[Role of probiotics in treatment of nonalcoholic fatty liver disease]

Nonalcoholic fatty liver disease (NAFLD) is one of the most common chronic liver diseases in China and manifests as simple fatty liver, non-alcoholic steatohepatitis, liver cirrhosis, and hepatocellular carcinoma. Studies have shown that intestinal flora can affect the development and progression of NAFLD via the "gut-liver axis" . Probiotics are active microorganisms with beneficial effects on the host, and more and more studies have found that probiotics play a positive role in improving NAFLD. They are cheaper, less harmful, and safer compared with antibiotics and surgery, and therefore, it may become a new method for the prevention and treatment of NAFLD. This article reviews the research advances in probiotics in the treatment of NAFLD, in order to provide a basis for the treatment of NAFLD using probiotics.

Mutation Detection in Patients With Advanced Cancer by Universal Sequencing of Cancer-Related Genes in Tumor and Normal DNA vs Guideline-Based Germline Testing

IMPORTANCE

Guidelines for cancer genetic testing based on family history may miss clinically actionable genetic changes with established implications for cancer screening or prevention.

OBJECTIVE

To determine the proportion and potential clinical implications of inherited variants detected using simultaneous sequencing of the tumor and normal tissue ("tumor-normal sequencing") compared with genetic test results based on current guidelines.

DESIGN, SETTING, AND PARTICIPANTS

From January 2014 until May 2016 at Memorial Sloan Kettering Cancer Center, 10 336 patients consented to tumor DNA sequencing. Since May 2015, 1040 of these patients with advanced cancer were referred by their oncologists for germline analysis of 76 cancer predisposition genes. Patients with clinically actionable inherited mutations whose genetic test results would not have been predicted by published decision rules were identified. Follow-up for potential clinical implications of mutation detection was through May 2017.

EXPOSURE

Tumor and germline sequencing compared with the predicted yield of targeted germline sequencing based on clinical guidelines.

MAIN OUTCOMES AND MEASURES

Proportion of clinically actionable germline mutations detected by universal tumor-normal sequencing that would not have been detected by guideline-directed testing.

RESULTS

Of 1040 patients, the median age was 58 years (interquartile range, 50.5-66 years), 65.3% were male, and 81.3% had stage IV disease at the time of genomic analysis, with prostate, renal, pancreatic, breast, and colon cancer as the most common diagnoses. Of the 1040 patients, 182 (17.5%; 95% CI, 15.3%-19.9%) had clinically actionable mutations conferring cancer susceptibility, including 149 with moderate- to high-penetrance mutations; 101 patients tested (9.7%; 95% CI, 8.1%-11.7%) would not have had these mutations detected using clinical guidelines, including 65 with moderate- to high-penetrance mutations. Frequency of inherited mutations was related to case mix, stage, and founder mutations. Germline findings led to discussion or initiation of change to targeted therapy in 38 patients tested (3.7%) and predictive testing in the families of 13 individuals (1.3%), including 6 for whom genetic evaluation would not have been initiated by guideline-based testing.

CONCLUSIONS AND RELEVANCE

In this referral population with selected advanced cancers, universal sequencing of a broad panel of cancer-related genes in paired germline and tumor DNA samples was associated with increased detection of individuals with potentially clinically significant heritable mutations over the predicted yield of targeted germline testing based on current clinical guidelines. Knowledge of these additional mutations can help guide therapeutic and preventive interventions, but whether all of these interventions would improve outcomes for patients with cancer or their family members requires further study.

TRIAL REGISTRATION

clinicaltrials.gov Identifier: NCT01775072.

Biomechanic Factors Associated With Orbital Floor Fractures

Importance

Orbital floor fractures are commonly seen in clinical practice, yet the etiology underlying the mechanism of fracture is not well understood. Current research focuses on the buckling theory and hydraulic theory, which implicate trauma to the orbital rim and the globe, respectively.

Objective

To elucidate and define the biomechanical factors involved in an orbital floor fracture.

