Temporal dynamics of the multi-omic response to endurance exercise training

Regular exercise promotes whole-body health and prevents disease, but the underlying molecular mechanisms are incompletely understood1-3. Here, the Molecular Transducers of Physical Activity Consortium4 profiled the temporal transcriptome, proteome, metabolome, lipidome, phosphoproteome, acetylproteome, ubiquitylproteome, epigenome and immunome in whole blood, plasma and 18 solid tissues in male and female Rattus norvegicus over eight weeks of endurance exercise training. The resulting data compendium encompasses 9,466 assays across 19 tissues, 25 molecular platforms and 4 training time points. Thousands of shared and tissue-specific molecular alterations were identified, with sex differences found in multiple tissues. Temporal multi-omic and multi-tissue analyses revealed expansive biological insights into the adaptive responses to endurance training, including widespread regulation of immune, metabolic, stress response and mitochondrial pathways. Many changes were relevant to human health, including non-alcoholic fatty liver disease, inflammatory bowel disease, cardiovascular health and tissue injury and recovery. The data and analyses presented in this study will serve as valuable resources for understanding and exploring the multi-tissue molecular effects of endurance training and are provided in a public repository ( https://motrpac-data.org/ ).

Senescent CAFs Mediate Immunosuppression and Drive Breast Cancer Progression

The tumor microenvironment (TME) profoundly influences tumorigenesis, with gene expression in the breast TME capable of predicting clinical outcomes. The TME is complex and includes distinct cancer-associated fibroblast (CAF) subtypes whose contribution to tumorigenesis remains unclear. Here, we identify a subset of myofibroblast CAFs (myCAF) that are senescent (senCAF) in mouse and human breast tumors. Utilizing the MMTV-PyMT;INK-ATTAC (INK) mouse model, we found that senCAF-secreted extracellular matrix specifically limits natural killer (NK) cell cytotoxicity to promote tumor growth. Genetic or pharmacologic senCAF elimination unleashes NK cell killing, restricting tumor growth. Finally, we show that senCAFs are present in HER2+, ER+, and triple-negative breast cancer and in ductal carcinoma in situ (DCIS) where they predict tumor recurrence. Together, these findings demonstrate that senCAFs are potently tumor promoting and raise the possibility that targeting them by senolytic therapy could restrain breast cancer development.

SIGNIFICANCE

senCAFs limit NK cell-mediated killing, thereby contributing to breast cancer progression. Thus, targeting senCAFs could be a clinically viable approach to limit tumor progression.

Induction of Multiple Alternative Mitogenic Signaling Pathways Accompanies the Emergence of Drug-Tolerant Cancer Cells

Drug resistance can evolve from a subpopulation of cancer cells that initially survive drug treatment and then gradually form a pool of drug-tolerant cells. Several studies have pinpointed the activation of a specific bypass pathway that appears to provide the critical therapeutic target for preventing drug tolerance. Here, we take a systems-biology approach, using proteomics and genomics to examine the development of drug tolerance to EGFR inhibitors in EGFR-mutant lung adenocarcinoma cells and BRAF inhibitors in BRAF-mutant melanoma cells. We found that there are numerous alternative mitogenic pathways that become activated in both cases, including YAP, STAT3, IGFR1, and phospholipase C (PLC)/protein kinase C (PKC) pathways. Our results suggest that an effective therapeutic strategy to prevent drug tolerance will need to take multiple alternative mitogenic pathways into account rather than focusing on one specific pathway.

Coordinated single-cell tumor microenvironment dynamics reinforce pancreatic cancer subtype

Bulk analyses of pancreatic ductal adenocarcinoma (PDAC) samples are complicated by the tumor microenvironment (TME), i.e. signals from fibroblasts, endocrine, exocrine, and immune cells. Despite this, we and others have established tumor and stroma subtypes with prognostic significance. However, understanding of underlying signals driving distinct immune and stromal landscapes is still incomplete. Here we integrate 92 single cell RNA-seq samples from seven independent studies to build a reproducible PDAC atlas with a focus on tumor-TME interdependence. Patients with activated stroma are synonymous with higher myofibroblastic and immunogenic fibroblasts, and furthermore show increased M2-like macrophages and regulatory T-cells. Contrastingly, patients with 'normal' stroma show M1-like recruitment, elevated effector and exhausted T-cells. To aid interoperability of future studies, we provide a pretrained cell type classifier and an atlas of subtype-based signaling factors that we also validate in mouse data. Ultimately, this work leverages the heterogeneity among single-cell studies to create a comprehensive view of the orchestra of signaling interactions governing PDAC.

Impact of preventive pill-based treatment on migraine days: A secondary outcome study of the Childhood and Adolescent Migraine Prevention (CHAMP) trial and a comparison of self-report to nosology-derived assessments

OBJECTIVE

To examine group differences in self-reported migraine days among youth who completed the Childhood and Adolescent Migraine Prevention (CHAMP) trial prior to its closure and explore the relationship between self-reported and "nosology-derived" (i.e., International Classification of Headache Disorders, 3rd edition [ICHD-3]) migraine days.

BACKGROUND

The CHAMP trial compared amitriptyline and topiramate to placebo for migraine prevention in youth and proposed to analyze change in migraine days as a secondary outcome. There is considerable variability in the field regarding what constitutes a "migraine day," how this is determined and reported in trials, and how consistent these measures are with diagnostic nosology.

METHODS

CHAMP trial completers (N = 175) were randomized to receive amitriptyline (n = 77), topiramate (n = 63), or placebo (n = 35). Participants maintained daily headache diaries where they reported each day with headache and if they considered that headache to be a migraine. For each headache day, participants completed a symptom record and reported about symptoms such as pain location(s) and presence of nausea/vomiting or photophobia and phonophobia. We examined group differences in self-reported migraine days at trial completion (summed from trial weeks 20-24) compared to baseline. We also used an algorithm to determine whether participants' symptom reports met ICHD-3 criteria for migraine without aura, and examined the association between self-reported and "nosology-derived" migraine days.

