Decoding Heterogenous Single-cell Perturbation Responses

Understanding diverse responses of individual cells to the same perturbation is central to many biological and biomedical problems. Current methods, however, do not precisely quantify the strength of perturbation responses and, more importantly, reveal new biological insights from heterogeneity in responses. Here we introduce the perturbation-response score (PS), based on constrained quadratic optimization, to quantify diverse perturbation responses at a single-cell level. Applied to single-cell transcriptomes of large-scale genetic perturbation datasets (e.g., Perturb-seq), PS outperforms existing methods for quantifying partial gene perturbation responses. In addition, PS presents two major advances. First, PS enables large-scale, single-cell-resolution dosage analysis of perturbation, without the need to titrate perturbation strength. By analyzing the dose-response patterns of over 2,000 essential genes in Perturb-seq, we identify two distinct patterns, depending on whether a moderate reduction in their expression induces strong downstream expression alterations. Second, PS identifies intrinsic and extrinsic biological determinants of perturbation responses. We demonstrate the application of PS in contexts such as T cell stimulation, latent HIV-1 expression, and pancreatic cell differentiation. Notably, PS unveiled a previously unrecognized, cell-type-specific role of coiled-coil domain containing 6 (CCDC6) in guiding liver and pancreatic lineage decisions, where CCDC6 knockouts drive the endoderm cell differentiation towards liver lineage, rather than pancreatic lineage. The PS approach provides an innovative method for dose-to-function analysis and will enable new biological discoveries from single-cell perturbation datasets.

One sentence summary

We present a method to quantify diverse perturbation responses and discover novel biological insights in single-cell perturbation datasets.

Comparison of Two Different Adjuvant High Dose Rate Vaginal Brachytherapy Fractionation Regimens in Early-Stage Endometrial Cancer

PURPOSE/OBJECTIVE(S)

Adjuvant vaginal brachytherapy (VBT) as monotherapy is commonly used as treatment for early-stage uterine cancer following hysterectomy. No ABS guidelines existed at the onset of our institution's high dose rate (HDR) brachytherapy program, so a regimen of 30 Gy in six fractions was adopted in this setting. Due to the COVID pandemic in 2020, we implemented the use of 22 Gy in four fractions as our primary regimen to reduce overall treatment duration and healthcare exposure risks. In this analysis, we seek to compare outcomes and toxicities between the two treatment regimens.

MATERIALS/METHODS

This is a single institution retrospective review of patients with Stage I-II endometrial cancer who received adjuvant VBT as monotherapy between 1998 and 2022. HDR VBT was delivered via a vaginal cylinder prescribed to a depth of 5 mm, to a dose of 22 or 30 Gy in four or six fractions, respectively. We evaluated maximum acute and chronic toxicities, defined as ≤6 months and ≥ 6 months following treatment completion, respectively. Toxicities were assessed using the Common Terminology Criteria for Adverse Events (CTCAE) criteria. We evaluated clinical outcomes including local recurrence (LR), distant metastasis (DM), cause-specific survival (CSS) and overall survival (OS). P-values <0.05 were considered significant.

RESULTS

A total of 270 patients were included in our analysis, with a median follow up of 4.98 years (7.7 and 1.3 years for six-fraction and 4-fraction regimen, respectively, p<0.001). The median age at the time of treatment was 66 (range 31-89). 195 patients (72.2%) were treated with six fractions and 75 (27.8%) were treated with four fractions. There was significantly less chronic vaginal dryness (p = 0.017) and vaginal stenosis (p<0.001) with the four-fraction compared to the 6-fraction regimen. There was no difference in acute toxicity (p = 0.468). There were no grade ≥3 toxicities in either group. The 2-year LR, DM, CSS, and OS rates for four/six fractions were 2.4%/3.7%, 6.8%/3.7%, 95.8%/97.9%, and 95.8%/95.8%, respectively. There were no significant differences in outcomes between the two groups.

CONCLUSION

Our experience supports that VBT in four fractions is well tolerated with minimal acute and chronic toxicities. When comparing to our institution's historical data for a six-fraction regimen, the use of a four-fraction regimen resulted in less chronic vaginal dryness and stenosis, supporting its continued use. The clinical outcomes have been similar thus far. Further analysis with a longer follow-up duration and a match-pair analysis is warranted.