Design, Setting, and Participants

A total of 10 orbits from 5 heads (3 male and 2 female) were used for this study. These came from fresh, unfixed human postmortem cadavers that were each selected so that the cause of death did not interfere with the integrity of orbital walls. Using a drop tower with an accelerometer, we measured impact force on the globe and rim of cadaver heads affixed with strain gauges.

Results

The mean impacts for rim and globe trauma were 3.9 J (95% CI, 3.4-4.3 J) and 3.9 J (95% CI, 3.5-4.3 J), respectively. Despite similar impact forces to the globe and rim, strain-gauge data displayed greater mean strain for globe impact (6563 μS) compared with rim impact (3530 μS); however, these data were not statistically significant (95% CI, 3598-8953 μS; P = .94).

Conclusions and Relevance

Our results suggest that trauma directly to the globe predisposes a patient to a more posterior fracture while trauma to the rim demonstrates an anterior predilection. Both the hydraulic and buckling mechanisms of fracture exist and demonstrate similar fracture thresholds.

Level of Evidence

NA.

The association of post-discharge adverse events with timely follow-up visits after hospital discharge

OBJECTIVE

There has been little research to examine the association of post-discharge adverse events (AEs) with timely follow-up visits after hospital discharge. We aimed to examine whether having a timely follow-up outpatient visit would reduce the risk for post-discharge AEs.

METHODS

This was a methods study of patients at risk for post-discharge AEs from December 2011 through October 2012. Five hundred and forty-five patients who were under the care of hospitalist physicians and were discharged home from a community hospital, spoke English, and could be contacted after discharge were evaluated. The aim of the study was to examine the association of post-discharge AEs with timely follow-up visits after hospital discharge based on structured telephone interviews, health record review, and adjudication by two blinded, trained physicians using a previously established methodology.

RESULTS

We observed a higher incidence of AEs with patients that had their first follow-up visit within 7 days after hospital discharge (33.5% vs. 23.0%, p = 0.007). This effect was attenuated somewhat but remained significant when adjusted for several patient factors (adjusted OR 1.33, 95% confidence interval 1.16-2.71).

CONCLUSION

This observational study paradoxically showed an increase in post-discharge AEs with early follow-up, likely a result of confounding by indication and/or information bias that could not be completely adjusted for. This study illustrates the potential hazards with conducting observational studies to determine the efficacy of various transitional care interventions, such as early follow-up, where risk for confounding by indication is high.

Descemet's Membrane Supports Corneal Endothelial Cell Regeneration in Rabbits

Descemet’s membrane (DM) helps maintain phenotype and function of corneal endothelial cells under physiological conditions, while little is known about the function of DM in corneal endothelial wound healing process. In the current study, we performed in vivo rabbit corneal endothelial cell (CEC) injury via CEC scraping, in which DM remained intact after CECs removal, or via DM stripping, in which DM was removed together with CECs. We found rabbit corneas in the CEC scraping group healed with transparency restoration, while there was posterior fibrosis tissue formation in the corneas after DM stripping on day 14. Following CEC scraping on day 3, cells that had migrated toward the central cornea underwent a transient fibrotic endothelial-mesenchymal transition (EMT) which was reversed back to an endothelial phenotype on day 14. However, in the corneas injured via DM stripping, most of the cells in the posterior fibrosis tissue did not originate from the corneal endothelium, and they maintained fibroblastic phenotype on day 14. We concluded that corneal endothelial wound healing in rabbits has different outcomes depending upon the presence or absence of Descemet’s membrane. Descemet’s membrane supports corneal endothelial cell regeneration in rabbits after endothelial injury.

