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My relationship with Ed Schein began with informal encounters during the summers of the late 1960s in Bethel, Maine, where the National Training Laboratories (NTL) held its programs. Our initial work together was co-training at NTL's Management Work Conference where I learned from a consummate professional in the sensitivity training world. Ed's contributions to the T Group movement were prolific, a significant example being the Addison Wesley Series of books on organization development. He defined the field of organizational psychology, provided the definitive work on organizational culture, and was the master of process consultation. A mild-mannered professor at MIT's Sloan School for his entire career, Ed was a copious writer, dedicated teacher, and skillful consultant.

The unfolded protein response (UPR) is a complex adaptive signaling pathway activated by the accumulation of misfolded proteins in the endoplasmic reticulum (ER). ER stress (ERS) triggers a cascade of responses that converge upon C/EBP homologous protein (CHOP) to drive inflammation and apoptosis. Herein, we sought to determine whether liver injury and fibrosis after small bowel resection (SBR) were mediated by a maladaptive hepatic ERS/UPR. C57BL/6 mice underwent 50% proximal SBR or sham operation. Markers of liver injury and UPR/ERS pathways were analyzed. These were compared with experimental groups including dietary fat manipulation, tauroursodeoxycholic acid (TUDCA) treatment, distal SBR, and global CHOP knockout (KO). At 10 wk, proximal SBR had elevated alanine aminotransferase/aspartate aminotransferase (ALT/AST) (

Supplementary Tables S1 - S9

Supplementary Figure S19 shows the complete switch of circulating tumor DNA profile in patient 026 between baseline and first progression timepoints

Supplementary Figure 12. Swimmer plot showing overall patient survival from initial cancer diagnosis.

Purpose:DNA mismatch repair defects (MMRd) and tumor hypermutation are rare and under-characterized in metastatic prostate cancer (mPC). Furthermore, because hypermutated MMRd prostate cancers can respond to immune checkpoint inhibitors, there is an urgent need for practical detection tools.Experimental Design:We analyzed plasma cell-free DNA-targeted sequencing data from 433 patients with mPC with circulating tumor DNA (ctDNA) purity ≥2%. Samples with somatic hypermutation were subjected to 185 × whole-exome sequencing and capture of mismatch repair gene introns. Archival tissue was analyzed with targeted sequencing and IHC.Results:Sixteen patients (3.7%) had somatic hypermutation with MMRd etiology, evidenced by deleterious alterations in MSH2, MSH6, or MLH1, microsatellite instability, and characteristic trinucleotide signatures. ctDNA was concordant with mismatch repair protein IHC and DNA sequencing of tumor tissue. Tumor suppressors such as PTEN, RB1, and TP53 were inactivated by mutation rather than copy-number loss. Hotspot mutations in oncogenes such as AKT1, PIK3CA, and CTNNB1 were common, and the androgen receptor (AR)-ligand binding domain was mutated in 9 of 16 patients. We observed high intrapatient clonal diversity, evidenced by subclonal driver mutations and shifts in mutation allele frequency over time. Patients with hypermutation and MMRd etiology in ctDNA had a poor response to AR inhibition and inferior survival compared with a control cohort.Conclusions:Hypermutated MMRd mPC is associated with oncogene activation and subclonal diversity, which may contribute to a clinically aggressive disposition in selected patients. In patients with detectable ctDNA, cell-free DNA sequencing is a practical tool to prioritize this subtype for immunotherapy.See related commentary by Schweizer and Yu, p. 981

Supplementary Methods, Figures, Table Legends Supplementary Figure 1: Representative Hematoxylin and Eosin stained photomicrographs of prostatectomy specimens demonstrating the effects of neoadjuvant chemohormonal therapy. Supplementary Figure 2: Quality metrics for targeted DNA sequencing of FFPE biopsy and RP specimens. Supplementary Figure 3: Somatic mutations detected pre- and post-treatment through targeted DNA sequencing. Supplementary Figure 4: Differences in the number and allelic frequency of somatic mutations between treated and untreated specimens. Supplementary Figure 5: Persistence of TP53 mutations in post-treated radical prostatectomy (RP) specimens. Supplementary Figure 6: Representative copy number plots from targeted sequencing of diagnostic biopsies and RP specimens from the untreated arm. Supplementary Figure 7: Pearson's correlation comparing the Nanostring platform (x axis) and RNA-seq (y axis) performed in 13 matched cases. Supplementary Figure 8: Scatterplots showing Pearson correlation between Nanostring data obtained from matched FFPE and fresh/frozen tissue in 7 patients. Supplementary Figure 9: Gene expression of PTEN (y axis) relative to genomic status (PTEN deletion or wild type (WT). Supplementary Figure 10: Left: Correlation of TMPRSS2-ERG fusion transcript expression (x axis) and ERG gene expression (y axis). Right: ERG expression vs. TMPRSS2-ERG fusion status with positive defined as normalized count> 50. Supplementary Figure 11: Principal component analysis plotted using the Biological Coefficient of Variation (BCV) distance as part of the edgeR package. Supplementary Figure 12: Unsupervised analysis of expression of all genes within the panel in radical prostatectomies from treated (green) and untreated (yellow) arms. Red= high expression; blue= low expression.