RESULTS

Results showed no significant differences between groups in self-reported migraine days over the course of the trial. Self-reported and "nosology-derived" migraine days during the baseline and treatment phases were strongly associated (r's = 0.73 and 0.83, respectively; p's < 0.001).

CONCLUSION

Regardless of treatment, CHAMP trial completers showed clinically important reductions in self-reported migraine days over the course of the trial (about 3.8 days less). The strong association between self-reported and "nosology-derived" migraine days suggests youth with migraine can recognize a day with migraine and reliably report their headache features and symptoms. Greater rigor and transparency in the calculation and reporting of migraine days in trials is needed.

Abstract 3639: Senescent stromal cells drive breast cancer tumorigenesis

Age is the largest risk factor for the development of cancer, including breast cancer, which is the most frequent malignancy in women. Investigation into how age impacts breast cancer development suggests that both the accumulation of oncogenic mutations within incipient tumor cells and age-related stromal changes conspire to drive tumorigenesis. While numerous physiologic changes arise with age, we posit that the accumulation of p16INKA4 (p16) positive senescent cells, which express various cytokines, chemokines, and enzymes collectively referred to as the senescence-associated secretory phenotype (SASP) contribute to cancer progression. SASP factors not only directly promote the proliferation of tumor cells, but also create an immunosuppressive microenvironment that contributes to robust tumor growth. Immunosuppressive SASP factors are detectable in human breast cancer stroma and high p16 positivity in stromal cells strongly correlates with breast cancer recurrence regardless of subtype. To investigate the role of senescent stroma in mammary tumor development, we crossed MMTV-PyMT (PyMT) transgenic mice that spontaneously develop mammary tumors to INK-ATTAC (INK) mice, which allows selective elimination of p16-positive cells. Depletion of senescent stromal cells in PyMT/INK mice led to significantly delayed mammary tumor onset and changes in various tumor-infiltrating immune cell populations. Analyses of single-cell RNA-sequencing (scRNA-seq) datasets of murine and human mammary tumor/breast cancer samples revealed that senescence is restricted to a cancer-associated fibroblasts (CAFs) subpopulation, which expresses high levels of immune-related and extracellular matrix (ECM)-related SASP factors and shows decreasing abundance in PyMT/INK mice upon the depletion of senescent stroma. Together, these data suggest that senescent CAFs contribute to mammary gland tumorigenesis by modulating tumor immunity and remodeling ECM in the microenvironment.

Citation Format: Jiayu (Jennifer) Ye, Ana Paula Delgado, Scott Powers, Sheila Stewart. Senescent stromal cells drive breast cancer tumorigenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3639.

Combinatorial CRISPR/Cas9 Screening Reveals Epistatic Networks of Interacting Tumor Suppressor Genes and Therapeutic Targets in Human Breast Cancer

The majority of cancers are driven by multiple genetic alterations, but how these changes collaborate during tumorigenesis remains largely unknown. To gain mechanistic insights into tumor-promoting genetic interactions among tumor suppressor genes (TSG), we conducted combinatorial CRISPR screening coupled with single-cell transcriptomic profiling in human mammary epithelial cells. As expected, different driver gene alterations in mammary epithelial cells influenced the repertoire of tumor suppressor alterations capable of inducing tumor formation. More surprisingly, TSG interaction networks were comprised of numerous cliques-sets of three or four genes such that each TSG within the clique showed oncogenic cooperation with all other genes in the clique. Genetic interaction profiling indicated that the predominant cooperating TSGs shared overlapping functions rather than distinct or complementary functions. Single-cell transcriptomic profiling of CRISPR double knockouts revealed that cooperating TSGs that synergized in promoting tumorigenesis and growth factor independence showed transcriptional epistasis, whereas noncooperating TSGs did not. These epistatic transcriptional changes, both buffering and synergistic, affected expression of oncogenic mediators and therapeutic targets, including CDK4, SRPK1, and DNMT1. Importantly, the epistatic expression alterations caused by dual inactivation of TSGs in this system, such as PTEN and TP53, were also observed in patient tumors, establishing the relevance of these findings to human breast cancer. An estimated 50% of differentially expressed genes in breast cancer are controlled by epistatic interactions. Overall, our study indicates that transcriptional epistasis is a central aspect of multigenic breast cancer progression and outlines methodologies to uncover driver gene epistatic networks in other human cancers. SIGNIFICANCE: This study provides a roadmap for moving beyond discovery and development of therapeutic strategies based on single driver gene analysis to discovery based on interactions between multiple driver genes.See related commentary by Fong et al., p. 6078.

KRAS drives immune evasion in a genetic model of pancreatic cancer

Immune evasion is a hallmark of KRAS-driven cancers, but the underlying causes remain unresolved. Here, we use a mouse model of pancreatic ductal adenocarcinoma to inactivate KRAS by CRISPR-mediated genome editing. We demonstrate that at an advanced tumor stage, dependence on KRAS for tumor growth is reduced and is manifested in the suppression of antitumor immunity. KRAS-deficient cells retain the ability to form tumors in immunodeficient mice. However, they fail to evade the host immune system in syngeneic wild-type mice, triggering strong antitumor response. We uncover changes both in tumor cells and host immune cells attributable to oncogenic KRAS expression. We identify BRAF and MYC as key mediators of KRAS-driven tumor immune suppression and show that loss of BRAF effectively blocks tumor growth in mice. Applying our results to human PDAC we show that lowering KRAS activity is likewise associated with a more vigorous immune environment.