The East Africa Consortium for human papillomavirus and cervical cancer in women living with HIV/AIDS

The East Africa Consortium was formed to study the epidemiology of human papillomavirus (HPV) infections and cervical cancer and the influence of human immunodeficiency virus (HIV) infection on HPV and cervical cancer, and to encourage collaborations between researchers in North America and East African countries. To date, studies have led to a better understanding of the influence of HIV infection on the detection and persistence of oncogenic HPV, the effects of dietary aflatoxin on the persistence of HPV, the benefits of antiretroviral therapy on HPV persistence, and the differences in HPV detections among HIV-infected and HIV-uninfected women undergoing treatment for cervical dysplasia by either cryotherapy or LEEP. It will now be determined how HPV testing fits into cervical cancer screening programs in Kenya and Uganda, how aflatoxin influences immunological control of HIV, how HPV alters certain genes involved in the growth of tumours in HIV-infected women. Although there have been challenges in performing this research, with time, this work should help to reduce the burden of cervical cancer and other cancers related to HIV infection in people living in sub-Saharan Africa, as well as optimized processes to better facilitate research as well as patient autonomy and safety. KEY MESSAGESThe East Africa Consortium was formed to study the epidemiology of human papillomavirus (HPV) infections and cervical cancer and the influence of human immunodeficiency virus (HIV) infection on HPV and cervical cancer.Collaborations have been established between researchers in North America and East African countries for these studies.Studies have led to a better understanding of the influence of HIV infection on the detection and persistence of oncogenic HPV, the effects of dietary aflatoxin on HPV detection, the benefits of antiretroviral therapy on HPV persistence, and the differences in HPV detections among HIV-infected and HIV-uninfected women undergoing treatment for cervical dysplasia by either cryotherapy or LEEP.

Abstract P5-09-06: Underdiagnosis of HBOC in breast cancer patients: Are genetic testing guidelines a tool or an obstacle?

Background: Pathogenic genetic variants are estimated to occur in 10-15% of all breast cancer patients, with BRCA 1/2 accounting for 40-50% of pathogenic/likely pathogenic (P/LP) variants. However, it is estimated that &lt;30% of breast cancer patients harboring a BRCA 1/2 variant have been identified, with the percentage being much less for ˜20 other breast cancer associated genes. Reasons for this are multifactorial and include complicated and restrictive testing guidelines developed at a time when the cost of testing was high and guidelines for management were limited. Today, cost has plummeted and there are definitive management guidelines for a broader range of genes. We created a community based Registry to determine the incidence of P/LP variants in breast cancer patients who meet and who do not meet the NCCN 2017 genetic testing criteria.

Methods: An IRB-approved multicenter prospective registry was initiated with 20 community and academic sites experienced incancer genetic testing and counseling.

Eligibility criteria included patients with a breast cancer diagnosis who had not been previously tested. Consecutive patients aged 18-90 were consented and underwent an 80 gene panel test (Invitae –Multi-Cancer Panel). The non-inferiority study was powered to detect a difference in P/LP variant rate of 4 percentage points with statistical significance (p&lt;0.05, Fisher's exact test).

HIPAA compliant electronic case report forms collected information on patient diagnosis, test results, and physician recommendations made after test results were received.

Results: Over 1000 patients were enrolled and data from 910 subjects analyzed to date. 50.4% met NCCN criteria and 49.5% did not. Median age for the enrolled patients is 60.5 and ranged from 22-93. 56.0% of patients were recently diagnosed with breast cancer. 10.9% of patients had a history of a prior non breast cancer. Overall, 8.9% of patients had a pathogenicvariant. 9.6% of patients who met NCCN criteria with test results had a P/LP variant. 8.2% of patients who did not meet criteria had a P/LP variant. The difference of positive cases among the two groups is not statistically significant (P = 0.49)

4.9% of patients had pathogenic variants if only an 11 gene standard breast cancer panel was considered.

The spectrum of mutated genes varied between the two groups, with some overlap.

Conclusions:

There was no statistically significant difference in the number of pathogenic/likely pathogenic variants between those patients who met and those who did not meet NCCN guidelines. Expanded panel testing yields more medically actionable P/LP variants than testing BRCA 1/2 alone or breast cancer panels with 11 genes. This study demonstrates that there will be a significant number of patients with P/LP variants are missed if NCCN guidelines are required for genetic testing. Current NCCN guidelines for the genetic testing of breast cancer patients are an obstacle to identifying patients with P/LP variants and should be removed.

Universal BC Genetic Testing RegistryNCCN Criteria (910 patients analyzed)#/% who have P/LP variants#/% who do not have P/LP variantsPatients who meet guidelines44/459 (9.6%)415/459 (90.4%)Patients who do not meet guidelines37/451 (8.2%)414/451 (91.8%)

Citation Format: Beitsch P, Whitworth P, Baron P, Rosen B, Compagnoni G, Simmons R, Smith LA, Holmes D, Brown E, Gold L, Clark P, Coomer C, Grady I, Barbosa K, Riley L, Kinney M, Lyons S, MacDonald H, Kahn S, Ruiz A, Patel R, Curcio L, Esplin E, Yang S. Underdiagnosis of HBOC in breast cancer patients: Are genetic testing guidelines a tool or an obstacle? [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-09-06.

