elongated protein B/C and Cul5 modules, and binded with the ring finger proteins to form active ubiquitin ligases, which mediated a series of cellular processes.2628 Our previous work has proved that RAB40C is a novel LDs-related RAB protein.11 This is because there is a unique SOCS box domain of RAB40C, which is necessary for LDs cluster.14 As the proadipocytes differentiate into adipocytes, the expression of RAB40C increased. During the formation and maturation of LDs in adipocytes, RAB40C gradually accumulated to the surface of LDs. RAB40C knockout moderately reduced the size of LDs, suggesting that RAB40C is involved in the biological genetic process of LDs.29

Alcohol induces cell differentiation into adipocytes.30 With the increase of alcohol exposure time and concentration, the number of adipocytes was increased.31 In the alcohol treatment group, intracellular lipid deposition also occurred, which eventually leaded to the death of osteocytes.31,33 These effective findings suggested that alcohol can directly induce adipogenesis, reduce bone marrow mesenchymal osteogenesis, and produce intracellular lipid deposition leading to osteocyte death, which may be related to the occurrence of alcohol-induced ONFH.31 In view of the research, rs62030917 of RAB40C significantly increased the risk of alcohol-induced ONFH. In subjects with unilateral lesions, rs62030917 and rs2269556 increased the alcohol-induced ONFH risk. Rs62030917 increased the risk of alcohol-induced ONFH in people 42 years old.

To sum up, the expression of RAB40C gene increases the risk of alcohol-induced ONFH, which indicates that the gene polymorphisms of RAB40C may increase its risk of disease. There are limitations in the scope and quantity of sample selection in this study. In this study, patients and people from Northwest China were selected, which may be biased. In addition, the sample size of this study is small, and further verification of our results needs larger samples to support. Finally, some polymorphic loci with alcohol-induced ONFH have been screened out at the DNA level, and the relationship between polymorphisms and gene expression level has not yet been evaluated. Therefore, the relationship between polymorphisms and gene expression level needs to be evaluated at the RNA level and protein level. The study only provides a direction for alcohol-induced ONFH research.

Our study indicated that RAB40C gene polymorphism rs62030917 significantly increased the risk of alcohol-induced ONFH and it may be a risk locus. Our study provides a direction for the research on the mechanism of alcoholic osteonecrosis, but it still needs intensive study.

No funds were received in support of this work.

Chang Liu and Xuan Liu are co-first authors for this study. The authors declare that they have no conflicts of interest.

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2. Abu-Shakra M, Buskila D, Shoenfeld Y. Osteonecrosis in patients with SLE. Clin Rev Allergy Immunol. 2003;25(1):1324. doi:10.1385/CRIAI:25:1:13

3. Yu H, Liu P, Zhu D, et al. Chrysophanic acid shifts the differentiation tendency of BMSCs to prevent alcohol-induced osteonecrosis of the femoral head. Cell Proliferation. 2020;53(8):e12871.

4. Klein RF, Fausti KA, Carlos AS, Ng EL, Tang BL. Ethanol inhibits human osteoblastic cell proliferation. Alcohol Clin Exp Res. 1996;20(3):572578. doi:10.1111/j.1530-0277.1996.tb01095.x

5. Guo YJ, Luo SH, Tang MJ, et al. Muscone exerts protective roles on alcohol-induced osteonecrosis of the femoral head. Biomed Pharmacother. 2018;97:825832. doi:10.1016/j.biopha.2017.11.025

6. Li YZ, Wang Y, Guo YC, et al. OPG and RANKL polymorphisms are associated with alcohol-induced osteonecrosis of the femoral head in the north area of China population in men. Medicine. 2016;95(25):7.

7. Gaddini GW, Turner RT, Grant KA, Iwaniec UT. Alcohol: a Simple Nutrient with Complex Actions on Bone in the Adult Skeleton. Alcohol Clin Exp Res. 2016;40(4):657671. doi:10.1111/acer.13000

8. Yoon BH, Jones LC, Chen CH, et al. Etiologic Classification Criteria of ARCO on Femoral Head Osteonecrosis Part 2: alcohol-Associated Osteonecrosis. J Arthroplasty. 2019;34(1):169174.e161. doi:10.1016/j.arth.2018.09.006

9. Chen J, Liu W, Cao Y, et al. MMP-3 and MMP-8 single-nucleotide polymorphisms are related to alcohol-induced osteonecrosis of the femoral head in Chinese males. Oncotarget. 2017;8(15):2517725188. doi:10.18632/oncotarget.15587

10. Ng EL, Tang BL, Rab GT. Pases and their roles in brain neurons and glia. Brain Res Rev. 2008;58(1):236246.

11. Tan R, Xu X, Hong W, Wang T. Analysis of biogenesis of lipid droplets by examining Rab40c associating with lipid droplets. Methods Mol Biol. 2015;1270:125135.