Human and Rodent Skeletal Muscles Express Angiotensin II Type 1 Receptors

Abundant evidence reveals that activation of the renin-angiotensin system promotes skeletal muscle atrophy in several conditions including congestive heart failure, chronic kidney disease, and prolonged mechanical ventilation. However, controversy exists about whether circulating angiotensin II (AngII) promotes skeletal muscle atrophy by direct or indirect effects; the centerpiece of this debate is the issue of whether skeletal muscle fibers express AngII type 1 receptors (AT1Rs). While some investigators assert that skeletal muscle expresses AT1Rs, others argue that skeletal muscle fibers do not contain AT1Rs. These discordant findings in the literature are likely the result of study design flaws and additional research using a rigorous experimental approach is required to resolve this issue. We tested the hypothesis that AT1Rs are expressed in both human and rat skeletal muscle fibers. Our premise was tested using a rigorous, multi-technique experimental design. First, we established both the location and abundance of AT1Rs on human and rat skeletal muscle fibers by means of an AngII ligand-binding assay. Second, using a new and highly selective AT1R antibody, we carried out Western blotting and determined the abundance of AT1R protein within isolated single muscle fibers from humans and rats. Finally, we confirmed the presence of AT1R mRNA in isolated single muscle fibers from rats. Our results support the hypothesis that AT1Rs are present in both human and rat skeletal muscle fibers. Moreover, our experiments provide the first evidence that AT1Rs are more abundant in fast, type II muscle fibers as compared with slow, type I fibers. Together, these discoveries provide the foundation for an improved understanding of the mechanism(s) responsible for AngII-induced skeletal muscle atrophy.

Digital Therapeutic Self-Management Intervention in Adolescents With Migraine: Feasibility and Preliminary Efficacy of "Migraine Manager"

OBJECTIVE

The objective of this study was to design, code, and pilot test the feasibility and preliminary efficacy of a self-management digital therapeutic tool for adolescents with migraine.

BACKGROUND

Self-management of migraine in adolescents is complex and has important implications for health outcomes. A comprehensive and accessible approach to self-management is needed for youth with migraine, their parents, and clinicians.

METHODS

An iterative co-design process was used to develop and optimize the Migraine Manager's digital therapeutic self-management tool. Subsequently, 40 adolescents, age 11-18 years, were enrolled in an 8-week single-arm open label trial (N = 36 analyzed). The primary outcome was headache days.

RESULTS

Usage data for Migraine Manager were similar to other health app usage data and feedback from participants was uniformly positive, indicating acceptable feasibility. Preliminary efficacy was demonstrated by a reduction in headache days from 17.2 ± 8.5 at baseline to 7.9 ± 7.2 at 8 weeks (95% CI, -13.0 to -7.8; P < .001). There was also statistically significant improvement in patient physical functioning quality of life reported by both patients (baseline = 55.7 ± 20.4; 8 weeks = 69.7 ± 21.9, P = .005) and parents (baseline = 58.5 ± 22.8; 8 weeks = 74.3 ± 18.1, P = .002), and in parent-reported ingestion issues subscale of the adherence barriers scale from baseline to 8 weeks (baseline = 6.0 ± 2.6; 8 weeks = 5.2 ± 3.0, P = .020).

CONCLUSIONS

A self-management digital therapeutic tool for adolescents with migraine can offer care to patients who might not otherwise receive such services. Migraine Manager demonstrated the feasibility and preliminary efficacy in this pilot trial, highlighting the potential beneficial impact of this tool. Larger controlled trials with long-term follow-up are needed to definitively determine the clinical efficacy of Migraine Manager.

Comparative single-cell RNA sequencing (scRNA-seq) reveals liver metastasis-specific targets in a patient with small intestinal neuroendocrine cancer

Genomic analysis of a patient's tumor is the cornerstone of precision oncology, but it does not address whether metastases should be treated differently. Here we tested whether comparative single-cell RNA sequencing (scRNA-seq) of a primary small intestinal neuroendocrine tumor to a matched liver metastasis could guide the treatment of a patient's metastatic disease. Following surgery, the patient was put on maintenance treatment with a somatostatin analog. However, the scRNA-seq analysis revealed that the neuroendocrine epithelial cells in the liver metastasis were less differentiated and expressed relatively little SSTR2, the predominant somatostatin receptor. There were also differences in the tumor microenvironments. RNA expression of vascular endothelial growth factors was higher in the primary tumor cells, reflected by an increased number of endothelial cells. Interestingly, vascular expression of the major VEGF receptors was considerably higher in the liver metastasis, indicating that the metastatic vasculature may be primed for expansion and susceptible to treatment with angiogenesis inhibitors. The patient eventually progressed on Sandostatin, and although consideration was given to adding an angiogenesis inhibitor to her regimen, her disease progression involved non-liver metastases that had not been characterized. Although in this specific case comparative scRNA-seq did not alter treatment, its potential to help guide therapy of metastatic disease was clearly demonstrated.

Abstract A42: Single-cell RNA-seq analysis of human pancreatic ductal adenocarcinoma identifies a novel cell type expressing the intestinal stem cell marker OLFM4

Pancreatic ductal adenomcarcinoma (PDAC) is one of the most lethal forms of cancer with a 5-year survival rate of 8%. To determine the composition of different cell types in PDAC, we performed single-cell RNA-sequencing (scRNA-seq) analysis of two resected patient tumors. Nine distinct cell types were identified: (1) ductal carcinoma cells expressing mutant KRAS, (2) normal pancreatic islet cells, (3) B-lymphocytes, (4) macrophages, (5) mast cells, (6) nerve cells, (7-8) two types of cancer-associated fibroblasts (CAFs), and (9) a previously unidentified epithelial type with distinctly high expression of OLFM4 and CRISP3. Histologic analysis of human PDAC and chronic pancreatitis (CP) tissue sections confirmed the presence of this distinct cell type and furthermore demonstrated that it corresponded to inflamed/injured ducts and early pancreatic intraepithelial neoplasms (PanINs) but that actual PDACs did not express OLFM4. CRISP3 was not always expressed in this new cell type, but the expression of OLFM4 was always detected in these histologic structures. This distinct pancreatic epithelial cell type was also observed in mouse models for chronic pancreatitis and in mutant-KRAS induced PanINs. We hypothesize that inflammation-induced OLFM4 expression helps drive PanIN formation, and that its expression could be exploited for early PDAC detection. We are currently performing functional studies using organoids to address the role that OLFM4 might play in generation of this distinct cell type.