Abstract P5-09-03: Expanded panel testing superior to BRCA1/2 and breast cancer panel in patients with breast cancer

Background: The testing of hereditary breast and ovarian cancer (HBOC) patients for BRCA1/2 only was established years ago to identify patients with clinically actionable variants and limit the economic burden. However, the cost of genetic testing has plummeted, and the number of breast cancer-risk genes with management guidelines has expanded. We created a community-based registry to test all breast cancer patients. A primary objective of this registry included accruing and comparing patients who did and did not meet NCCN guidelines and determining if providing all breast cancer patients with comprehensive multi-gene panel testing yields additional clinical value than testing BRCA1/2 alone.

Methods: An IRB-approved multicenter prospective registry was initiated with 20 community-based and academic breast sites, selected to insure geographic and ethnic diversity. Consecutive patients ages 18-90 with current or prior breast cancer were offered testing with an 80-gene panel (Invitae, San Francisco, CA). HIPAA-compliant case report forms collected patient diagnosis, test results, and physician recommendations made after test results.

Results: Over 1,000 patients were enrolled and data on 911 have been analyzed to date. Median age of patients is 60.5 (range 22 to 93). 56.0% were recently diagnosed with breast cancer. Of these patients, 50.54% met NCCN criteria, and 49.5% did not. 10.9% had history of a prior non-breast cancer. The pathogenic/likely pathogenic (P/LP) variant rate for patients on a comprehensive 80-gene panel was 8.9%. When restricted to a guidelines-based 11-gene breast cancer panel (BRCA1/2, ATM, CDH1, CHEK2, NBN, NF1, PTEN, STK11, TP53, PALB2), 4.9% had P/LP variants; when limited to BRCA1/2, 1.6% had P/LP variants. Of all patients with P/LP findings, 93% had variants in cancer-risk genes with established management recommendations (Table 1) and 80% had germline variants conferring eligibility for precision medicine-based cancer treatments, such as PARP inhibitors, through actively enrolling clinical trials.

Conclusions: This study demonstrates that comprehensive panel testing of breast cancer patients provides a higher yield of clinically actionable P/LP variants than BRCA1/2 testing alone. Limited panels may miss clinically relevant P/LP variants, leaving risk for preventable cancers undiscovered and unnecessarily restricting patients' treatment options. These results also suggest that variants in tumor suppressor genes, not previously thought related to breast cancer, may contribute to its etiology. A comprehensive panel strategy reveals untapped clinical utility and can impact breast cancer patient care by informing implementation of precision medicine treatment interventions and guiding long-term medical management and surveillance for patients and their family members.

 PatientsVariantsWith breast cancer management guidelines (including variants ATM*, BRCA1*, BRCA2*, CHEK2*, NBN*, NF1, PALB2*, TP53*)45 (56%)46 (55%)With cancer guidelines and clinical management implications (including variants BARD1*, FH, MITF, MSH6*, MUTYH*, PTCH1, RAD50*, RAD51C*, RAD51D*, RB1, RET, VHL)31 (38%)33 (39%)Evidence of actionability accruing (including variants BLM, DIS3L2, RECQL4)5 (6%)5 (6%)Totals8184*P/LP variants in these genes confer potential clinical trial eligibility, e.g. NCT02401347.

Citation Format: Beitsch P, Whitworth P, Baron P, Rosen B, Compagnoni G, Simmons R, Smith LA, Holmes D, Brown E, Gold L, Clark P, Coomer C, Grady I, Barbosa K, Riley L, Kinney M, Lyons S, MacDonald H, Kahn S, Ruiz A, Patel R, Curcio L, Esplin E, Yang S, Michalski S. Expanded panel testing superior to BRCA1/2 and breast cancer panel in patients with breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-09-03.