Profuse color-evolution-based fluorescent test paper sensor for rapid and visual monitoring of endogenous Cu2+ in human urine

The fluorescent paper for colorimetric detection of metal ions has been widely fabricated using various sensing probes, but it still remains an elusive task to design a test paper with multicolor variation with target dosages for accurate determination. Herein, we report a profuse color-evolution-based fluorescent test paper sensor for rapid and visual monitoring of Cu²⁺ in human urine by printing tricolor probe onto filter paper. The tricolor probe consists of blue-emission carbon dots (bCDs), green-emission quantum dots (gQDs) and red-emission quantum dots (rQDs), which is based on the principle that the fluorescence of gQDs and rQDs are simultaneously quenched by Cu²⁺, whereas the bCDs as the photostable internal standard is insensitive to Cu²⁺. Upon the addition of different amounts of Cu²⁺, the ratiometric fluorescence intensity of the tricolor probe continuously varied, leading to color changes from shallow pink to blue with a detection limit of 1.3nM. When the tricolor probe solution was printed onto a sheet of filter paper, as-obtained test paper displayed a more profuse color evolution from shallow pink to light salmon to dark orange to olive drab to dark olive green to slate blue to royal blue and to final dark blue with the increase of Cu²⁺ concentration compared with dual-color probe-based test paper, and dosage scale as low as 6.0nM was clearly discriminated. The sensing test paper is simple, rapid and inexpensive, and serves as a visual platform for ultrasensitive monitoring of endogenous Cu²⁺ in human urine.

Overall survival in lower IPSS risk MDS by receipt of iron chelation therapy, adjusting for patient-related factors and measuring from time of first red blood cell transfusion dependence: an MDS-CAN analysis

Analyses suggest iron overload in red blood cell (RBC) transfusion-dependent (TD) patients with myleodysplastic syndrome (MDS) portends inferior overall survival (OS) that is attenuated by iron chelation therapy (ICT) but may be biassed by unbalanced patient-related factors. The Canadian MDS Registry prospectively measures frailty, comorbidity and disability. We analysed OS by receipt of ICT, adjusting for these patient-related factors. TD International Prognostic Scoring System (IPSS) low and intermediate-1 risk MDS, at RBC TD, were included. Predictive factors for OS were determined. A matched pair analysis considering age, revised IPSS, TD severity, time from MDS diagnosis to TD, and receipt of disease-modifying agents was conducted. Of 239 patients, 83 received ICT; frailty, comorbidity and disability did not differ from non-ICT patients. Median OS from TD was superior in ICT patients (5·2 vs. 2·1 years; P < 0·0001). By multivariate analysis, not receiving ICT independently predicted inferior OS, (hazard ratio for death 2·0, P = 0·03). In matched pair analysis, OS remained superior for ICT patients (P = 0·02). In this prospective, non-randomized analysis, receiving ICT was associated with superior OS in lower IPSS risk MDS, adjusting for age, frailty, comorbidity, disability, revised IPSS, TD severity, time to TD and receiving disease-modifying agents. This provides additional evidence that ICT may confer clinical benefit.

Abstract 4280: FH (rs367543046, chr1:241661227 A/ATTT) heterozygous carrier status does not confer risk to hereditary leiomyomatosis and renal cell cancer (HLRCC) and prostate cancer

Fumarate Hydratase (FH) mutations underpin the autosomal recessive syndrome Fumarate Hydratase deficiency and the autosomal dominant syndrome Hereditary Leiomyomatous and Renal Cell Carcinoma (HLRCC). The variant rs367543046, a duplication leading to p. Lys477_Asn478insLys in FH has strong evidence for risk towards fumarate hydratase deficiency when occurring in trans to another germline alteration in the FH gene. In addition, this variant in the heterozygous state has been reported in ClinVar to predispose to the autosomal dominant condition HLRCC, given other heterozygous mutations have shown to be pathogenic. Population level data is sparse to determine the variant’s impact in the heterozygous state. Here, we show in a series of 1375 cancer cases the (rs367543046, chr1: 241661227 A/ATTT), variant detected in 7 (0.5%) individuals with cancer. One patient with bladder cancer had a history of uterine leiomyomas, but the immunohistochemistry for 2SC was negative, suggesting that the leiomyomas were not associated with HLRCC. None of the other 6 carriers of this variant had any features of HLRCC. Notably, this variant was not detected in any of the patients with renal cancer (n=178) participating in the study. Since 4/7 prostrate cancer patients of Ashkenazi ethnicity harbored this variant, we performed a genetic epidemiology study using 856 Ashkenazi Jewish prostate cancer patients. The allele frequencies were compared with 557 Ashkenazi Jewish non-cancer controls. A fisher’s two sided exact test showed that the variant is not associated with prostate cancer in Jews (P=1, OR 1.12(CI 95% 0.21-7.25). Our findings suggest that the variant, which is pathogenic for autosomal recessive fumarate hydratase deficiency does not confer pathogenicity in the heterozygous form for Hereditary Leiomyomatous and Renal Cell Carcinoma or prostate cancer.