Citation Format: Manisha Rao, Alice Nemajerova, Jinyu Li, Mei Gao, Ki Oh, Richard Moffit, Joseph Kim, George Georgakis, Aaron Sasson, Agnieszka Bialkowkska, Scott Powers. Single-cell RNA-seq analysis of human pancreatic ductal adenocarcinoma identifies a novel cell type expressing the intestinal stem cell marker OLFM4 [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2019 Sept 6-9; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2019;79(24 Suppl):Abstract nr A42.

Identification of targetable BRAF ΔN486_P490 variant by whole-genome sequencing leading to dabrafenib-induced remission of a BRAF-mutant pancreatic adenocarcinoma

The tumor genome of a patient with advanced pancreatic cancer was sequenced to identify potential therapeutic targetable mutations after standard of care failed to produce any significant overall response. Matched tumor-normal whole-genome sequencing revealed somatic mutations in BRAF, TP53, CDKN2A, and a focal deletion of SMAD4 The BRAF variant was an in-frame deletion mutation (ΔN486_P490), which had been previously demonstrated to be a kinase-activating alteration in the BRAF kinase domain. Working with the Novartis patient assistance program allowed us to treat the patient with the BRAF inhibitor, dabrafenib. The patient's overall clinical condition improved dramatically with dabrafenib. Levels of serum tumor marker dropped immediately after treatment, and a subsequent CT scan revealed a significant decrease in the size of both primary and metastatic lesions. The dabrafenib-induced remission lasted for 6 mo. Preclinical studies published concurrently with the patient's treatment showed that the BRAF in-frame mutation (ΔNVTAP) induces oncogenic activation by a mechanism distinct from that induced by V600E, and that this difference dictates the responsiveness to different BRAF inhibitors. This study describes a dramatic instance of how high-level genomic technology and analysis was necessary and sufficient to identify a clinically logical treatment option that was then utilized and shown to be of clinical value for this individual.

Factors Related to Migraine Patients' Decisions to Initiate Behavioral Migraine Treatment Following a Headache Specialist's Recommendation: A Prospective Observational Study

Objective

To evaluate the frequency with which migraine patients initiated behavioral migraine treatment following a headache specialist recommendation and the predictors for initiating behavioral migraine treatment.

Methods

We conducted a prospective cohort study of consecutive patients diagnosed with migraine to examine whether the patients initiated behavioral migraine treatment following a provider recommendation. The primary outcome was scheduling the initial visit for behavioral migraine treatment. Patients who initiated behavioral migraine treatment were compared with those who did not (demographics, migraine characteristics, and locus of control) with analysis of variance and chi-square tests.

Results

Of the 234 eligible patients, 69 (29.5%) were referred for behavioral treatment. Fifty-three (76.8%) patients referred for behavioral treatment were reached by phone. The mean duration from time of referral to follow-up was 76  (median 76, SD = 45) days. Thirty (56.6%) patients initiated behavioral migraine treatment. There was no difference in initiation of behavioral migraine treatment with regard to sex, age, age of diagnosis, years suffered with headaches, health care utilization visits, Migraine Disability Assessment Screen, and locus of control (P > 0.05). Patients who had previously seen a psychologist for migraine were more likely to initiate behavioral migraine treatment than patients who had not. Time constraints were the most common barrier cited for not initiating behavioral migraine treatment.

Conclusions

Less than one-third of eligible patients were referred for behavioral treatment, and only about half initiated behavioral migraine treatment. Future research should further assess patients' decisions regarding behavioral treatment initiation and methods for behavioral treatment delivery to overcome barriers to initiating behavioral migraine treatment.

Barriers to Behavioral Treatment Adherence for Headache: An Examination of Attitudes, Beliefs, and Psychiatric Factors

BACKGROUND/OBJECTIVES

Nonpharmacological interventions, such as biofeedback, cognitive behavioral therapy, and relaxation techniques are Level-A evidence-based treatments for headache. The impact of these interventions is often equivalent to or greater than pharmacological interventions, with fewer side effects. Despite such evidence, the rate of participation in nonpharmacological interventions for headache remains low. Once obstacles to optimizing use of behavioral interventions, such as local access to nonpharmacological treatment and primary headache providers are traversed, identification of barriers contributing to low adherence is imperative given the high levels of disability and cost associated with treating headache disorders. In this review of factors in adults associated with underuse of nonpharmacological interventions, we discuss psychological factors relevant to participation in nonpharmacological treatment, including attitudes and beliefs, motivation for change, awareness of triggers, locus of control, self-efficacy, acceptance, coping styles, personality traits, and psychiatric comorbidities associated with treatment adherence. Finally, future prospects and approaches to optimizing treatment matching and minimizing adherence issues are addressed.

METHODS

An interdisciplinary team conducted this narrative review. Neuropsychologists conducted a literature search during the month of July 2017 using a combination of the keywords ("headache" or "migraine") and ("adherence" or "compliance") or "barriers to treatment" or various "psychological factors" discussed in this narrative review. Content experts, a psychiatrist, and a complementary and integrative health specialist provided additional commentary and input to this narrative review resulting in integration of additional noteworthy studies, book chapters and books.