Loss to Follow-Up in a Cervical Cancer Screening and Treatment Program in Western Kenya

Background: Increasingly, evidence is emerging from developing countries like Kenya on the burden of loss to follow-up care after a positive cervical cancer screening/diagnosis, which impacts negatively on cervical cancer prevention and control. Unfortunately little or no information exists on the subject in the western region of Kenya. This study is designed to determine the proportion of and predictors and reasons for defaulting from follow-up care after positive cervical cancer screen. Aim: To determine the rates and factors associated with loss to follow-up in a multivisit cervical cancer screening and treatment program in western Kenya. Methods: We conducted a prospective study of women, who presented for cervical cancer screening at Chulaimbo and Webuye subcounty hospitals, and screened positive by VIA. A 2-3 weeks appointment was then set for review by a gynae-oncologist. A total of 100 women, scheduled for review, were recruited in the study and followed between August 2016 and May 2017. LTFU was defined as failure to keep a second rescheduled appointment or being unreachable for 3 consecutive months and failure to confirm that a woman sought for care in another health facility. Descriptive statistics was used for summary and the Cox regression model was used to estimate the risk of LTFU for different covariates. Results: The age range was 21-77 years, with a mean of 44.45 years. 39% of the women defaulted from scheduled follow-up appointment of which 25 (64%) were LTFU. Univariate Cox regression was conducted for HIV cases (HR=2.7, P value=0.021), clinic revisits (HR=2.6, P value=0.026), married (HR=0.63, P value=0.237) and previously screened women (HR=1.67, P value=0.198). Increased risk of LTFU was observed for HIV cases (HR=2.4, P value=0.04) and revisits (HR=7.5, P value=0.014) in an adjusted model. Conclusion: LTFU affects cervical cancer management due to several factors some of which are beyond the control of the women. We recommend a larger study be replicated for ease of generalizability of results; awareness and strategies are required to retain them to obey the treatment appointment since they are the highly vulnerable.

MeCP2-regulated miRNAs control early human neurogenesis through differential effects on ERK and AKT signaling

Rett syndrome (RTT) is an X-linked, neurodevelopmental disorder caused primarily by mutations in the methyl-CpG-binding protein 2 (MECP2) gene, which encodes a multifunctional epigenetic regulator with known links to a wide spectrum of neuropsychiatric disorders. Although postnatal functions of MeCP2 have been thoroughly investigated, its role in prenatal brain development remains poorly understood. Given the well-established importance of microRNAs (miRNAs) in neurogenesis, we employed isogenic human RTT patient-derived induced pluripotent stem cell (iPSC) and MeCP2 short hairpin RNA knockdown approaches to identify novel MeCP2-regulated miRNAs enriched during early human neuronal development. Focusing on the most dysregulated miRNAs, we found miR-199 and miR-214 to be increased during early brain development and to differentially regulate extracellular signal-regulated kinase (ERK)/mitogen-activated protein kinase and protein kinase B (PKB/AKT) signaling. In parallel, we characterized the effects on human neurogenesis and neuronal differentiation brought about by MeCP2 deficiency using both monolayer and three-dimensional (cerebral organoid) patient-derived and MeCP2-deficient neuronal culture models. Inhibiting miR-199 or miR-214 expression in iPSC-derived neural progenitors deficient in MeCP2 restored AKT and ERK activation, respectively, and ameliorated the observed alterations in neuronal differentiation. Moreover, overexpression of miR-199 or miR-214 in the wild-type mouse embryonic brains was sufficient to disturb neurogenesis and neuronal migration in a similar manner to Mecp2 knockdown. Taken together, our data support a novel miRNA-mediated pathway downstream of MeCP2 that influences neurogenesis via interactions with central molecular hubs linked to autism spectrum disorders.

Abstract P4-06-09: Addition of a remote genetic counselor to the breast specialist's team improves clinical decision-making

Background: There is a shortage of trained genetic counselors (GC) and often long wait times for appointments, resulting in other specialists frequently ordering genetic testing. However, non-genetic specialists, including breast surgeons, find it difficult to stay current in genetics due to rapid advances in gene discovery, expanded panel offerings, and frequent changes to professional guidelines. We tested a novel model for hereditary cancer risk assessment where breast surgeons had “on demand” access to a remote laboratory-based genetic counselor for peer to peer consultation. In this study we sought to determine the impact this model has on breast surgeons' routinely ordering genetic testing including test identification, ordering patterns, and medical management.

Methods: An IRB approved multi-center prospective study involved 14 community-based breast cancer surgeons experienced with hereditary cancer risk assessment without a genetic counselor as part of their practice. Cases were all discussed with a remote Invitae GC to determine testing eligibility and selection. Physicians had the option to utilize remote GCs to discuss results or to refer to traditional genetic counseling services. Pre and post-test surveys were completed for each patient by the testing physician. To protect patient privacy, a unique case ID was used to link patient test data with identifying data.

Results: A total of 192 patients were evaluated with median age of 52. Risk assessment via BRCAPRO and the Hughes Risk model were performed on 98% of patients by the physicians. 65% of patients met NCCN guidelines for testing. Pathogenic mutations were found in 14% of patients. Breast surgeons changed their test selection 21% of the time after discussion with a GC. They called to discuss results in 47% of cases and medical management changes were incorporated in 15% of these cases based on discussion with a remote GC.

