Walter Bodmer

University of Oxford | OX · Department of Oncology

Elevated cancer metabolism releases lactic acid and CO 2 into the under-perfused tumor microenvironment, resulting in extracellular acidosis. The surviving cancer cells must adapt to this selection pressure; thus, targeting tumor acidosis is a rational therapeutic strategy to manage tumor growth. However, none of the major approved treatments are b...

The naked mole rat (NMR), Heterocephalus glaber, the longest-living rodent, provides a unique opportunity to explore how evolution has shaped adult stem cell (ASC) activity and tissue function with increasing lifespan. Using cumulative BrdU labelling and a quantitative imaging approach to track intestinal ASCs (Lgr5+) in their native in vivo state,...

Acidic environments reduce the intracellular pH (pHi) of most cells to levels that are sub-optimal for growth and cellular functions. Yet, cancers maintain an alkaline cytoplasm despite low extracellular pH (pHe). Raised pHi is thought to be beneficial for tumor progression and invasiveness. However, the transport mechanisms underpinning this adapt...

The founder population of Newfoundland and Labrador (NL) is a unique genetic resource, in part due to its geographic and cultural isolation, where historical records describe a migration of European settlers, primarily from Ireland and England, to NL in the 18th and 19th centuries. Whilst its historical isolation, and increased prevalence of certai...

Background Cancer evolution consists of a stepwise acquisition of genetic and epigenetic changes, which alter the gene expression profiles of cells in a particular tissue and result in phenotypic alterations acted upon by natural selection. The recurrent appearance of specific genetic lesions across individual cancers and cancer types suggests the...

Growth of cancer cells in vitro can be attenuated by genetically inactivating selected metabolic pathways. However, loss-of-function mutations in metabolic pathways are not negatively selected in human cancers, indicating that these genes are not essential in vivo . We hypothesize that spontaneous mutations in 'metabolic genes' will not necessarily...

Epidermal growth factor (EGF) signalling regulates normal epithelial and other cell growth, with EGF receptor (EGFR) overexpression reported in many cancers. However, the role of EGFR clusters in cancer and their dependence on EGF binding is unclear. We present novel single-molecule total internal reflection fluorescence microscopy of (i) EGF and E...

Short tandem repeat (STR) polymorphisms are traditionally assessed by measuring allele lengths via capillary electrophoresis (CE). Massively parallel sequencing (MPS) reveals differences among alleles of the same length, thus improving discrimination, but also identifying groups of alleles likely related by descent. These may have relatively restri...

Experimental inactivation of certain genes involved in metabolism attenuates cancer cell growth in vitro . However, loss-of-function mutations in metabolic pathways are not negatively selected in human cancers, indicating that these genes are not essential in vivo . We hypothesize that spontaneous mutations affecting metabolic pathways do not neces...

Background: Cancer evolution consists of a stepwise acquisition of genetic and epigenetic changes, which alter the gene expression profiles of cells in a particular tissue and result in phenotypic alterations acted upon by natural selection. The recurrent appearance of specific genetic lesions across individual cancers and cancer types suggests the...

Motivation Cancer evolution consists of a stepwise acquisition of genetic and epigenetic changes, which alter the gene expression profiles of cells in a particular tissue and result in phenotypic alterations acted upon by natural selection. The recurrent appearance of specific genetic lesions across individual cancers and cancer types suggests the...

The influence of Viking-Age migrants to the British Isles is obvious in archaeological and place-names evidence, but their demographic impact has been unclear. Autosomal genetic analyses support Norse Viking contributions to parts of Britain, but show no signal corresponding to the Danelaw, the region under Scandinavian administrative control from...

Background/aim: Interactions between colorectal cancer (CRC) cells and myofibroblasts govern many processes such as cell growth, migration, invasion and differentiation, and contribute to CRC progression. Robust experimental tests are needed to investigate the nature of these interactions for future anticancer studies. The purpose of the study was...

Placental alkaline phosphatase, PLAP encoded by ALPP gene in humans is mainly expressed in placenta and testis, and not expressed in any other normal tissues. PLAP is overexpressed in a proportion of colorectal cancers which makes it an attractive target for CAR (chimeric antigen receptor)-T cell therapy. PLAP mRNA expression was detected in 21.4%...

The reconciliation between Mendelian inheritance of discrete traits and the genetically based correlation between relatives for quantitative traits was Fisher’s infinitesimal model of a large number of genetic variants, each with very small effects, whose causal effects could not be individually identified. The development of genome-wide genetic as...