RESULTS

Various psychological factors, such as attitudes and beliefs, lack of motivation, poor awareness of triggers, external locus of control, poor self-efficacy, low levels of acceptance, and engagement in maladaptive coping styles can contribute to nonadherence.

CONCLUSIONS

To maximize adherence, clinicians can assess and address an individual's level of treatment acceptance, beliefs that may present as barriers, readiness for change, locus of control, self-efficacy and psychiatric comorbidities. Identification of barriers to adherence as well as the application of relevant assessment and intervention techniques have the potential to facilitate adherence and ultimately improve treatment success.

Tandem Duplications May Supply the Missing Genetic Alterations in Many Triple-Negative Breast and Gynecological Cancers

In this issue of Cancer Cell, Menghi et al. show that tandem duplications (TDs) are a common genetic feature of gynecological and triple-negative breast cancers. They also provide evidence that these TDs generate genetic alterations driving these cancers, which, if substantiated, will fundamentally change our understanding of their oncogenesis.

Development of Patient-Derived Gastric Cancer Organoids from Endoscopic Biopsies and Surgical Tissues

BACKGROUND

Organoids are three-dimensional in vitro models of human disease developed from benign and malignant gastrointestinal tissues with tremendous potential for personalized medicine applications. We sought to determine whether gastric cancer patient-derived organoids (PDOs) could be safely established from endoscopic biopsies for rapid drug screening.

METHODS

Patients underwent esophagogastroduodenoscopy (EGD) for surveillance or staging and had additional forceps biopsies taken for PDO creation. Cancer tissues from operative specimens were also used to create PDOs. To address potential tumor heterogeneity, we performed low-coverage whole-genome sequencing of endoscopic-derived PDOs with paired surgical PDOs and whole-tumor lysates. The stability of genomic alterations in endoscopic organoids was assessed by next-generation sequencing and nested polymerase chain reaction (PCR) assay. The feasibility and potential accuracy of drug sensitivity screening with endoscopic-derived PDOs were also evaluated.

RESULTS

Gastric cancer PDOs (n = 15) were successfully established from EGD forceps biopsies (n = 8) and surgical tissues (n = 7) from five patients with gastric adenocarcinoma. Low-coverage whole-genomic profiling of paired EGD and surgical PDOs along with whole-tumor lysates demonstrated absence of tumor heterogeneity. Nested PCR assay identified similar KRAS alterations in primary tumor and paired organoids. Drug sensitivity testing of endoscopic-derived PDOs displayed standard dose-response curves to current gastric cancer cytotoxic therapies.

CONCLUSIONS

Our study results demonstrate the feasibility of developing gastric cancer PDOs from EGD biopsies. These results also indicate that endoscopic-derived PDOs are accurate surrogates of the primary tumor and have the potential for drug sensitivity screening and personalized medicine applications.

Some methods for heterogeneous treatment effect estimation in high dimensions

When devising a course of treatment for a patient, doctors often have little quantitative evidence on which to base their decisions, beyond their medical education and published clinical trials. Stanford Health Care alone has millions of electronic medical records that are only just recently being leveraged to inform better treatment recommendations. These data present a unique challenge because they are high dimensional and observational. Our goal is to make personalized treatment recommendations based on the outcomes for past patients similar to a new patient. We propose and analyze 3 methods for estimating heterogeneous treatment effects using observational data. Our methods perform well in simulations using a wide variety of treatment effect functions, and we present results of applying the 2 most promising methods to data from The SPRINT Data Analysis Challenge, from a large randomized trial of a treatment for high blood pressure.

Nuclear penalized multinomial regression with an application to predicting at bat outcomes in baseball

We propose the nuclear norm penalty as an alternative to the ridge penalty for regularized multinomial regression. This convex relaxation of reduced-rank multinomial regression has the advantage of leveraging underlying structure among the response categories to make better predictions. We apply our method, nuclear penalized multinomial regression (NPMR), to Major League Baseball play-by-play data to predict outcome probabilities based on batter-pitcher matchups. The interpretation of the results meshes well with subject-area expertise and also suggests a novel understanding of what differentiates players.

Challenges in Ras therapeutics in pancreatic cancer

Pancreatic cancer is considered among the most aggressive and the least curable of all human malignancies. It is usually characterized by multiple aberrations in tumor suppressor genes and oncogenes, most notably activating mutations in KRAS. This review examines the various attempts that have been made to inhibit Kras and its downstream signaling pathways in pancreatic cancer with an emphasis on challenges related to clinical trials. Attempts include preventing the localization of Ras protein to the plasma membrane, inhibiting downstream oncogenic signaling by targeting Kras effectors such as MEK1/2, Erk1/2 or Akt singly or in combination, and directly inhibiting Kras protein. Most clinical trials have focused on inhibiting downstream effector pathways and clinical benefit has been limited due to compensatory mechanisms and toxicity associated with small therapeutic windows. Additionally, genetic screens have been conducted to identify gene or genes that could provide therapeutic vulnerabilities in mutant KRAS cells and provide a way to target mutant Kras protein only. We also discuss how potentially transforming clinical trials have failed in the past and what new strategies are on-going in clinical trials for pancreas cancer. For long-term success in targeting Kras, future efforts should focus on combinatorial strategies to more effectively block Kras pathways at multiple points, and improve translational application of pre-clinical data to the clinic.

