1
|
Chappidi MR, Sjöström M, Greenland NY, Cowan JE, Baskin AS, Shee K, Simko JP, Chan E, Stohr BA, Washington SL, Nguyen HG, Quigley DA, Davicioni E, Feng FY, Carroll PR, Cooperberg MR. Transcriptomic Heterogeneity of Expansile Cribriform and Other Gleason Pattern 4 Prostate Cancer Subtypes. Eur Urol Oncol 2024; 7:222-230. [PMID: 37474400 DOI: 10.1016/j.euo.2023.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 06/04/2023] [Accepted: 06/26/2023] [Indexed: 07/22/2023]
Abstract
BACKGROUND Prostate cancers featuring an expansile cribriform (EC) pattern are associated with worse clinical outcomes following radical prostatectomy (RP). However, studies of the genomic characteristics of Gleason pattern 4 subtypes are limited. OBJECTIVE To explore transcriptomic characteristics and heterogeneity within Gleason pattern 4 subtypes (fused/poorly formed, glomeruloid, small cribriform, EC/intraductal carcinoma [IDC]) and the association with biochemical recurrence (BCR)-free survival. DESIGN, SETTING, AND PARTICIPANTS This was a retrospective cohort study including 165 men with grade group 2-4 prostate cancer who underwent RP at a single academic institution (2016-2020) and Decipher testing of the RP specimen. Patients with Gleason pattern 5 were excluded. IDC and EC patterns were grouped. Median follow-up was 2.5 yr after RP for patients without BCR. OUTCOMES MEASUREMENTS AND STATISTICAL ANALYSIS Prompted by heterogeneity within pattern 4 subtypes identified via exploratory analyses, we investigated transcriptomic consensus clusters using partitioning around medoids and hallmark gene set scores. The primary clinical outcome was BCR, defined as two consecutive prostate-specific antigen measurements >0.2 ng/ml at least 8 wk after RP, or any additional treatment. Multivariable Cox proportional-hazards models were used to determine factors associated with BCR-free survival. RESULTS AND LIMITATIONS In this cohort, 99/165 patients (60%) had EC and 67 experienced BCR. Exploratory analyses and clustering demonstrated transcriptomic heterogeneity within each Gleason pattern 4 subtype. In the multivariable model controlled for pattern 4 subtype, margin status, Cancer of the Prostate Risk Assessment Post-Surgical score, and Decipher score, a newly identified steroid hormone-driven cluster (hazard ratio 2.35 95% confidence interval 1.01-5.47) was associated with worse BCR-free survival. The study is limited by intermediate follow-up, no validation cohort, and lack of accounting for intratumoral and intraprostatic heterogeneity. CONCLUSIONS Transcriptomic heterogeneity was present within and across each Gleason pattern 4 subtype, demonstrating there is additional biologic diversity not captured by histologic subtypes. This heterogeneity can be used to develop novel signatures and to classify transcriptomic subtypes, which may help in refining risk stratification following RP to further guide decision-making on adjuvant and salvage treatments. PATIENT SUMMARY We studied prostatectomy specimens and found that tumors with similar microscopic appearance can have genetic differences that may help to predict outcomes after prostatectomy for prostate cancer. Our results demonstrate that further gene expression analysis of prostate cancer subtypes may improve risk stratification after prostatectomy. Future studies are needed to develop novel gene expression signatures and validate these findings in independent sets of patients.
Collapse
Affiliation(s)
- Meera R Chappidi
- Department of Urology, University of California-San Francisco, San Francisco, CA, USA.
| | - Martin Sjöström
- Department of Radiation Oncology, University of California-San Francisco, San Francisco, CA, USA
| | - Nancy Y Greenland
- Department of Anatomic Pathology, University of California-San Francisco, San Francisco, CA, USA
| | - Janet E Cowan
- Department of Urology, University of California-San Francisco, San Francisco, CA, USA
| | - Avi S Baskin
- Department of Urology, University of California-San Francisco, San Francisco, CA, USA
| | - Kevin Shee
- Department of Urology, University of California-San Francisco, San Francisco, CA, USA
| | - Jeffry P Simko
- Department of Anatomic Pathology, University of California-San Francisco, San Francisco, CA, USA
| | - Emily Chan
- Department of Anatomic Pathology, University of California-San Francisco, San Francisco, CA, USA
| | - Bradley A Stohr
- Department of Anatomic Pathology, University of California-San Francisco, San Francisco, CA, USA
| | - Samuel L Washington
- Department of Urology, University of California-San Francisco, San Francisco, CA, USA; Department of Epidemiology & Biostatistics, University of California-San Francisco, San Francisco, CA, USA
| | - Hao G Nguyen
- Department of Urology, University of California-San Francisco, San Francisco, CA, USA
| | - David A Quigley
- Department of Urology, University of California-San Francisco, San Francisco, CA, USA; Department of Epidemiology & Biostatistics, University of California-San Francisco, San Francisco, CA, USA
| | | | - Felix Y Feng
- Department of Urology, University of California-San Francisco, San Francisco, CA, USA; Department of Radiation Oncology, University of California-San Francisco, San Francisco, CA, USA