12. Yang Q, Jie Z, Cao H, et al. Low-level expression of let-7a in gastric cancer and its involvement in tumorigenesis by targeting RAB40C. Carcinogenesis. 2011;32(5):713722. doi:10.1093/carcin/bgr035

13. Geybels MS, Alumkal JJ, Luedeke M, et al. Epigenomic profiling of prostate cancer identifies differentially methylated genes in TMPRSS2:ERG fusion-positive versus fusion-negative tumors. Clin Epigenetics. 2015;7:128. doi:10.1186/s13148-015-0161-6

14. Luo X, Li C, Tan R, et al. A RasGAP, DAB2IP, regulates lipid droplet homeostasis by serving as GAP toward RAB40C. Oncotarget. 2017;8(49):8541585427. doi:10.18632/oncotarget.19960

15. Song Y, Du Z, Ren M, et al. Association of gene variants of transcription factors PPARgamma, RUNX2, Osterix genes and COL2A1, IGFBP3 genes with the development of osteonecrosis of the femoral head in Chinese population. Bone. 2017;101:104112. doi:10.1016/j.bone.2017.05.002

16. Zhao D, Zhang F, Wang B, et al. Guidelines for clinical diagnosis and treatment of osteonecrosis of the femoral head in adults (2019 version). J Orthopaedic Translation. 2020;21:100110. doi:10.1016/j.jot.2019.12.004

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18. Gabriel S, Ziaugra L, Tabbaa D. SNP genotyping using the Sequenom MassARRAY iPLEX platform. Curr Protocols Human Genetics. 2009;2:12. doi:10.1002/0471142905.hg0212s60

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Mechanism of alcoholic osteonecrosis of the femoral head | IJGM - Dove Medical Press

Scientists have long contemplated a future where genome editing could alter the building blocks of our world to help humans live longer, healthier lives.

That dream is no longer a possibility, but a reality, thanks largely to the discovery of CRISPR and its ability to edit DNA. In 2020, Emmanuelle Charpentier and Jennifer A. Doudna won the Nobel Prize in Chemistry for the discovery, the first pair of women to do so.

In late June, scientists took a leap forward in proving CRISPRs power as a medical tool. Study results published in The New England Journal of Medicine showed that a one-time injection of the gene-editing system was extremely effective at treating patients with a rare genetic disease.

CRISPR is also being widely used in agriculture. Scientists are building genetically modifiedcrops that are better suited to the changing climate.

However, the hopes of CRISPR also bring significant, ethical hurdles that the international scientific community will have to face.

Genome editing is a powerful, scientific technology that can reshape medical treatments and peoples lives, but it can also harmfully reduce human diversity and increase social inequality by editing out the kinds of people that medical science, and the society it has shaped, categorize as diseased or genetically contaminatedpeoplewho are understood as having bad genes.

What promise does CRISPR hold in the coming years? And how do we manage its possible perils?

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The Hopes And Hurdles Of CRISPR And Gene Editing - New Hampshire Public Radio

DALLAS July 6, 2021 Using artificial intelligence, UT Southwestern scientists have identified thousands of genetic mutations likely to affect the immune system in mice. The work is part of one Nobel laureates quest to find virtually all such variations in mammals.

Bruce Beutler, M.D., director of the Center for the Genetics of Host Defense (CGHD)

This study identifies 101 novel gene candidates with greater than 95% chance of being required for immunity, says Bruce Beutler, M.D., director of the Center for the Genetics of Host Defense (CGHD) and corresponding author of the study published this week in the Proceedings of the National Academy of Sciences. Many of these candidates we have already verified by re-creating the mutations or knocking out the genes. Lead author Darui Xu, a computational biologist at CGHD, wrote the software.