Ashkenazi Jewish Prostate Cancer Patients vs Ashkenazi Jewish Non-Cancer PatientsAttributeAshkenazi Jewish Prostate Cancer PatientsAshkenazi Jewish Non-Cancer patientsCT53CC17071151

Citation Format: Michael F. Walsh, Diana Mandelker, Joseph Vijai, David Musheyev, Jennifer Kennedy, Zsofia Stadler, Yelena Kemel, Sabine Topka, Karen Cadoo, Maria Carlo, Marc Ladanyi, Mark Robson, Kenneth Offit, Liying Zhang. FH (rs367543046, chr1:241661227 A/ATTT) heterozygous carrier status does not confer risk to hereditary leiomyomatosis and renal cell cancer (HLRCC) and prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4280. doi:10.1158/1538-7445.AM2017-4280

Prospective Genomic Profiling of Prostate Cancer Across Disease States Reveals Germline and Somatic Alterations That May Affect Clinical Decision Making

PURPOSE

A long natural history and a predominant osseous pattern of metastatic spread are impediments to the adoption of precision medicine in patients with prostate cancer. To establish the feasibility of clinical genomic profiling in the disease, we performed targeted deep sequencing of tumor and normal DNA from patients with locoregional, metastatic non-castrate, and metastatic castration-resistant prostate cancer (CRPC).

METHODS

Patients consented to genomic analysis of their tumor and germline DNA. A hybridization capture-based clinical assay was employed to identify single nucleotide variations, small insertions and deletions, copy number alterations and structural rearrangements in over 300 cancer-related genes in tumors and matched normal blood.

RESULTS

We successfully sequenced 504 tumors from 451 patients with prostate cancer. Potentially actionable alterations were identified in DNA damage repair (DDR), PI3K, and MAP kinase pathways. 27% of patients harbored a germline or a somatic alteration in a DDR gene that may predict for response to PARP inhibition. Profiling of matched tumors from individual patients revealed that somatic TP53 and BRCA2 alterations arose early in tumors from patients who eventually developed metastatic disease. In contrast, comparative analysis across disease states revealed that APC alterations were enriched in metastatic tumors, while ATM alterations were specifically enriched in CRPC.

CONCLUSION

Through genomic profiling of prostate tumors representing the disease clinical spectrum, we identified a high frequency of potentially actionable alterations and possible drivers of disease initiation, metastasis and castration-resistance. Our findings support the routine use of tumor and germline DNA profiling for patients with advanced prostate cancer, for the purpose of guiding enrollment in targeted clinical trials and counseling families at increased risk of malignancy.

Abstract 1281: Germline mutations in NBN conferring DNA damage response defects are found in patients with multiple cancer types