Epidermal growth factor (EGF) signaling regulates normal cell development, however EGF receptor (EGFR) overexpression is reported in several carcinomas. Despite structural and biochemical evidence that EGF-EGFR ligation activates signaling through monomer-dimer transitions, live cell mechanistic details remain contentious. We report single-molecule...

Placental alkaline phosphatase, PLAP encoded by ALPP gene in humans is mainly expressed in placenta and testis, and not expressed in any other normal tissues. PLAP is overexpressed in colorectal cancers which makes it an attractive target for CAR (chimeric antigen receptor)-T cell therapy. PLAP mRNA expression was detected in 21.5% (25 out of 116)...

Any replicating system in which heritable variants with differing replicative potentials can arise is subject to a Darwinian evolutionary process. The continually replicating adult tissue stem cells that control the integrity of many tissues of long-lived, multicellular, complex vertebrate organisms, including humans, constitute such a replicating...

Any replicating system in which heritable variants with differing replicative potentials can arise is subject to a Darwinian evolutionary process. The continually replicating adult tissue stem cells that control the integrity of many tissues of long-lived, multicellular, complex vertebrate organisms, including humans, constitute such a replicating...

Supplementary figure and movie legends

Figure S1. Immunostaining for polarity markers actin, ezrin, villin and myosin IIc, in six parental tumours and daughter primary serum‐free suspension cultures. (A) Haematoxylin/eosin staining of parental tumour sections. (B) Anti‐actin (red)/anti‐ezrin (green)/DAPI co‐staining or (C) anti‐villin (green)/anti‐myosin IIC (red)/DAPI (blue) of parenta...

Figure S2. Apical‐in orientation of brush border proteins is restored in primary cultures grown in Matrigel with serum. Primary suspension cultures were cultured as either serum‐free suspensions or serum‐containing Matrigel cultures for 1 week, followed by fixation, sectioning and immunolabelling. (A) Anti‐actin (red)/DAPI (blue) and anti‐ezrin (gr...

Figure S3. ABCB1 is polarised to outer colony cell membranes in serum‐free suspension but relocates to central apical membranes in cultures grown in Matrigel/serum. (A) Immunolabelling for F‐actin (red) and ABCB1 (green), with DAPI (blue) in various serum‐free primary cultures. (B) Immunolabelling for F‐actin (red) and ABCB1 (green), with DAPI (blu...

Figure S4. Established colorectal cancer cell lines have polarised ABCB1. (A) F‐actin/anti‐ABCB1 labelling of C80 colonies embedded in Matrigel with serum or grown as serum‐free suspensions. (B) Similar experiment to (A) but with the SW1222 cell line. Scale bars = 100 μm.

Figure S5. C80 colonies grown in Matrigel/serum accumulate the ABCB1 substrate TMRE in lumens in an ABCB1‐dependent manner. C80 colonies grown in Matrigel with serum or as serum‐free suspension cultures for 2 weeks and labelled with 100 μm ABCB1 substrate TMRE for 1 h, with or without ABCB1 inhibitors. Cultures were pre‐incubated with drug vehicle...

Figure S6. ABCB1 distribution in colonies under different culture conditions. (A) Mean ABCB1 fluorescence of 17 (from same image) C105251 colonies cultured as serum‐free suspensions or in Matrigel with serum for 1 week (p = 0.312 Student's t‐test). Error bars = SEM. (B) Anti‐ABCB1 labelling of collagen‐embedded C2284 colonies incubated with AIIB2 (...

Movie S1. Z‐stack of red F‐actin and blue DAPI staining of primary culture C2661 cultured in Matrigel with 10% serum for 1 week. Steps are 5 μm.

Table S1. Microarray data used in Figures 2 and 4

Movie S2. Three‐dimensional reconstruction of a C105251 monolayer grown on plastic in serum‐containing medium for 2 weeks, labelled for ABCB1 (green), F‐actin (red) and with DAPI (blue). The scales show microns.

Movie S3. Primary cultures have collagen‐contracting capacity

CEL files. Four .CEL files each with raw microarray data from a cell line

Significance We report optical mapping of DNA from a single cell. Notably, we demonstrate isolation of single cells, DNA extraction, and optical mapping, all within a single integrated micro-/nanofluidic device. Single-cell optical mapping is less complex than sequencing, which we performed after whole-genome amplification of DNA extracted from a s...