Table S1: Targeted gene panel for DNA sequencing Table S2: List of genes in the custom Nanostring gene panel Table S3: Clinical characteristics of the patient cohort. Table S4: Predicted minimum tumor cellularity estimated by targeted DNA sequencing. Table S5: Somatic mutation calls from targeted DNA-sequencing. Table S6: Germline mutation calls from targeted DNA sequencing. Table S7: Comparison of non-silent mutations detected by targeted sequencing and whole exome sequencing (WES). Table S8: Differential gene expression between treated and untreated specimens Table S9: Gene expression values (normalized counts) of radical prostatectomy specimens Table S10: Gene expression values (normalized counts) of tumor biopsies Table S11: Gene expression values (normalized counts) of benign prostate specimens

Supplementary Table 1: Somatic mutation count across all samples within meta-cohort. Counts of mutations in all ctDNA positive samples. 95th and 90th percentile are highlighted. Samples are named as a function of their relative mutation count. Supplementary Table 2: Evidence for mismatch repair deficiency by patient. See also Figure 2 Supplementary Table 3: Somatic mismatch repair gene alterations detected in patients with hypermutation. The status of key mismatch repair genes with respect to mutations and copynumber events. ClinVar version 20180603 annotations are included. *Clinvar annotation absent; **Diploid or lack of evidence for deviation from diploid ploidy; blue colour indicates the patients without MMRd etiology Supplementary Table 4: Whole exome sequencing summary statistics. Read depth and subsequent frequency calculations are based on unique read depth, post duplicate removal. Supplementary Table 5: Frequency of mutation and copy number changes in key genes. Comparison of gene and copy number frequencies in mimsatch repair cohort compared to control. P value and odds ratio generated using scipy.stats.fisher_exact verion 1.2.1 Supplementary Table 6: Somatic coding region altering mutations detected through targeted DNA sequencing (all cases in 95th percentile). Mutation annotation format with refseq protein change annotation. Supplementary Table 7: AR and other oncogene mutations detected across serial cfDNA collections. Protein changes are annotated with all refseq isoform amino acid changes. Variant allele frequency (VAF) is provided for each mutation. Supplementary Table 8: Distribution of variant allele frequencies for somatic mutations in each sample. Column D indicates the proportion of mutations in each sample that are considered subclonal. Predicted ctDNA fractions are calculated on max allele frequency of mutations in gene panel. Other columns contain descriptive statistics that summarize the central tendency, dispersion and shape of the distribution of variant allele frequencies per sample. Supplementary Table 9: CtDNA fraction by sample. The highest allele frequency mutation from each sample which does not belong to copy altered segment of the genome is used in the calculation of ctDNA fraction. Supplementary Table 10: Comparison of variant allele frequencies between tissue and ctDNA samples from patients P04 and P10. Supplementary Table 11: Clinical characteristics and PSA response to first-line AR-pathway inhibitor in the MMRd and control (MMR intact) cohort.