| | - Peter R Carroll
- Department of Urology, University of California-San Francisco, San Francisco, CA, USA
| | - Matthew R Cooperberg
- Department of Urology, University of California-San Francisco, San Francisco, CA, USA; Department of Epidemiology & Biostatistics, University of California-San Francisco, San Francisco, CA, USA
| |
Collapse
|
2
|
Augello MA, Chen X, Liu D, Lin K, Hakansson A, Sjöström M, Khani F, Deonarine LD, Liu Y, Travascio-Green J, Wu J, Loda M, Feng FY, Robinson BD, Davicioni E, Sboner A, Barbieri CE. Canonical AREs are tumor suppressive regulatory elements in the prostate. bioRxiv 2024:2024.02.23.581466. [PMID: 38464162 PMCID: PMC10925218 DOI: 10.1101/2024.02.23.581466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The androgen receptor (AR) is the central determinant of prostate tissue identity and differentiation, controlling normal, growth-suppressive prostate-specific gene expression 1 . It is also a key driver of prostate tumorigenesis, becoming "hijacked" to drive oncogenic transcription 2-5 . However, the regulatory elements determining the execution of the growth suppressive AR transcriptional program, and whether this can be reactivated in prostate cancer (PCa) cells remains unclear. Canonical androgen response element (ARE) motifs are the classic DNA binding element for AR 6 . Here, we used a genome-wide strategy to modulate regulatory elements containing AREs to define distinct AR transcriptional programs. We find that activation of these AREs is specifically associated with differentiation and growth suppressive transcription, and this can be reactivated to cause death in AR + PCa cells. In contrast, repression of AREs is well tolerated by PCa cells, but deleterious to normal prostate cells. Finally, gene expression signatures driven by ARE activity are associated with improved prognosis and luminal phenotypes in human PCa patients. This study demonstrates that canonical AREs are responsible for a normal, growth-suppressive, lineage-specific transcriptional program, that this can be reengaged in PCa cells for potential therapeutic benefit, and genes controlled by this mechanism are clinically relevant in human PCa patients.
Collapse
|
3
|
Kelk P, Fasth A, Holgerson PL, Sjöström M. Successful complete oral rehabilitation of a patient with osteopetrosis with extensive pre-treatments, bone grafts, dental implants and fixed bridges: a multidisciplinary case report. BMC Oral Health 2023; 23:940. [PMID: 38017429 PMCID: PMC10683162 DOI: 10.1186/s12903-023-03707-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 11/23/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND Osteopetrosis comprises a group of inherited disorders that are rare and result in abnormal bone structure. Bone remodeling is extremely inhibited because osteoclasts are nonfunctional or lacking. This condition causes overgrowth of bone with disappearance of the bone marrow, leading to aplastic anemia; obstruction of nerve passages in the skull leads to blindness and often hearing impairment. In most cases, osteopetrosis results in oral complications such as tooth deformation, hypomineralization, and delayed or absent tooth eruption. The only curative treatment is hematopoietic stem cell transplantation (HSCT). The main treatment of the oral complications during childhood and adolescence consists in protecting the erupted teeth against caries disease through prophylactic treatment aimed at optimal oral hygiene through frequent regular dental visits throughout life. Many patients with osteopetrosis require major oral rehabilitation to treat complications of the disease. Improved results of HSCT increase the likelihood that dental professionals will encounter patients with osteopetrosis. CASE PRESENTATION In this case report, we show that individuals with osteopetrosis who have severe oral complications can be treated successfully if they are treated for osteopetrosis at an early age. The boy had his dental care in pedodontics, and regular multidisciplinary meetings were held for future treatment planning. At the age of 15, he was then referred for rehabilitation. The initial evaluations revealed no further growth in the alveolar bone. The rehabilitation was done stepwise, with extraction of malformed and malpositioned teeth. Initially, the patient received a removable partial denture followed by reconstruction of the width of the alveolar process, titanium implants, temporary fixed bridges, and finally screw-retained titanium-ceramic bridges with titanium frames for the upper and lower jaws. CONCLUSIONS The three-year follow-up after loading indicated a stable marginal bone level and optimal oral hygiene as a result of frequent professional oral hygiene care. The patient showed no signs of symptoms from the temporomandibular joint and has adapted to the new jaw relation without any functional or phonetical issues.
Collapse
Affiliation(s)
- P Kelk
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
| | - A Fasth
- Department of Pediatrics, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - PLif Holgerson
- Department of Odontology, Umeå University, Umeå, 901 85, Sweden
| | - M Sjöström
- Department of Odontology, Umeå University, Umeå, 901 85, Sweden.