Evaluating disease prediction models using a cohort whose covariate distribution differs from that of the target population

Personal predictive models for disease development play important roles in chronic disease prevention. The performance of these models is evaluated by applying them to the baseline covariates of participants in external cohort studies, with model predictions compared to subjects' subsequent disease incidence. However, the covariate distribution among participants in a validation cohort may differ from that of the population for which the model will be used. Since estimates of predictive model performance depend on the distribution of covariates among the subjects to which it is applied, such differences can cause misleading estimates of model performance in the target population. We propose a method for addressing this problem by weighting the cohort subjects to make their covariate distribution better match that of the target population. Simulations show that the method provides accurate estimates of model performance in the target population, while un-weighted estimates may not. We illustrate the method by applying it to evaluate an ovarian cancer prediction model targeted to US women, using cohort data from participants in the California Teachers Study. The methods can be implemented using open-source code for public use as the R-package RMAP (Risk Model Assessment Package) available at http://stanford.edu/~ggong/rmap/ .

New Views into the Genetic Landscape of Metastatic Breast Cancer

Whether metastasis-specific genetic alterations exist remains controversial. The study by Yates et al. in this issue of Cancer Cell provides evidence that metastases emerge late during primary breast cancer progression and that additional driver mutations are often acquired, posing both challenges and opportunities for precision treatment of metastatic breast cancer.

Abstract 1762: Keratin 17 identifies prognostic subtypes of pancreatic ductal adenocarcinoma

Recent RNA sequencing (RNASeq) studies from Bailey et al., 2016, Moffitt et al., 2015 and Collisson et al., 2011 reported that mRNA expression from bulk tumor defines molecular subtypes of pancreatic ductal adenocarcinoma (PDAC) that are highly correlated with patient survival. These studies independently identified Keratin 17 (K17) mRNA overexpression as one of over 20 upregulated transcripts that define the RNA signature of the most lethal PDACs. Studies in our lab determined that neither K17 gene missense mutations nor copy-number alterations explain the upregulation of K17 mRNA expression by malignant cells. In addition, we found that K17 expression, measured at the protein level by immunohistochemistry or at the level of mRNA by RNASeq, is sufficient to stratify patients by short- vs long- term survival at baseline after resection. These retrospective survival analyses were performed in four independent patient cohorts using a uniform threshold to define low- vs high- K17 patients (total n= 558). High-K17 cases were twice as likely to die from this disease compared to stage-matched low-K17 cases (P values &lt; 0.05). Furthermore, we determined that K17 expression is associated with outcome after Gemcitabine treatment using the Bailey et al., 2016 patient cohort (n= 94). This is the first study to show that the expression of a single gene, K17, can accurately subtype PDAC at initial diagnosis. In conclusion, K17 was identified as a robust and independent, clinically relevant, prognostic and predictive biomarker to stratify clinical outcome at the time of initial diagnosis and to potentially inform clinical decisions regarding chemotherapeutic intervention.

Citation Format: Luisa F. Escobar-Hoyos, Cindy Leiton, Elizabeth Vanner, Lucia Roa-Pena, Jinyu Li, Scott Powers, Ali Akalin, Jela Bandovic, Peter Bailey, David Chang, Richard Moffitt, Jen Jen Yeh, Andrew Biankin, Kenneth Shroyer. Keratin 17 identifies prognostic subtypes of pancreatic ductal adenocarcinoma [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 1762. doi:10.1158/1538-7445.AM2017-1762

A systematic evaluation of nucleotide properties for CRISPR sgRNA design

BACKGROUND

CRISPR is a versatile gene editing tool which has revolutionized genetic research in the past few years. Optimizing sgRNA design to improve the efficiency of target/DNA cleavage is critical to ensure the success of CRISPR screens.

RESULTS

By borrowing knowledge from oligonucleotide design and nucleosome occupancy models, we systematically evaluated candidate features computed from a number of nucleic acid, thermodynamic and secondary structure models on real CRISPR datasets. Our results showed that taking into account position-dependent dinucleotide features improved the design of effective sgRNAs with area under the receiver operating characteristic curve (AUC) >0.8, and the inclusion of additional features offered marginal improvement (∼2% increase in AUC).

CONCLUSION

Using a machine-learning approach, we proposed an accurate prediction model for sgRNA design efficiency. An R package predictSGRNA implementing the predictive model is available at http://www.ams.sunysb.edu/~pfkuan/softwares.html#predictsgrna .

The nuclear transport receptor Importin-11 is a tumor suppressor that maintains PTEN protein

Phosphatase and tensin homologue (PTEN) protein levels are critical for tumor suppression. However, the search for a recurrent cancer-associated gene alteration that causes PTEN degradation has remained futile. In this study, we show that Importin-11 (Ipo11) is a transport receptor for PTEN that is required to physically separate PTEN from elements of the PTEN degradation machinery. Mechanistically, we find that the E2 ubiquitin-conjugating enzyme and IPO11 cargo, UBE2E1, is a limiting factor for PTEN degradation. Using in vitro and in vivo gene-targeting methods, we show that Ipo11 loss results in degradation of Pten, lung adenocarcinoma, and neoplasia in mouse prostate with aberrantly high levels of Ube2e1 in the cytoplasm. These findings explain the correlation between loss of IPO11 and PTEN protein in human lung tumors. Furthermore, we find that IPO11 status predicts disease recurrence and progression to metastasis in patients choosing radical prostatectomy. Thus, our data introduce the IPO11 gene as a tumor-suppressor locus, which is of special importance in cancers that still retain at least one intact PTEN allele.

The DNA Damage Transducer RNF8 Facilitates Cancer Chemoresistance and Progression through Twist Activation

Twist has been shown to cause treatment failure, cancer progression, and cancer-related death. However, strategies that directly target Twist are not yet conceivable. Here we reveal that K63-linked ubiquitination is a crucial regulatory mechanism for Twist activation. Through an E3 ligase screen and biochemical studies, we unexpectedly identified that RNF8 functions as a direct Twist activator by triggering K63-linked ubiquitination of Twist. RNF8-promoted Twist ubiquitination is required for Twist localization to the nucleus for subsequent EMT and CSC functions, thereby conferring chemoresistance. Our histological analyses showed that RNF8 expression is upregulated and correlated with disease progression, EMT features, and poor patient survival in breast cancer. Moreover, RNF8 regulates cancer cell migration and invasion and cancer metastasis, recapitulating the effect of Twist. Together, our findings reveal a previously unrecognized tumor-promoting function of RNF8 and provide evidence that targeting RNF8 is an appealing strategy to tackle tumor aggressiveness and treatment resistance.