Purpose:Cross-resistance renders multiple lines of androgen receptor (AR) signaling inhibitors increasingly futile in metastatic castration-resistant prostate cancer (mCRPC). We sought to determine acquired genomic contributors to cross-resistance.Experimental Design:We collected 458 serial plasma cell-free DNA samples at baseline and progression timepoints from 202 patients with mCRPC receiving sequential AR signaling inhibitors (abiraterone and enzalutamide) in a randomized phase II clinical trial (NCT02125357). We utilized deep targeted and whole-exome sequencing to compare baseline and posttreatment somatic genomic profiles in circulating tumor DNA (ctDNA).Results:Patient ctDNA abundance was correlated across plasma collections and independently prognostic for sequential therapy response and overall survival. Most driver alterations in established prostate cancer genes were consistently detected in ctDNA over time. However, shifts in somatic populations after treatment were identified in 53% of patients, particularly after strong treatment responses. Treatment-associated changes converged upon the AR gene, with an average 50% increase in AR copy number, changes in AR mutation frequencies, and a 2.5-fold increase in the proportion of patients carrying AR ligand binding domain truncating rearrangements.Conclusions:Our data show that the dominant AR genotype continues to evolve during sequential lines of AR inhibition and drives acquired resistance in patients with mCRPC.

An excel file containing Supplementary Tables S1 - S10

Purpose: The combination of docetaxel chemotherapy and androgen deprivation therapy (ADT) has become a standard treatment for patients with metastatic prostate cancer. The recently accrued phase III CALGB 90203 trial was designed to investigate the clinical effectiveness of this treatment approach earlier in the disease. Specimens from this trial offer a unique opportunity to interrogate the acute molecular response to docetaxel and ADT and identify potential biomarkers.Experimental Design: We evaluated baseline clinical data, needle biopsies, and radical prostatectomy (RP) specimens from 52 (of 788) patients enrolled on CALGB 90203 at one high volume center. Pathology review, tumor and germline-targeted DNA sequencing (n = 72 genes), and expression profiling using NanoString platform (n = 163 genes) were performed to explore changes in critical prostate cancer pathways linked to aggression and resistance.Results: Three of 52 patients had only microfocal residual cancer at prostatectomy. The most common alterations included TMPRSS2-ERG fusion (n = 32), TP53 mutation or deletion (n = 11), PTEN deletion (n = 6), FOXA1 (n = 6), and SPOP (n = 4) mutation, with no significant enrichment in posttreated specimens. We did not observe AR amplification or mutations. The degree of AR signaling suppression varied among treated tumors and there was upregulation of both AR and AR-V7 expression as well as a subset of neuroendocrine and plasticity genes.Conclusions: These data support the feasibility of targeted and temporal genomic and transcriptome profiling of neoadjuvant-treated prostate cancer with limited formalin-fixed paraffin embedded tissue requirement. Characterization of the heterogeneity of treatment response and molecular outliers that arise posttreatment provides new insight into potential early markers of resistance. Clin Cancer Res; 23(22); 6802–11. ©2017 AACR.

Loss of functional small bowel surface area causes short bowel syndrome (SBS), intestinal failure, and parenteral nutrition (PN) dependence. The gut adaptive response following resection may be difficult to predict, and it may take up to 2 yr to determine which patients will wean from PN. Here, we examined features of gut microbiota and bile acid (BA) metabolism in determining adaptation and ability to wean from PN. Stool and sera were collected from healthy controls and from patients with SBS (n = 52) with ileostomy, jejunostomy, ileocolonic, and jejunocolonic anastomoses fed with PN plus enteral nutrition or who were exclusively enterally fed. We undertook 16S rRNA gene sequencing, BA profiling, and 7α-hydroxy-4-cholesten-3-one (C4) quantitation with LC-MS/MS and serum amino acid analyses. Patients with SBS exhibited altered gut microbiota with reduced gut microbial diversity compared with healthy controls. We observed differences in the microbiomes of patients with SBS with ileostomy versus jejunostomy, jejunocolonic versus ileocolonic anastomoses, and PN dependence compared with those who weaned from PN. Stool and serum BA composition and C4 concentrations were also altered in patients with SBS, reflecting adaptive changes in enterohepatic BA cycling. Stools from patients who were weaned from PN were enriched in secondary BAs including deoxycholic acid and lithocholic aicd. Shifts in gut microbiota and BA metabolites may generate a favorable luminal environment in select patients with SBS, promoting the ability to wean from PN. Proadaptive microbial species and select BA may provide novel targets for patient-specific therapies for SBS. NEW & NOTEWORTHY Loss of intestinal surface area causes short bowel syndrome, intestinal failure, and parenteral nutrition dependence. We analyzed the gut microbiota and bile acid metabolome of a large cohort of short bowel syndrome adult patients with different postsurgical anatomies. We report a novel analysis of the microbiome of patients with ileostomy and jejunostomy. Enrichment of specific microbial and bile acid species may be associated with the ability to wean from parenteral nutrition.