Conclusions: Remote GC provider support assisted physicians in facilitating customized test selection, aided in navigating challenging counseling cases, and impacted clinical management. This service may serve as a viable, effective model for 'on demand' genetic counseling support and may be a novel opportunity to expand genetic testing in a breast surgery setting.

Citation Format: Rosen B, O'Leary E, Shan Y, Pat W, Peter B. Addition of a remote genetic counselor to the breast specialist's team improves clinical decision-making [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-06-09.

Abstract P4-06-05: Not presented

This abstract was not presented at the symposium.

Initial characterization of a gel patch dosimeter for in vivo dosimetry

In vivo dosimetry is a greatly underutilized tool for patient safety in clinical external beam radiotherapy treatments, despite being recommended by several national and international organizations (AAPM, ICRU, IAEA, NACP). The reasons for this underutilization mostly relate to the feasibility and cost of in vivo dosimetry methods. Due to the increase in the number of beam angles and dose per fraction in modern treatments, there is a compelling need for a novel dosimeter that is robust and affordable while able to operate properly in these complex conditions. This work presents a gel patch dosimeter as a novel method of in vivo dosimetry. DEFGEL, a 6% T normoxic polyacrylamide gel, was injected into 1 cm thick acrylic molds to create 1 cm thick small cylindrical patch dosimeters. To evaluate the change in optical density due to radiation induced polymerization, dosimeters were scanned before and after irradiation using an in-house developed laser densitometer. The dose-responses of three separate batches of gel were evaluated and compared to check for linearity and repeatability. The response development time was evaluated to ensure that the patch dosimeter could be high throughput. Additionally, the potential of this system to be used as an in vivo dosimeter was tested with a clinically relevant end-to-end in vivo phantom test. All irradiations were performed with a Varian Clinac 21EX at the University of Wisconsin Medical Radiation Research Center (UWMRRC). The dose-response of all three batches of gel was found to be linear within the range of 2-20 Gy. At doses below 0.5 Gy the statistical uncertainties were prohibitively large to make quantitative assessments of the results. The three batches demonstrated good repeatability in the range of 2 Gy to up to 10 Gy, with only slight variations in response at higher doses. For low doses the dosimeter fully developed within an hour while at higher doses they fully developed within four hours. During the in vivo phantom test the predicted patch absorbed dose was 4.23 Gy while the readout dose was evaluated to be 4.37 Gy, which corresponds to a 3.2% discrepancy. The dosimeter and densitometer pairing shows promise as an in vivo dosimetry system, especially for hypofractionated or MRI-guided radiotherapy treatments where higher doses are prescribed.

Beyond knockouts: the International Knockout Mouse Consortium delivers modular and evolving tools for investigating mammalian genes

The International Knockout Mouse Consortium (IKMC; http://www.mousephenotype.org ) has generated mutations in almost every protein-coding mouse gene and is completing the companion Cre driver resource to expand tissue-specific conditional mutagenesis. Accordingly, the IKMC has carried out high-throughput gene trapping and targeting producing conditional mutations in murine embryonic stem cells in more than 18,500 genes, from which at least 4900 mutant mouse lines have been established to date. This resource is currently being upgraded with more powerful tools, such as visualization and manipulation cassettes that can be easily introduced into IKMC alleles for multifaceted functional studies. In addition, we discuss how existing IKMC products can be used in combination with CRISPR technology to accelerate genome engineering projects. All information and materials from this extraordinary biological resource together with coordinated phenotyping efforts can be retrieved at www.mousephenotype.org . The comprehensive IKMC knockout resource in combination with an extensive set of modular gene cassettes will continue to enhance functional gene annotation in the future and solidify its impact on biomedical research.

Genetic testing for BRCA1 and BRCA2 in the Province of Ontario

In 2001, genetic testing for BRCA1 and BRCA2 was introduced in Ontario, for women at high-risk of breast or ovarian cancer. To date over 30,000 individuals have been tested throughout Ontario. Testing was offered to all Ontario residents who were eligible under any of 13 criteria. We report the results of tests conducted at Mount Sinai Hospital from 2007 to 2014. A total of 4726 individuals were tested, 764 (16.2%) were found to carry a pathogenic variant (mutation). Among 3684 women and men who underwent testing without a known familial BRCA mutation, 331 (9.0%) were found to carry a mutation. Among 1042 women and men tested for a known family mutation, 433 (41.6%) were positive. There were 603 female mutation carriers, of these, 303 were affected with breast or ovarian cancer (50%) and 16 with another cancer (2.3%). Of 284 unaffected female carriers, 242 (85%) were tested for a known family mutation and 42 (15%) were the first person in the family to be tested. By placing greater emphasis on recruiting unaffected female relatives of known mutation carriers for testing, greater than one-half of newly identified carriers will be unaffected.