Functionally Assessing Candidate Drivers Advances Precision Cancer Medicine

The complexity of genomic alterations in cancer has made it difficult to identify oncogenic drivers for the development of targeted therapies. The study by Berger et al. in this issue of Cancer Cell demonstrates that high-throughput functional profiling can uncover impactful mutations and oncogenic driver alleles.

Abstract 2589: Dissecting extrinsic and intrinsic cancer risk

Cancers were once thought to originate from mature tissue cells that underwent dedifferentiation in response to cancer progression. Today, cancers are proposed to originate from the malignant transformation of normal tissue progenitor and stem cells, although this is not uniformly accepted. Nevertheless, recent research has highlighted a strong correlation between tissue-specific cancer risk and the lifetime population size and cumulative number of cell divisions of tissue-specific stem cells. However, there has been extensive controversy regarding the conclusion that this correlation implies that there is a very high unavoidable risk for many specific cancers that are due solely to the intrinsic baseline population size of tissue-specific stem cells. This issue has become a key public health debate with dissemination of the ‘bad luck’ hypothesis. Here we provide strong evidence that unavoidable intrinsic risk factors contribute only modestly (&lt;10-30%) to the development of many common cancer types. In an initial approach, we demonstrate that the correlation between stem-cell division and cancer risk does not distinguish between the effects of intrinsic and extrinsic factors. We then develop a novel data-driven approach to estimate intrinsic risk by considering the lower bound risk value for most cancers as a limiting condition for contribution of intrinsic processes. Furthermore, we present an independent mathematical model that capitalizes on the accumulation of endogenous mutations in stem cells. Using mutation rates as a starting point, we found that rates of intrinsic mutations are not sufficient to account for the observed lifetime cancer risk, even in the conservative estimate that all these mutations are due to intrinsic processes alone. Our results are consistent with vast epidemiological data at population level and also mutational signature data at molecular level. The consensus suggests that cancer risk is likely to be heavily influenced by extrinsic factors, and therefore is possibly modifiable and preventable. These results carry immense consequences for strategizing cancer prevention, research, and public health. [Note: this work is in press in Nature.]

Citation Format: Song Wu, Scott Powers, Wei Zhu, Yusuf Hannun. Dissecting extrinsic and intrinsic cancer risk. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2589.

Migraine and its psychiatric comorbidities

Migraine is a highly prevalent and disabling neurological disorder associated with a wide range of psychiatric comorbidities. In this manuscript, we provide an overview of the link between migraine and several comorbid psychiatric disorders, including depression, anxiety and post-traumatic stress disorder. We present data on psychiatric risk factors for migraine chronification. We discuss the evidence, theories and methods, such as brain functional imaging, to explain the pathophysiological links between migraine and psychiatric disorders. Finally, we provide an overview of the treatment considerations for treating migraine with psychiatric comorbidities. In conclusion, a review of the literature demonstrates the wide variety of psychiatric comorbidities with migraine. However, more research is needed to elucidate the neurocircuitry underlying the association between migraine and the comorbid psychiatric conditions and to determine the most effective treatment for migraine with psychiatric comorbidity.

Effectors and potential targets selectively upregulated in human KRAS-mutant lung adenocarcinomas

Genetic and proteomic analysis of human tumor samples can provide an important compliment to information obtained from model systems. Here we examined protein and gene expression from the Cancer Genome and Proteome Atlases (TCGA and TCPA) to characterize proteins and protein-coding genes that are selectively upregulated in KRAS-mutant lung adenocarcinomas. Phosphoprotein activation of several MAPK signaling components was considerably stronger in KRAS-mutants than any other group of tumors, even those with activating mutations in receptor tyrosine kinases (RTKs) and BRAF. Co-occurring mutations in KRAS-mutants were associated with differential activation of PDK1 and PKC-alpha. Genes showing strong activation in RNA-seq data included negative regulators of RTK/RAF/MAPK signaling along with potential oncogenic effectors including activators of Rac and Rho proteins and the receptor protein-tyrosine phosphatase genes PTPRM and PTPRE. These results corroborate RAF/MAPK signaling as an important therapeutic target in KRAS-mutant lung adenocarcinomas and pinpoint new potential targets.

Electronic behavioral interventions for headache: a systematic review

BACKGROUND

There is increasing interest in using electronic behavioral interventions as well as mobile technologies such as smartphones for improving the care of chronic disabling diseases such as migraines. However, less is known about the current clinical evidence for the feasibility and effectiveness of such behavioral interventions.

OBJECTIVE

To review the published literature of behavioral interventions for primary headache disorders delivered by electronic means suitable for use outside of the clinician's office.

METHODS

An electronic database search of PubMed, PsycINFO, and Embase was conducted through December 11, 2015. All eligible studies were systematically reviewed to examine the modality in which treatment was delivered (computer, smartphone, watch and other), types of behavioral intervention delivered (cognitive behavioral therapy [CBT], biofeedback, relaxation, other), the headache type being treated, duration of treatment, adherence, and outcomes obtained by the trials to examine the overall feasibility of electronic behavioral interventions for headache.