Colonic epithelial cells are highly polarised with a lumen‐facing apical membrane, termed the brush border, and a basal membrane in contact with the underlying extracellular matrix (ECM). This polarity is often maintained in cancer tissue in the form of neoplastic glands and has prognostic value. We compared the cellular polarity of several ex vivo...

Introduction Colorectal cancer is a highly preventable disease as early detection increases rates of patient survival to near 100%. Also during therapy colorectal tumors can develop resistance due to mutations in cellular growth factor receptor signaling pathway genes such as KRAS and BRAF. Herein we report new validation studies of a novel multige...

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

Central-western Asia has often been underrepresented in population genetic studies, but it is important for the clarification of the peopling of Eurasia and the relationship between its western and eastern extremities. We genotyped individuals from over 40 population groups, mostly central Eurasian, for mitochondrial HVR1, CCR5del32 and five functi...

Epidermal growth factor (EGF) signalling regulates cell growth, differentiation and proliferation in epithelium and EGF receptor (EGFR) overexpression has been reported in several carcinoma types. Structural and biochemical evidence suggests EGF binding stimulates EGFR monomer-dimer transitions, activating downstream signalling. However, mechanisti...

Significance The human face is extraordinarily variable, and the extreme similarity of the faces of identical twins indicates that most of this variability is genetically determined. We have devised an approach to increase the chance of identifying specific large genetic effects on particular facial features, by choosing features with high heritabi...

The extent of population structure within Ireland is largely unknown, as is the impact of historical migrations. Here we illustrate fine-scale genetic structure across Ireland that follows geographic boundaries and present evidence of admixture events into Ireland. Utilising the ‘Irish DNA Atlas’, a cohort (n = 194) of Irish individuals with four g...

In order to discover specific variants with relatively large effects on the human face we have devised an approach to identifying facial features with high heritability. This is based on using twin data to estimate the additive genetic value of each point on a face, as provided by a 3D camera system. In addition, we have used the ethnic difference...

Significance Metabolism energizes cancer growth, but only if its end product, acid, is removed effectively. A bottleneck for acid handling is slow diffusion across the underperfused extracellular milieu of hypoxic tumors. Here, we characterize the acid-handling mechanisms operating in stromal myofibroblasts that can improve the flow of acid through...

Pericryptal myofibroblasts in the colon and rectum play an important role in regulating the normal colorectal stem cell niche and facilitating tumor progression.Myofibroblasts previously have been distinguished from normal fibroblasts mostly by the expression of α; smooth muscle actin (α;SMA). We now have identified AOC3 (amine oxidase, copper cont...

Significance Myofibroblasts surround the epithelial cells of the crypts that form the surface of the gut. They play an important role in controlling the normal epithelium and influence the development of colorectal and other epithelial cancers. The definition of myofibroblasts previously depended almost entirely on the expression of smooth muscle a...

Purpose: CEA TCB is a novel IgG-based T Cell Bispecific antibody for the treatment of CEA-expressing solid tumors currently in Phase 1 clinical trials (NCT02324257). Its format incorporates bivalent binding to CEA, a head-to-tail fusion of CEA and CD3e binding Fab domains and an engineered Fc region with completely abolished binding to FcγRs and C...

Fine-scale genetic variation between human populations is interesting as a signature of historical demographic events and because of its potential for confounding disease studies. We use haplotype-based statistical methods to analyse genome-wide single nucleotide polymorphism (SNP) data from a carefully chosen geographically diverse sample of 2,039...

Significance In the colon, stem cell self-renewal and multipotency is regulated by the polycomb complex protein BMI1, among other genes. Differentiation is regulated by the transcription factor caudal-type homeobox 1 (CDX1), expression of which coincides with repression of BMI1. Colorectal cancer stem cells (CSCs) express BMI1 but not CDX1. Tumors...

Human colorectal cancer (CRC) cell lines are an important model system for studying the biology of this malignancy as well as therapeutic and biomarker discovery. However, data on the degree to which established CRC cell lines reflect the somatic diversity of primary cancers at the genome level are limited. Using whole exome sequencing and SNP micr...

We have developed a simple procedure for deriving pure cultures of growing cancer cells from colorectal cancers, including material refrigerated overnight, for pathological characterisation and cytotoxicity assays. 46 cancers were processed and cultures set up under varying culture conditions. Use of a Rho kinase (ROCK1) inhibitor markedly increase...