The optimal organization of gynecologic oncology services: a systematic review

BACKGROUND

A system-level organizational guideline for gynecologic oncology was identified by a provincial cancer agency as a key priority based on input from stakeholders, data showing more limited availability of multidisciplinary or specialist care in lower-volume than in higher-volume hospitals in the relevant jurisdiction, and variable rates of staging for ovarian and endometrial cancer patients.

METHODS

A systematic review assessed the relationship of the organization of gynecologic oncology services with patient survival and surgical outcomes. The electronic databases medline and embase (ovid: 1996 through 9 January 2015) were searched using terms related to gynecologic malignancies combined with organization of services, patterns of care, and various facility and physician characteristics. Outcomes of interest included overall or disease-specific survival, short-term survival, adequate staging, and degree of cytoreduction or optimal cytoreduction (or both) for ovarian cancer patients by hospital or physician type, and rate of discrepancy in initial diagnoses and intraoperative consultation between non-specialist pathologists and gyne-oncology-specialist pathologists.

RESULTS

One systematic review and sixteen additional primary studies met the inclusion criteria. The evidence base as a whole was judged to be of lower quality; however, a trend toward improved outcomes with centralization of gynecologic oncology was found, particularly with respect to the gynecologic oncology care of patients with advanced-stage ovarian cancer.

CONCLUSIONS

Improvements in outcomes with centralization of gynecologic oncology services can be attributed to a number of factors, including access to specialist care and multidisciplinary team management. Findings of this systematic review should be used with caution because of the limitations of the evidence base; however, an expert consensus process made it possible to create recommendations for implementation.

The sooner the better: Genetic testing following ovarian cancer diagnosis

OBJECTIVE

As treatment based genetic testing becomes a reality, it is important to assess the attitudes and preferences of women newly diagnosed with ovarian cancer regarding genetic testing. The objective of this study was to determine when women with a diagnosis of high grade serous ovarian cancer would prefer to undergo genetic testing and factors that influence this preference.

METHODS

Women over 18years of age with a known diagnosis of high grade serous ovarian cancer diagnosed between October 2010-2013 were identified via the Princess Margaret Cancer Center Registry. Participants completed a questionnaire, which obtained preferences and attitudes towards genetic testing, cancer history, and demographic information.

RESULTS

120 of the 355 women identified (33.8%) completed the questionnaires. The median age at time of ovarian cancer diagnosis was 57years (range 35-84). The majority of participants in this study were offered (94.6%) and pursued (84.8%) genetic testing. In this cohort, testing was most frequently offered at diagnosis (41.8%) or during treatment (19.1%). In this study, women with high grade serous ovarian cancer felt that genetic testing should be offered before or at the time of diagnosis (67.8%). Having a family history of breast or ovarian cancer was significantly (p=0.012) associated with preferring genetic testing at an earlier time point in the disease course.

CONCLUSIONS

Our results demonstrate that women with high grade serous ovarian cancer acknowledge the personal and clinical utility of genetic testing and support test implementation at the time of cancer diagnosis.

Prognostic value of INPP4B protein immunohistochemistry in ovarian cancer

PURPOSE OF INVESTIGATION

Ovarian cancer is associated with poor prognosis and altered protein expression patterns may be useful for identifying patients likely to have poor disease outcomes. The impact of altered INPP4B protein expression on prognosis is unclear. The aim of this study was to evaluate the implication of INPP4B expression changes in a large series of ovarian cancer tissue samples.

MATERIALS AND METHODS

Tissue microarrays were constructed from 599 epithelial ovarian tumors and stained with antibodies for INPP4B, p53, and PTEN. Proportional hazard models were used to estimate survival hazard ratios (HRs) associated with altered protein expression.

RESULTS

Seventy-nine percent of the ovarian cancers demonstrated loss of INPP4B, whereas 53% showed aberrant p53 expression (i.e., complete loss of p53 or over-expression of p53) and 8% showed loss of PTEN. INPP4B was frequently lost in serous and endometrioid cancer subtypes, aberrant p53 expression was most common among serous subtype, and loss of PTEN was most common among endometrioid tumors (p for all three proteins across histologic subtypes ≤ 0.0001). INPP4B loss or aberrant p53 expression were both associated with increased mortality (HR = 1.84; 95% CI 1.27 - 2.68 and HR = 3.10; 95% CI 2.33 - 4.11, respectively); however, in multivariate models, only the relationship with p53 achieved statistical significance (HR = 1.20; 95% CI 0.82 - 1.76 for INPP4B and HR = 1.73; 95% CI 1.28 - 2.34 for p53). Conclusion: The INPP4B protein is frequently lost in serous and endometrioid subtypes of ovarian cancer. A possible prognostic role of INPP4B for endometrioid ovarian tumors requires further evaluation.