Weve developed software called Candidate Explorer (CE) that uses a machine-learning algorithm to identify chemically induced mutations likely to cause traits related to immunity. The software determines the probability that any mutation weve induced will be verified as causative after further testing, Beutler says. His discovery of an important family of receptors that allow mammals to quickly sense infection and trigger an inflammatory response led to the 2011 Nobel Prize in Physiology or Medicine.

The purpose of CE is to help researchers predict whether a mutation associated with a phenotype (trait or function) is a truly causative mutation. CE has already helped us to identify hundreds of genes with novel functions in immunity. This will improve our understanding of the immune system so that we can find new ways to keep it robust, and also know the reason it sometimes falters, says Beutler, Regental Professor, and professor of immunology and internal medicine at UT Southwestern.

CE provides a score that tells us the likelihood that a particular mutation-phenotype association will be verified for cause and effect if we re-create the mutation or knock out the gene, he says.

CE examines 67 features of the primary genetic mapping data to arrive at an estimate of the likelihood of causation. For some mutations, causation is very clear; for others, less so. Over time, the program learns from experiments in which researchers re-create the mutation in a fresh pedigree and verify or exclude the hypothesis of causation. All mutations are made available to the scientific community through a public repository, and the data supporting causation are viewable within the Candidate Explorer program on the CGHD website, Mutagenetix.

The team used CE to evaluate about 87,000 mutation/trait associations that passed the initial statistical threshold for candidacy. The traits examined were flow cytometry data collected on circulating immune cells of third-generation mutant mice. In this screen, Candidate Explorer ranked a total of 2,336 mutations in 1,279 genes as good or excellent candidates for causation of traits, the team reports.

Beutler adds that this work is part of a research program he set out on nearly a decade ago to identify every mutation that may affect the mouse immune system.

Weve now worked through about 60% of the genome and have identified thousands of genes hundreds of them novel that participate in immunity in the mouse, he says.The vast majority of these also contribute to human immunity.

Beutler adds that the mouse and human genome are very similar in size and content of genes. Almost all mouse genes have a human counterpart, and vice versa, he says.

The current study focused on changes in cells known to be tied to immunity such as B cells, T cells, macrophages, and natural killer cells.

UTSW co-authors include: Stephen Lyon, Chun Hui Bu, Sara Hildebrand, Jin Huk Choi, Xue Zhong, Aijie Liu, Emre E. Turer, Zhao Zhang, Jamie Russell, Sara Ludwig, Elena Mahrt, Evan Nair-Gill, Hexin Shi, Ying Wang, Duanwu Zhang, Tao Yue, Kuan-wen Wang, Jeffrey A. SoRelle, Lijing Su, Takuma Misawa, William McAlpine, Lei Sun, Jianhui Wang, Xiaoming Zhan, Mihwa Choi, Roxana Farokhnia, Andrew Sakla, Sara Schneider, Hannah Coco, Gabrielle Coolbaugh, Braden Hayse, Sara Mazal, Dawson Medler, Brandon Nguyen, Edward Rodriguez, Andrew Wadley, Miao Tang, Xiaohong Li, Priscilla Anderton, Katie Keller, Amanda Press, Lindsay Scott, Jiexia Quan, Sydney Cooper, Tiffany Collie, Baifang Qin, Jennifer Cardin, Rochelle Simpson, Meron Tadesse, Qihua Sun, Carol A. Wise, Jonathan J. Rios, and Eva Marie Y. Moresco. Researchers in Japan and China also contributed to the study.

The work received support from the National Institutes of Health (grants R01 AI125581 and U19 AI100627).

Beutler holds the Raymond and Ellen Willie Distinguished Chair in Cancer Research, in Honor of Laverne and Raymond Willie, Sr.

About UTSouthwestern Medical Center

UTSouthwestern, one of the premier academic medical centers in the nation, integrates pioneering biomedical research with exceptional clinical care and education. The institutions faculty has received six Nobel Prizes, and includes 24 members of the National Academy of Sciences, 16 members of the National Academy of Medicine, and 13 Howard Hughes Medical Institute Investigators. The full-time faculty of more than 2,800 is responsible for groundbreaking medical advances and is committed to translating science-driven research quickly to new clinical treatments. UTSouthwestern physicians provide care in about 80 specialties to more than 117,000 hospitalized patients, more than 360,000 emergency room cases, and oversee nearly 3 million outpatient visits a year.