Human colorectal cancer (CRC) cell lines are used widely to investigate tumor biology, experimental therapy and biomarkers. However, to what extent these established cell lines represent and maintain the genetic diversity of primary cancers is uncertain. In this study, we profiled 70 CRC cell lines for mutations and DNA copy-number by whole-exome s...

Despite the millions of dollars spent on target validation and drug optimization in preclinical models, most therapies still fail in phase III clinical trials. Our current model systems, or the way we interpret data from them, clearly do not have sufficient clinical predictive power. Current opinion suggests that this is because the cell lines and...

Single cancer stem-like cells (CSCs) from colorectal cancers can be functionally identified by their ability to form large lumen-containing colonies in 3D Matrigel cultures. These colonies contain the three types of differentiated colorectal epithelial cells, and single cells obtained from them can reproduce themselves and form tumors efficiently i...

Background: Myofibroblasts have an important role in regulating the normal colorectal stem cell niche. While the activation of myofibroblasts in primary colorectal cancers has been previously described, myofibroblast activation in lymph node metastases has not been described before. Methods: Paraffin-embedded lymph node sections from patients with...

A significant proportion of colorectal cancer (CRC) patients are resistant to anti-ERBB1 [avian erythroblastic leukemia viral (v-erb-b) oncogene homolog, receptor for EGF] monoclonal antibodies (Mabs). We evaluated both immune and nonimmune effects of cetuximab (anti-ERBB1 Mab), trastuzumab (anti-ERBB2 Mab), pertuzumab (anti-ERBB2 Mab), and lapatin...

Some 15-20% of multiple adenomatous polyposis have no genetic explanation and 20-30% of colorectal cancer (CRC) cases are thought to be due to inherited multifactorial causes. Accumulation of deleterious effects of low-frequency dominant and independently acting variants may be a partial explanation for such patients. The aim of this study was to t...

Recently, the debate on the origins of the major European Y chromosome haplogroup R1b1b2-M269 has reignited, and opinion has moved away from Palaeolithic origins to the notion of a younger Neolithic spread of these chromosomes from the Near East. Here, we address this debate by investigating frequency patterns and diversity in the largest collectio...

There is a great deal of interest in a fine-scale population structure in the UK, both as a signature of historical immigration events and because of the effect population structure may have on disease association studies. Although population structure appears to have a minor impact on the current generation of genome-wide association studies, it i...

Hypoxia is an important regulator of normal and cancer stem cell (CSC) differentiation. Colorectal CSCs from SW1222, LS180, and CCK81 colorectal cancer-derived cell lines are able to differentiate into complex 3D lumen-containing structures in normoxia, whereas in hypoxia, they form undifferentiated dense colonies that have reduced expression of th...

We examined the influence that rare variants and low-frequency polymorphisms in the cancer candidate gene CCND1 have on the development of multiple intestinal adenomas and the early onset of colorectal cancer. Individuals with <100 multiple polyps and patients with colorectal cancer diagnosed before 50 years of age were recruited in UK, and screene...

MYH associated polyposis is a hereditary syndrome responsible for early colorectal cancer with a distinct genetic pathway from the Familial Adenomatous Polyposis or the Hereditary Non Polyposis Colorectal Cancer syndrome. We have studied a family with three members bearing a biallelic mutation in MYH at c.1185_1186dup. One patient who developed col...

Replication error deficient (RER+) colorectal cancers are a distinct subset of colorectal cancers, characterized by inactivation of the DNA mismatch repair system. These cancers are typically pseudodiploid, accumulate mutations in repetitive sequences as a result of their mismatch repair deficiency, and have distinct pathologies. Regulatory sequenc...

It is now generally accepted that cancers contain a sub-population, the cancer stem cells (CSCs), which initiate and drive a tumour's growth. At least until recently it has been widely assumed that only a small proportion of the cells in a tumour are CSCs. Here we use a mathematical model, supported by experimental evidence, to show that such an as...

Colorectal cancer is (CRC) one of the commonest cancers and its therapy is still based on few drugs. Currently, no biological criteria are used to choose the most effective of the established drugs for treatment. A panel of 77 CRC cell lines was tested for sensitivity to 5-fluorouracil (5FU) using the SRB assay. The responses were grouped into thre...

There are good reasons to expect that common genetic variants do not explain all of the inherited risk of the common cancers, not least of these being the relatively low proportion of familial relative risk that common cancer SNPs currently explain. One promising source of the unexplained risk is rare, low-penetrance genetic variants, a class that...