Nibrin, the protein encoded by the NBN gene forms a complex with Mre11 and Rad51 (MRN complex) that is crucial for DNA damage repair. Mutations in NBN are found in &gt;90% of patients with Nimjegen breakage syndrome (NBS), an autosomal recessive disorder characterized by growth retardation, microcephaly, radiosensitivity, immunodeficiency and increased cancer risk. Most of NBS patients harbor the common founder mutation c.657del5 that leads to expression of a hypomorphic 70kDa C-terminal fragment produced by alternative translation initiation. Cell lines derived from these patients show increased sensitivity to DNA-damaging agents, chromosome instability, and abnormal cell cycle checkpoint function. Several studies have addressed cancer incidence in individuals with germline NBN mutations, showing increased cancer risk for individuals harboring the c.657del5 founder mutation and for carriers of the R215W missense mutation across multiple cancer types. For other NBN mutations conflicting reports exist as to their association with cancer risk. Here, we report newly identified NBN germline frameshift and truncating mutations in patients with multiple cancer types, including prostate, lung, breast cancer, acute lymphocytic leukemia, and chronic lymphocytic leukemia. Modeling these mutations in an NBN-deficient cellular background showed expression of a novel C-terminal truncated fragment that can bind to Mre11. Cells expressing these mutant proteins display attenuated DNA damage repair function and decreased overall survival following induction of DNA damage. Impaired Chk2 phosphorylation was also observed, indicating cell cycle checkpoint deficiencies. Thus, the NBN germline mutations identified here could contribute to genomic instability predisposing to tumorigenesis. Further in vitro studies with these and additional germline mutations occurring in cancer patients are ongoing, in order to better understand the role of this pathway of DNA damage repair in susceptibility to malignancies.

Citation Format: Sabine Topka, Michael F. Walsh, Ann Maria, Annie Lincoln, Diana Mandelker, Liying Zhang, Marc Ladanyi, Michael F. Berger, Mark E. Robson, Joseph Vijai, Kenneth Offit. Germline mutations in NBN conferring DNA damage response defects are found in patients with multiple cancer types [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1281. doi:10.1158/1538-7445.AM2017-1281

Ectodysplasin A protein promotes corneal epithelial cell proliferation

The EDA gene encodes ectodysplasin A (Eda), which if mutated causes X-linked hypohidrotic ectodermal dysplasia (XLHED) disease in humans. Ocular surface changes occur in XLHED patients whereas its underlying mechanism remains elusive. In this study, we found Eda was highly expressed in meibomian glands, and it was detected in human tears but not serum. Corneal epithelial integrity was defective and the thickness was reduced in the early postnatal stage of Eda mutant Tabby mice. Corneal epithelial cell proliferation decreased and the epithelial wound healing was delayed in Tabby mice, whereas it was restored by exogenous Eda. Eda exposure promoted mouse corneal epithelial wound healing during organ culture, whereas scratch wound assay showed that it did not affect human corneal epithelial cell line migration. Epidermal growth factor receptor (EGFR), phosphorylated EGFR (p-EGFR), and phosphorylated ERK1/2 (p-ERK) were down-regulated in Tabby mice corneal epithelium. Eda treatment up-regulated the expression of Ki67, EGFR, p-EGFR, and p-ERK in human corneal epithelial cells in a dose-dependent manner. In conclusion, Eda protein can be secreted from meibomian glands and promotes corneal epithelial cell proliferation through regulation of the EGFR signaling pathway. Eda release into the tears plays an essential role in the maintenance of corneal epithelial homeostasis.

Discovery and prevalence of cancer-susceptibility germline mutations (Mts) in patients (Pts) with advanced renal cell carcinoma (aRCC)

4524

Background: About 5% of RCC is thought to be familial, but recent studies suggest this may be an underestimate (Int. J. Cancer;100:476). We studied the prevalence of germline cancer-susceptibility mts in pts with aRCC. Methods: Pts with aRCC (stage III or IV), unselected for suspicion of an inherited cancer syndrome, were offered germline testing for 76 cancer-associated genes between 10/2015 and 12/2016. Germline sequencing was done as part of MSK-IMPACT, a matched tumor-normal next-generation sequencing platform. Results: 203/213 pts accepted testing (median age 55, range 13-55) of whom 73% had clear cell RCC (ccRCC), 92% had metastases, 20% were early onset (≤46 yrs at diagnosis), 9% had a family history of RCC, 6% multifocal RCC at diagnosis, and 15% ≥2 primary malignancies. Pathogenic/likely pathogenic mts were found in 35 pts (17%): 12 (6%) with mts in genes associated with familial RCC; 10 (5%) mts in high/moderate penetrance genes not linked to RCC (Table).13 (6%) had mts in genes of low/uncertain penetrance or for autosomal recessive disease. Mts were present in 15% of ccRCC and 19% of non-ccRCC. Mts were not more common in pts with early onset, family history, multifocal RCC, or ≥2 malignancies (p>0.1 for each by Fisher’s exact test). Notably, 4/12 pts with mts in familial RCC genes did not meet the American College of Medical Genetics (ACMG) criteria for testing (1 each VHL, BAP1, SDHA, FH). Prevalence of CHEK2 mts was compared to population databases (ExAC); CHEK2 conferred a relative risk of 10.9 (p< 0. 002; CI=3.9-24.7) for RCC. Conclusions: 17% of aRCC pts had a germline mutation in a cancer-associated gene of which 33% of the high penetrance RCC germline mts were not identified using standard clinical criteria, providing rationale for broad testing. Once the increased risk is confirmed, CHEK2 should be included in RCC genetic testing. [Table: see text]