Survival in women with ovarian cancer with and without microsatellite instability

PURPOSE OF INVESTIGATION

Microsatellite instability (MSI) is a hallmark of defective mismatch repair and is present in approximately 20% of ovarian cancers. It is not known if the presence of MSI predicts survival in women with epithelial ovarian cancer.

MATERIALS AND METHODS

Cases of epithelial ovarian cancer were ascertained from a population-based study in Ontario and tumour samples were tested for MSI, using five MSI markers. Patients were divided into MSI-high and MSI-low/normal, according to National Cancer Institute criteria. The authors compared the prevalence of specific prognostic factors in the two subgroups, including age, grade, stage, and histology. They estimated the hazard ratio for death from ovarian cancer associated with MSI-high and with other prognostic factors using a multi-variate analysis.

RESULTS

A total of 418 ovarian cancer patients were included. One hundred and twenty-seven (19.7%) cancers were MSI- high. Subgroup analyses did not reveal any statistically significant differences for pathologic features associated with MSI status. No survival difference was seen according to MSI status.

CONCLUSIONS

The presence of MSI in ovarian cancer is not associated with survival.

Evidence for a time-dependent association between FOLR1 expression and survival from ovarian carcinoma: implications for clinical testing. An Ovarian Tumour Tissue Analysis consortium study

BACKGROUND

Folate receptor 1 (FOLR1) is expressed in the majority of ovarian carcinomas (OvCa), making it an attractive target for therapy. However, clinical trials testing anti-FOLR1 therapies in OvCa show mixed results and require better understanding of the prognostic relevance of FOLR1 expression. We conducted a large study evaluating FOLR1 expression with survival in different histological types of OvCa.

METHODS

Tissue microarrays composed of tumour samples from 2801 patients in the Ovarian Tumour Tissue Analysis (OTTA) consortium were assessed for FOLR1 expression by centralised immunohistochemistry. We estimated associations for overall (OS) and progression-free (PFS) survival using adjusted Cox regression models. High-grade serous ovarian carcinomas (HGSC) from The Cancer Genome Atlas (TCGA) were evaluated independently for association between FOLR1 mRNA upregulation and survival.

RESULTS

FOLR1 expression ranged from 76% in HGSC to 11% in mucinous carcinomas in OTTA. For HGSC, the association between FOLR1 expression and OS changed significantly during the years following diagnosis in OTTA (Pinteraction=0.01, N=1422) and TCGA (Pinteraction=0.01, N=485). In OTTA, particularly for FIGO stage I/II tumours, patients with FOLR1-positive HGSC showed increased OS during the first 2 years only (hazard ratio=0.44, 95% confidence interval=0.20-0.96) and patients with FOLR1-positive clear cell carcinomas (CCC) showed decreased PFS independent of follow-up time (HR=1.89, 95% CI=1.10-3.25, N=259). In TCGA, FOLR1 mRNA upregulation in HGSC was also associated with increased OS during the first 2 years following diagnosis irrespective of tumour stage (HR: 0.48, 95% CI: 0.25-0.94).

CONCLUSIONS

FOLR1-positive HGSC tumours were associated with an increased OS in the first 2 years following diagnosis. Patients with FOLR1-negative, poor prognosis HGSC would be unlikely to benefit from anti-FOLR1 therapies. In contrast, a decreased PFS interval was observed for FOLR1-positive CCC. The clinical efficacy of FOLR1-targeted interventions should therefore be evaluated according to histology, stage and time following diagnosis.

Evidence for a time-dependent association between FOLR1 expression and survival from ovarian carcinoma: implications for clinical testing. An Ovarian Tumour Tissue Analysis consortium study

BACKGROUND

Folate receptor 1 (FOLR1) is expressed in the majority of ovarian carcinomas (OvCa), making it an attractive target for therapy. However, clinical trials testing anti-FOLR1 therapies in OvCa show mixed results and require better understanding of the prognostic relevance of FOLR1 expression. We conducted a large study evaluating FOLR1 expression with survival in different histological types of OvCa.

METHODS

Tissue microarrays composed of tumour samples from 2801 patients in the Ovarian Tumour Tissue Analysis (OTTA) consortium were assessed for FOLR1 expression by centralised immunohistochemistry. We estimated associations for overall (OS) and progression-free (PFS) survival using adjusted Cox regression models. High-grade serous ovarian carcinomas (HGSC) from The Cancer Genome Atlas (TCGA) were evaluated independently for association between FOLR1 mRNA upregulation and survival.