The WHO Nomenclature Committee for Factors of the HLA System met following the 14th International HLA and Immunogenetics Workshop in Melbourne, Australia in December 2005 and Buzios, Brazil during the 15th International HLA and Immunogenetics Workshop in September 2008. This report documents the additions and revisions to the nomenclature of HLA sp...

The role of transforming growth factor beta receptor type 1 (TGFBR1) polymorphisms, particularly a coding CGC insertion (rs11466445, TGFBR1*6A/9A) in exon 1, has been extensively investigated in regard to colorectal cancer (CRC) risk. These investigations have generated conflicting results. More recently, allele-specific expression (ASE) of TGFBR1...

The WHO Nomenclature Committee for Factors of the HLA System met during the 15th International Histocompatibility and Immunogenetics Workshop in Buzios, Brazil in September 2008. This update is an extract of the main report that documents the additions and revisions to the nomenclature of human leukocyte antigen (HLA) specificities following the pr...

The HLA region on chromosome 6 is gene-rich and under selective pressure because of the high proportion of immunity-related genes. Linkage disequilibrium (LD) patterns and allele frequencies in this region are highly differentiated across broad geographical populations, making it a region of interest for population genetics and immunity-related dis...

Cancer stem cells (CSCs) are the subpopulation of cells within a tumor that can self-renew, differentiate into multiple lineages, and drive tumor growth. Here we describe a two-pronged approach for the identification and characterization of CSCs from colorectal cancer cell lines, using a Matrigel-based differentiation assay, and cell surface marker...

My second formally published paper, written with Peter Parsons and entitled ‘The analogy between factorial experimentation and balanced multi-point linkage tests’, 1 opens with the sentence ‘It was pointed out by Fisher 2 in the Bateson lecture that the factorial method of experimentation, now used extensively in agriculture and other fields of res...

The effect of glycoengineering a membrane specific anti-carcinoembryonic antigen (CEA) (this paper uses the original term CEA for the formally designated CEACAM5) antibody (PR1A3) on its ability to enhance killing of colorectal cancer (CRC) cell lines by human immune effector cells was assessed. In vivo efficacy of the antibody was also tested. The...

The capacity of platelets, lymphocytes, leukocytes (mixed lymphocytes and granulocytes) and erythrocytes to absorb 12 leukocyte agglutinins from multiparous women was investigated. Erythrocytes did not absorb these agglutinins. Platelets, lymphocytes and granulocytes appeared to share antigens identified by representative antisera belonging to the...

In the 1960s Karlin and Bodmer established an active programme in mathematical population genetics with NIH support that, in turn, supported the work of Ewens and Feldman with Karlin. Subsequently Karlin established a similar programme in Israel. The overall contributions of Karlin to population genetics and molecular biology are briefly reviewed f...

4124 Background: Cancer stem cells are defined as cells within a tumour that are able to self-renew and differentiate into all cell lineages within that tumour. With our extensive panel of colorectal cell lines, our aims are: 1) To characterise and isolate cancer stem cells based on stem cell markers, morphological appearances and the ability to fo...

The WHO Nomenclature Committee for factors of the HLA system met in Hakone after the Eleventh International Histocompatibility Workshop and Conference during November 1991 to consider additions and revisions to the nomenclature of specificities defined by both molecular and serological techniques following the principles established in previous rep...

CDX1 is a transcription factor that plays a key role in intestinal development and differentiation. However, the downstream targets of CDX1 are less well defined than those of its close homologue, CDX2. We report here the identification of downstream targets of CDX1 using microarray gene-expression analysis and other approaches. Keratin 20 (KRT20),...

The lymphoblastoid cell line Daudi lacks both HLA—A and B antigens and β2 microglobulin. Somatic cell hybrids derived from a fusion between this line and D98/AH-2 were shown to express four HLA antigens not detectable on either parent cell, A1, A10(Aw26), Bw16(Bw38, Bw17. The initial definition by direct cytotoxicity assay was confirmed by absorpti...

We have developed an automated, highly sensitive and specific method for identifying and enumerating circulating tumour cells (CTCs) in the blood. Blood samples from 10 prostate, 25 colorectal and 4 ovarian cancer patients were analysed. Eleven healthy donors and seven men with elevated serum prostate-specific antigen (PSA) levels but no evidence o...