Cancer predisposing germline mutations in patients (pts) with urothelial cancer (UC) of the renal pelvis (R-P), ureter (U) and bladder (B)

4510

Background: Urothelial cancers (UC) are suspected to have a substantial hereditary component, but other than highly penetrant genes such as those in mismatch-repair pathway (e.g. MSH2) typically associated with R-P/U primaries, heritable gene mutations have not been systematically studied. We sought to investigate the prevalence of known cancer pre-disposing germline mutations in pts with UC originating from all sites within the urinary tract. Methods: Pts with R-P, U and B primaries, unselected for suspicion of inherited cancer syndrome, were prospectively enrolled from medical oncology and urology clinics to a germline sequencing protocol from June 2016 to January 2017. Germline gene analysis was performed in a CLIA-certified lab using a next generation sequencing (NGS) platform (MSK-IMPACT) that analyzes tumor-normal DNA pairs. The germline gene panel consisted of 76 genes associated with hereditary cancer predisposition. Results: As of January 24, 2017, 101 pts have NGS results available, with median age 63 (31-87), 76% male, 24% female. Primary sites were B (67%), R-P/U (31%), or both (3%). 73% had organ-confined disease and 27% had metastases. 8% had early onset (≤45 yrs at diagnosis), 10% had a family history of UC, 25% had documented non-UC cancers. 25 pathogenic or likely pathogenic (P-LP) mutations were identified in 22 patients. P-LP mutations were present in 29% of pts with R-P/U primaries and 18% of pts with B primaries. 12 DNA damage response gene alterations were found (4 CHEK2, 3 BRCA1, 2 BRCA2, 1 ATM, 1 BRIP1, 1 NBN) and 8 in Lynch syndrome associated genes (5 MSH2, 2 MSH6, 1 MLH1). Other mutations include 2 APC, 1 TP53, and 1 FH. Notably 3 pts had 2 alterations each ( MSH6/ APC, BRCA2/ APC, BRCA1/ CHEK2). 9/22 pts with P-LP mutations did not meet American College of Medical Genetics criteria for genetic screening. Conclusions: 22% of UC pts had a germline mutation in a cancer-associated gene. There was an unexpectedly high frequency of pts with DNA-repair pathway mutations. Active accrual is ongoing to define the full spectrum of alterations. These results have profound implications for genetic counseling and screening and further studies are warranted.

Multi gene panel testing in unselected patients (pts) with endometrial cancer (EC)