RESULTS

FOLR1 expression ranged from 76% in HGSC to 11% in mucinous carcinomas in OTTA. For HGSC, the association between FOLR1 expression and OS changed significantly during the years following diagnosis in OTTA (Pinteraction=0.01, N=1422) and TCGA (Pinteraction=0.01, N=485). In OTTA, particularly for FIGO stage I/II tumours, patients with FOLR1-positive HGSC showed increased OS during the first 2 years only (hazard ratio=0.44, 95% confidence interval=0.20-0.96) and patients with FOLR1-positive clear cell carcinomas (CCC) showed decreased PFS independent of follow-up time (HR=1.89, 95% CI=1.10-3.25, N=259). In TCGA, FOLR1 mRNA upregulation in HGSC was also associated with increased OS during the first 2 years following diagnosis irrespective of tumour stage (HR: 0.48, 95% CI: 0.25-0.94).

CONCLUSIONS

FOLR1-positive HGSC tumours were associated with an increased OS in the first 2 years following diagnosis. Patients with FOLR1-negative, poor prognosis HGSC would be unlikely to benefit from anti-FOLR1 therapies. In contrast, a decreased PFS interval was observed for FOLR1-positive CCC. The clinical efficacy of FOLR1-targeted interventions should therefore be evaluated according to histology, stage and time following diagnosis.

Sphingosine kinase 1 is regulated by peroxisome proliferator-activated receptor α in response to free fatty acids and is essential for skeletal muscle interleukin-6 production and signaling in diet-induced obesity

We previously demonstrated that sphingosine kinase 1 (Sphk1) expression and activity are up-regulated by exogenous palmitate (PAL) in a skeletal muscle model system and in diet-induced obesity in mice; however, potential functions and in vivo relevance of this have not been addressed. Here, we aimed to determine the mechanism by which PAL regulates SphK1 in muscle, and to determine potential roles for its product, sphingosine-1-phosphate (S1P), in muscle biology in the context of obesity. Cloning and analysis of the mouse Sphk1 promoter revealed a peroxisome proliferator-activated receptor (PPAR) α cis-element that mediated activation of a reporter under control of the Sphk1 promoter; direct interaction of PPARα was demonstrated by chromatin immunoprecipitation. PAL treatment induced the proinflammatory cytokine interleukin (IL)-6 in a manner dependent on SphK1, and this was attenuated by inhibition of the sphingosine-1-phosphate receptor 3 (S1PR3). Diet-induced obesity in mice demonstrated that IL-6 expression in muscle, but not adipose tissue, increased in obesity, but this was attenuated in Sphk1(-/-) mice. Moreover, plasma IL-6 levels were significantly decreased in obese Sphk1(-/-) mice relative to obese wild type mice, and muscle, but not adipose tissue IL-6 signaling was activated. These data indicate that PPARα regulates Sphk1 expression in the context of fatty acid oversupply and links PAL to muscle IL-6 production. Moreover, this function of SphK1 in diet-induced obesity suggests a potential role for SphK1 in obesity-associated pathological outcomes.

Keeping it simple: genetics referrals for all invasive serous ovarian cancers

OBJECTIVE

In the province of Ontario, all women diagnosed with invasive serous ovarian cancer are eligible for genetic testing for mutations in the BRCA1 and BRCA2 genes. This study aimed to determine the proportion of these women who are seen for genetic counseling and to identify potential predictors and barriers to having genetic counseling.

METHODS

All women who were diagnosed with invasive serous ovarian cancer and had genetic counseling at Princess Margaret Hospital (PMH) between 2002 and 2009 were identified. Logistic regressions and trend analyses explored age at diagnosis, year at diagnosis, and the time between diagnosis and genetic counseling. Genetic counseling outcomes were also examined.

RESULTS

Of 623 women diagnosed with invasive serous ovarian cancer, 144 (23%) were seen for genetic counseling. As age at diagnosis increased, the likelihood of genetic counseling decreased (p=0.005). With a more recent date of diagnosis, the probability of having genetic counseling increased (p=0.032) while the time to genetic counseling decreased (p=0.001). Of women who pursued genetic testing, 31% were found to have a BRCA1 or BRCA2 mutation, 16% of whom had no family history of breast or ovarian cancer.

CONCLUSIONS

Despite the availability of genetic testing, only a small proportion of women with invasive serous ovarian cancer were seen for genetic counseling. Over time, an improvement in the proportion of women being seen for genetic counseling was noted; however barriers to seeing women with a later age at diagnosis or those with no family history of breast or ovarian cancer clearly exist.