Purpose:Cross-resistance renders multiple lines of androgen receptor (AR) signaling inhibitors increasingly futile in metastatic castration-resistant prostate cancer (mCRPC). We sought to determine acquired genomic contributors to cross-resistance.Experimental Design:We collected 458 serial plasma cell-free DNA samples at baseline and progression timepoints from 202 patients with mCRPC receiving sequential AR signaling inhibitors (abiraterone and enzalutamide) in a randomized phase II clinical trial (NCT02125357). We utilized deep targeted and whole-exome sequencing to compare baseline and posttreatment somatic genomic profiles in circulating tumor DNA (ctDNA).Results:Patient ctDNA abundance was correlated across plasma collections and independently prognostic for sequential therapy response and overall survival. Most driver alterations in established prostate cancer genes were consistently detected in ctDNA over time. However, shifts in somatic populations after treatment were identified in 53% of patients, particularly after strong treatment responses. Treatment-associated changes converged upon the AR gene, with an average 50% increase in AR copy number, changes in AR mutation frequencies, and a 2.5-fold increase in the proportion of patients carrying AR ligand binding domain truncating rearrangements.Conclusions:Our data show that the dominant AR genotype continues to evolve during sequential lines of AR inhibition and drives acquired resistance in patients with mCRPC.

There is increasing interest in the watch-and-wait approach for patients with rectal cancer who have had a complete clinical response following neoadjuvant long course chemoradiotherapy. This study is a cost analysis of expenditure on patients in the watch-and-wait program versus patients who underwent standard rectal resection followed by routine surveillance.Data were prospectively collated and retrospectively analysed in all patients who presented with rectal cancer from January 2016 to January 2018 at Sir Charles Gairdner Hospital, Perth, Western Australia. Software developed by the North Metropolitan Health Service was used to capture comprehensive data to calculate the in-hospital expenditure for an individual patient throughout their treatment journey.For a patient enrolled in the watch-and-wait pathway, the total cost of surveillance over a 5-year period was $45 246. This was compared with the cost of an ultra-low anterior resection/loop ileostomy/closure of loop and routine postoperative surveillance which came to a total of $87 473. While a patient who had an abdominoperineal resection followed by routine 5-year surveillance had an expenditure of $82 290.There is growing evidence that the watch-and-wait strategy is a valid management option. In the cost-conscious environment of the current health care system, the watch-and-wait pathway is a cost-effective and economically advantage treatment.

Intestinal failure-associated liver disease is a major morbidity associated with short bowel syndrome. We sought to determine if the obesity-resistant mouse strain (129S1/SvImJ) conferred protection from liver injury after small bowel resection (SBR). Using a parenteral nutrition-independent model of resection-associated liver injury, C57BL/6J and 129S1/SvImJ mice underwent a 50% proximal SBR or sham operation. At postoperative week 10, hepatic steatosis, fibrosis, and cholestasis were assessed. Hepatic and systemic inflammatory pathways were evaluated using oxidative markers and abundance of tissue macrophages. Potential mechanisms of endotoxin resistance were also explored. Serum lipid levels were elevated in all mouse lines. Hepatic triglyceride levels were no different between mouse strains, but there was an increased accumulation of free fatty acids in the C57BL/6J mice. Histological and serum markers of hepatic fibrosis, steatosis, and cholestasis were significantly elevated in resected C57BL/6J SBR mice as well as oxidative stress markers and macrophage recruitment in both the liver and visceral white fat in C57BL/6J mice compared with sham controls and the 129S1/SvImJ mouse line. Serum endotoxin levels were significantly elevated in C57BL/6J mice with significant elevation of hepatic TLR4 and reduction in PPARα expression levels. Despite high levels of serum lipids, 129S1/SvImJ mice did not develop liver inflammation, fibrosis, or cholestasis after SBR, unlike C57BL/6J mice. These data suggest that the accumulation of hepatic free fatty acids as well as increased endotoxin-driven inflammatory pathways through PPARα and TLR4 contribute to the liver injury seen in C57BL/6J mice with short bowel syndrome. NEW & NOTEWORTHY Unlike C57BL/6 mice, the 129S1/SvImJ strain is resistant to liver inflammation and injury after small bowel resection. These disparate outcomes are likely due to the accumulation of hepatic free fatty acids as well as increased endotoxin-driven inflammatory pathways through PPARα and TLR4 in C57BL/6 mice with short bowel syndrome.