e17119

Background: Inherited mutations (muts) in Lynch Syndrome genes (LS) & PTEN are associated with EC. The prevalence of other cancer predisposition genes is unclear. The majority of studies have selected pts by age, family history or specific tumor features. We sought the prevalence of cancer predisposition genes in unselected pts attending for surgical consultation. Methods: 03/2016-10/2016, pts with new EC diagnosis were offered to consent to an IRB approved protocol. Tumor-normal sequencing, was performed via a custom next-generation sequencing panel (MSK-IMPACT) with return of results for 76 cancer predisposition genes. Per institutional standard, all ECs undergo reflex screening for LS with IHC for mismatch repair proteins (MMR P). Results:77 pts consented, median age 60 (27-84), median BMI 27 (16-66), 27% Ashkenazi Jewish (AJ) descent. Tumors: 56 (73%) stage 1, remainder stage 3 or 4, majority (52, 68%) endometrioid histology, of which 31 (60%) grade 1. 15 pathogenic germline variants were identified in 14 pts (18%) including 3 (4%) in LS genes (2 MSH6, 1 MLH1) with corresponding abnormal MMR P. One pt with a known BRCA1 mutation, without prior cancer, with prior risk reducing salpingo-oophorectomy had stage III grade 3 endometrioid EC at 47 yo, tumor LOH at BRCA1 was identified. Of the 4 pts with high-penetrance muts, 3 met criteria for genetic testing for the implicated gene due to personal/family cancer history, 1 pt with MSH6 mutation was identified via absent MMR P only. The remaining 11 pathogenic variants were incremental findings in moderate penetrance ( CHEK2 I157T, MRE11, ATM, APC I1307K, MUTYH) or autosomal recessive genes ( MUTYH, RECQL4, ATM). 5 pt had moderate penetrance variants in known AJ founder muts. Conclusions: In this cohort of unselected EC pts the prevalence of LS was as expected & reflex IHC screening captured all pts appropriately. While all high-penetrance muts were captured by clinical criteria, the incremental identification of moderate penetrance muts in these largely early stage/ low risk EC pts may alter personal & at-risk family member breast & colon cancer screening recommendations. Continuing accrual will reveal the extent to which additional high penetrance genes are seen in unselected EC pts.

Next-generation sequencing (NGS) of tissue and cell free DNA (cfDNA) to identify somatic and germline alterations in advanced prostate cancer

5010

Background: With the goal of accelerating enrollment onto appropriate clinical trials, we performed prospective genomic characterization of pts with advanced prostate cancer. Given the long natural history and osseous disease predominance, we also analyzed plasma cfDNA to assess the feasibility of identifying targetable alterations in pts for whom adequate tumor tissue was unavailable. Methods: 1038 tumors from 896 pts along with matched normal DNA were analyzed with a capture-based NGS assay (MSK-IMPACT) targeting 341–468 genes. In 5/2015, the protocol was amended to allow pts to opt-in for a formal germline analysis of 76 genes associated with heritable cancer risk. In select pts, plasma cfDNA was collected and analyzed using the same assay. Results: Between 2/2014 and 2/2017, 576 primary tumors and 462 metastases were sequenced. The most notable finding was the high frequency of known or likely pathogenic germline and somatic mutations in genes that regulate DNA damage response (DDR). In the subset with both tumor and germline analysis, 28.84% (169/586) had a DDR mutation identified compared to only 10.65% (33/310) of pts with somatic only analysis. In the subset with tumor and germline analysis, 9.39% (55/586) had somatic only DDR mutations and 16.38% (96/586) had germline only DDR mutations, including 8 pts with two germline mutations. 3.07% (18/586) had co-occurring somatic and germline DDR mutations, with only 0.68% (4/586) involving the same DDR gene (all BRCA2). Prostate cancer had the highest tissue failure rate among the overall MSK-IMPACT solid tumor cohort, and bone biopsy-derived tissue was successfully sequenced in only 42% of pts. Profiling of cfDNA did identify somatic DDR or AR mutations in 12.5% (4/32) of pts without adequate tumor for analysis. Conclusions: This prospective genomic profiling effort identified frequent somatic and germline DDR mutations that may guide PARPi or platinum therapy. Both somatic and germline analyses were required to identify all pts with likely pathogenic DDR alterations. NGS-based cfDNA analysis is feasible in advanced prostate cancer and may identify mutations missed by tumor only sequencing.