RESULTS

Our search produced 291 results from which 23 eligible articles were identified. Fourteen studies used the internet via the computer, 2 used Personal Digital Assistants, 2 used CD ROM and 5 used other types of devices. None used smartphones or wearable devices. Four were pilot studies (N ≤ 10) which assessed feasibility. For the behavioral intervention, CBT was used in 11 (48 %) of the studies, relaxation was used in 8 (35 %) of the studies, and biofeedback was used in 5 (22 %) of the studies. The majority of studies (14/23, 61 %) used more than one type of behavioral modality. The duration of therapy ranged from 4-8 weeks for CBT with a mean of 5.9 weeks. The duration of other behavioral interventions ranged from 4 days to 60 months. Outcomes measured varied widely across the individual studies.

CONCLUSIONS

Despite the move toward individualized medicine and mHealth, the current literature shows that most studies using electronic behavioral intervention for the treatment of headache did not use mobile devices. The studies examining mobile devices showed that the behavioral interventions that employed them were acceptable to patients. Data are limited on the dose required, long term efficacy, and issues related to the security and privacy of this health data. This study was registered at the PROSPERO International Prospective Register of Systematic Reviews (CRD42015032284) (Prospero, 2015).

Inducing stable reversion to achieve cancer control

How can we stop cancer progression? Current strategies depend on modelling progression as the balanced outcome of mutations in, and expression of, tumour suppressor genes and oncogenes. New treatments emerge from successful attempts to tip that balance, but secondary mutational escape from those treatments has become a major impediment because it leads to resistance. In this Opinion article, we argue for a return to an earlier stratagem: tumour cell reversion. Treatments based on selection and analysis of stable revertants could create more durable remissions by reducing the selective pressure that leads to rapid drug resistance.

CUSTOMIZED TRAINING WITH AN APPLICATION TO MASS SPECTROMETRIC IMAGING OF CANCER TISSUE

We introduce a simple, interpretable strategy for making predictions on test data when the features of the test data are available at the time of model fitting. Our proposal-customized training-clusters the data to find training points close to each test point and then fits an ℓ ₁-regularized model (lasso) separately in each training cluster. This approach combines the local adaptivity of k-nearest neighbors with the interpretability of the lasso. Although we use the lasso for the model fitting, any supervised learning method can be applied to the customized training sets. We apply the method to a mass-spectrometric imaging data set from an ongoing collaboration in gastric cancer detection which demonstrates the power and interpretability of the technique. Our idea is simple but potentially useful in situations where the data have some underlying structure.

Oncogenic Myc Induces Expression of Glutamine Synthetase through Promoter Demethylation

c-Myc is known to promote glutamine usage by upregulating glutaminase (GLS), which converts glutamine to glutamate that is catabolized in the TCA cycle. Here we report that in a number of human and murine cells and cancers, Myc induces elevated expression of glutamate-ammonia ligase (GLUL), also termed glutamine synthetase (GS), which catalyzes the de novo synthesis of glutamine from glutamate and ammonia. This is through upregulation of a Myc transcriptional target thymine DNA glycosylase (TDG), which promotes active demethylation of the GS promoter and its increased expression. Elevated expression of GS promotes cell survival under glutamine limitation, while silencing of GS decreases cell proliferation and xenograft tumor growth. Upon GS overexpression, increased glutamine enhances nucleotide synthesis and amino acid transport. These results demonstrate an unexpected role of Myc in inducing glutamine synthesis and suggest a molecular connection between DNA demethylation and glutamine metabolism in Myc-driven cancers.

Cautions about the reliability of pairwise gene correlations based on expression data

BACKGROUND

Rapid growth in the availability of genome-wide transcript abundance levels through gene expression microarrays and RNAseq promises to provide deep biological insights into the complex, genome-wide transcriptional behavior of single-celled organisms. However, this promise has not yet been fully realized.

RESULTS

We find that computation of pairwise gene associations (correlation; mutual information) across a set of 2782 total genome-wide expression samples from six diverse bacteria produces unexpectedly large variation in estimates of pairwise gene association-regardless of the metric used, the organism under study, or the number and source of the samples. We pinpoint the cause to sampling bias. In particular, in repositories of expression data (e.g., Gene Expression Omnibus, GEO), many individual genes show small differences in absolute gene expression levels across the set of samples. We demonstrate that these small differences are due mainly to "noise" instead of "signal" attributable to environmental or genetic perturbations. We show that downstream analysis using gene expression levels of genes with small differences yields biased estimates of pairwise association.

CONCLUSIONS

We propose flagging genes with small differences in absolute, RMA-normalized, expression levels (e.g., standard deviation less than 0.5), as potentially yielding biased pairwise association metrics. This strategy has the potential to substantially improve the confidence in genome-wide conclusions about transcriptional behavior in bacterial organisms. Further work is needed to further refine strategies to identify genes with small difference in expression levels prior to computing gene-gene association metrics.

Reciprocal interaction of Wnt and RXR-α pathways in hepatocyte development and hepatocellular carcinoma

Genomic analysis of human hepatocellular carcinoma (HCC) is potentially confounded by the differentiation state of the hepatic cell-of-origin. Here we integrated genomic analysis of mouse HCC (with defined cell-of-origin) along with normal development. We found a major shift in expression of Wnt and RXR-α pathway genes (up and down, respectively) coincident with the transition from hepatoblasts to hepatocytes. A combined Wnt and RXR-α gene signature categorized HCCs into two subtypes (high Wnt, low RXR-α and low Wnt, high RXR-α), which matched cell-of-origin in mouse models and the differentiation state of human HCC. Suppression of RXR-α levels in hepatocytes increased Wnt signaling and enhanced tumorigenicity, whereas ligand activation of RXR-α achieved the opposite. These results corroborate that there are two main HCC subtypes that correspond to the degree of hepatocyte differentation and that RXR-α, in part via Wnt signaling, plays a key functional role in the hepatocyte-like subtype and potentially could serve as a selective therapeutic target.