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UT Southwestern scientists closing in on map of the mammalian immune system - UT Southwestern

Researchers at OHSU have devised a method that delivers a 10-fold improvement in the amount of DNA that can be recovered from a single cell to be sequenced and interpreted. The finding, published in the journal Nature Biotechnology, is a big leap forward in the effort to understand cancer development, brain function and immunity. (Getty Images)

Researchers have devised a way to multiply by more than ten-fold the accessible details of gene activity in individual cells. Its a big leap in the effort to understand cancer development, brain function, immunity and other biological processes driven by the complex interactions of multitudes of different cell types.

Organs and tissues are made up of cells that may look the same, but individual cells can actually differ dramatically. Single-cell analysis allows the study of this cell-to-cell variation within an organ, tissue or cancerous tumor. But the research has been hampered by limits on the depth of information that can be gleaned at the single-cell level when working with large numbers of cells.

Andrew Adey, PH.D.

The downside has been the low-quality of single-cell profiles. Our method allows us to get a much more complete profile of any given single cell, said Andrew Adey, Ph.D., senior author of a paper in Nature Biotechnology describing the innovation. Adey is an associate professor of molecular and medical genetics in the OHSU School of Medicine.

He said the new method delivers about a ten-fold improvement in the amount of DNA that can be recovered from a single cell to be sequenced and interpreted. The genetic code is written in DNA in a sequence of units, called bases, that are like letters of an alphabet. Sequencing DNA reveals the order of the bases, and it is the first step to understanding the genetic makeup of a cell and whether particular genes are active or silent.

Single-cell studies are particularly important in understanding cancer. The cells of a tumor can be strikingly diverse. Different cells pick up different DNA mutations as the tumor grows, and some of the mutations and changes in gene activity give rise to sub-populations of tumor cells with new qualities, such as the ability to spread to other body parts or resist anti-cancer drugs.

Adey and colleagues showed that their method can be used to reveal DNA alterations that have emerged in a subset of cells in tumor samples taken from patients with pancreatic cancer. Thats important because it can help researchers understand how populations of tumor cells evolve and become deadly.

For example, you can potentially identify rare cell subtypes within a tumor that are resistant to therapy, Adey said. His team has already begun working with OHSU Knight Cancer Institute researchers testing the single-cell method as a way find out if some of the cells in a patients tumor have evolved resistance to a particular chemo drug or targeted therapy. That knowledge could be used to develop individualized treatment plans for patients.

If you are working with something like a cancer biopsy from a patient, a very small piece of tissue, you really want to make every cell count, you really have to get a lot of info from each single cell, Adey said.

The new method builds on a technique called single-cell combinatorial indexed sequencing, which Adey and colleagues developed earlier. Its a way to generate DNA libraries collections of DNA fragments that can be used to analyze genes and mutations for thousands of single cells at the same time. The process uses an enzymatic reaction to attach primers to the ends of the DNA fragments. They are kind of like handles the sequencer uses to start reading, Adey says.

While the technique greatly increases the number of single cells that can be analyzed in one experiment, it comes with the tradeoff of sparse coverage of readable DNA sequences per cell. To be readable, a primer must be attached at both ends of the DNA fragment, which the reaction accomplishes only half of the time.

The new method results in all library fragments having primers on both ends, while also improving efficiency in other ways. The researchers said the efficiency has the added benefit of reducing sequencing costs by about one third.

The adapters are designed such that standard sequencing recipes can be used instead of the custom workflows and primers that are required for competing methods. That makes the method compatible with many different tests commonly used to explore the state of single cells.

This chemistry can just slot into many other assays, Adey said. People can just start using it.

This research was supported by the National Institutes of Health (grants R01DA047237, R35GM124704, and R01MH113926).

In our interest of ensuring the integrity of our research and as part of our commitment to public transparency, OHSU actively regulates, tracks and manages relationships that our researchers may hold with entities outside of OHSU. In regards to this research, Andrew Adey and OHSU colleague Ryan M. Mulqueen are authors on licensed patents that cover components of the technologies described here. Review details of OHSU's conflict of interest program to find out more about how we manage these business relationships.

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Innovation massively expands view into workings of single cells - OHSU News