Comprehensive detection of germline variants by MSK-IMPACT, a clinical diagnostic platform for solid tumor molecular oncology and concurrent cancer predisposition testing

Background

The growing number of Next Generation Sequencing (NGS) tests is transforming the routine clinical diagnosis of hereditary cancers. Identifying whether a cancer is the result of an underlying disease-causing mutation in a cancer predisposition gene is not only diagnostic for a cancer predisposition syndrome, but also has significant clinical implications in the clinical management of patients and their families.

Methods

Here, we evaluated the performance of MSK-IMPACT (Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets) in detecting genetic alterations in 76 genes implicated in cancer predisposition syndromes. Output from hybridization-based capture was sequenced on an Illumina HiSeq 2500. A custom analysis pipeline was used to detect single nucleotide variants (SNVs), small insertions/deletions (indels) and copy number variants (CNVs).

Results

MSK-IMPACT detected all germline variants in a set of 233 unique patient DNA samples, previously confirmed by previous single gene testing. Reproducibility of variant calls was demonstrated using inter- and intra- run replicates. Moreover, in 16 samples, we identified additional pathogenic mutations other than those previously identified through a traditional gene-by-gene approach, including founder mutations in BRCA1, BRCA2, CHEK2 and APC, and truncating mutations in TP53, TSC2, ATM and VHL.

Conclusions

This study highlights the importance of the NGS-based gene panel testing approach in comprehensively identifying germline variants contributing to cancer predisposition and simultaneous detection of somatic and germline alterations.

Electronic supplementary material

The online version of this article (doi:10.1186/s12920-017-0271-4) contains supplementary material, which is available to authorized users.

Kinetics of iron absorption by in situ ligated small intestinal loops of broilers involved in iron transporters

Two experiments were conducted with 28-d-old commercial male broilers to study the kinetics of iron (Fe) absorption and the effect of Fe treatment on divalent metal transporter 1 (DMT1) and ferroportin 1 (FPN1) mRNA levels in in situ ligated segments from different small intestinal regions of broilers. In Exp. 1, we compared Fe absorption in 3 small intestinal segments at different post-perfusion time points after perfusion with 0.45 m of Fe as Fe sulfate (FeSO ∙ 7HO), and found that the Fe absorption in the duodenum at 30, 45, and 60 min was greater ( < 0.006) than that in the jejunum, and at 60 min, the Fe absorption in the duodenum was greater ( = 0.034) than that in the ileum. In addition, the Fe absorption at 30 min was more than 85.0% of the maximum absorption in each segment. In Exp. 2, a kinetic study of Fe absorption was performed with the duodenal, jejunal, and ileal loops perfused with solutions containing 0 (control), 0.11, 0.22, 0.45, 0.80, 1.79, or 3.58 m of Fe as FeSO 7HO. The Fe concentrations in perfusates were measured at 30 min after perfusion, and in the control group and the group treated with 0.45 m Fe as FeSO 7HO, the DMT1 and FPN1 mRNA levels in the ligated duodenum, jejunum, and ileum were analyzed. The kinetic curves of Fe absorption showed that Fe absorption in the duodenum and jejunum depended on a saturated carrier-mediated process. The maximum absorption rate in the duodenal segment was greater ( < 0.0001) than that in the jejunum (42.75 vs. 8.16 nmol × cm × min), and the Michaelis-Menten constant value was higher ( < 0.0001) in the duodenum than in the jejunum (6.16 vs. 1.31 m). In the ileum, however, the Fe absorption was a non-saturated diffusion process, and the diffusive constant was 3.54 × 10 cm × min. The DMT1 and FPN1 mRNA levels in the duodenum were greater ( < 0.0001) than those in the jejunum and ileum, and greater ( < 0.009) in the jejunum than in the ileum. No differences ( > 0.25) were detected in the DMT1 and FPN1 mRNA levels of the duodenum or jejunum and the DMT1 mRNA level of the ileum between the control and the 0.45 m Fe group, but Fe perfusion increased ( < 0.03) FPN1 mRNA level in the ileum. The above results indicate that the duodenum is the main site of Fe absorption in the small intestine of broilers, and Fe absorption in the duodenum and jejunum is a saturated carrier-mediated process, but a non-saturated diffusion process in the ileum.