| |
Collapse
|
4
|
Xu Y, Wang Z, Sjöström M, Deng S, Wang C, Johnson NA, Gonzalez J, Li X, Metang LA, Tirado CR, Mukherji A, Wainwright G, Yu X, Yang Y, Barnes S, Hofstad M, Zhu H, Hanker A, He HH, Chen Y, Wang Z, Raj G, Arteaga C, Feng F, Wang Y, Wang T, Mu P. ZNF397 Loss Triggers TET2-driven Epigenetic Rewiring, Lineage Plasticity, and AR-targeted Therapy Resistance in AR-dependent Cancers. bioRxiv 2023:2023.10.24.563645. [PMID: 37961351 PMCID: PMC10634771 DOI: 10.1101/2023.10.24.563645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Cancer cells exhibit phenotypical plasticity and epigenetic reprogramming, which allows them to evade lineage-dependent targeted treatments by adopting lineage plasticity. The underlying mechanisms by which cancer cells exploit the epigenetic regulatory machinery to acquire lineage plasticity and therapy resistance remain poorly understood. We identified Zinc Finger Protein 397 (ZNF397) as a bona fide co-activator of the androgen receptor (AR), essential for the transcriptional program governing AR-driven luminal lineage. ZNF397 deficiency facilitates the transition of cancer cell from an AR-driven luminal lineage to a Ten-Eleven Translocation 2 (TET2)-driven lineage plastic state, ultimately promoting resistance to therapies inhibiting AR signaling. Intriguingly, our findings indicate that TET2 inhibitor can eliminate the AR targeted therapies resistance in ZNF397-deficient tumors. These insights uncover a novel mechanism through which prostate and breast cancers acquire lineage plasticity via epigenetic rewiring and offer promising implications for clinical interventions designed to overcome therapy resistance dictated by lineage plasticity. Statement of Significance This study reveals a novel epigenetic mechanism regulating tumor lineage plasticity and therapy response, enhances understanding of drug resistance and unveils a new therapeutic strategy for prostate cancer and other malignancies. Our findings also illuminate TET2's oncogenic role and mechanistically connect TET2-driven epigenetic rewiring to lineage plasticity and therapy resistance.
Collapse
|
5
|
Sjöström M, Bjartell A. Re: Niraparib and Abiraterone Acetate for Metastatic Castration-resistant Prostate Cancer. Eur Urol 2023; 84:437-438. [PMID: 37179239 DOI: 10.1016/j.eururo.2023.04.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Affiliation(s)
- Martin Sjöström
- Department of Radiation Oncology, University of California-San Francisco, San Francisco, CA, USA
| | - Anders Bjartell
- Department of Urology, Skåne University Hospital, Lund University, Malmö, Sweden.
| |
Collapse
|
6
|
Helzer KT, Sharifi MN, Sperger JM, Shi Y, Annala M, Bootsma ML, Reese SR, Taylor A, Kaufmann KR, Krause HK, Schehr JL, Sethakorn N, Kosoff D, Kyriakopoulos C, Burkard ME, Rydzewski NR, Yu M, Harari PM, Bassetti M, Blitzer G, Floberg J, Sjöström M, Quigley DA, Dehm SM, Armstrong AJ, Beltran H, McKay RR, Feng FY, O'Regan R, Wisinski KB, Emamekhoo H, Wyatt AW, Lang JM, Zhao SG. Fragmentomic analysis of circulating tumor DNA-targeted cancer panels. Ann Oncol 2023; 34:813-825. [PMID: 37330052 PMCID: PMC10527168 DOI: 10.1016/j.annonc.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 05/30/2023] [Accepted: 06/06/2023] [Indexed: 06/19/2023] Open
Abstract
BACKGROUND The isolation of cell-free DNA (cfDNA) from the bloodstream can be used to detect and analyze somatic alterations in circulating tumor DNA (ctDNA), and multiple cfDNA-targeted sequencing panels are now commercially available for Food and Drug Administration (FDA)-approved biomarker indications to guide treatment. More recently, cfDNA fragmentation patterns have emerged as a tool to infer epigenomic and transcriptomic information. However, most of these analyses used whole-genome sequencing, which is insufficient to identify FDA-approved biomarker indications in a cost-effective manner. PATIENTS AND METHODS We used machine learning models of fragmentation patterns at the first coding exon in standard targeted cancer gene cfDNA sequencing panels to distinguish between cancer and non-cancer patients, as well as the specific tumor type and subtype. We assessed this approach in two independent cohorts: a published cohort from GRAIL (breast, lung, and prostate cancers, non-cancer, n = 198) and an institutional cohort from the University of Wisconsin (UW; breast, lung, prostate, bladder cancers, n = 320). Each cohort was split 70%/30% into training and validation sets. RESULTS In the UW cohort, training cross-validated accuracy was 82.1%, and accuracy in the independent validation cohort was 86.6% despite a median ctDNA fraction of only 0.06. In the GRAIL cohort, to assess how this approach performs in very low ctDNA fractions, training and independent validation were split based on ctDNA fraction. Training cross-validated accuracy was 80.6%, and accuracy in the independent validation cohort was 76.3%. In the validation cohort where the ctDNA fractions were all <0.05 and as low as 0.0003, the cancer versus non-cancer area under the curve was 0.99. CONCLUSIONS To our knowledge, this is the first study to demonstrate that sequencing from targeted cfDNA panels can be utilized to analyze fragmentation patterns to classify cancer types, dramatically expanding the potential capabilities of existing clinically used panels at minimal additional cost.
Collapse
Affiliation(s)
- K T Helzer
- Department of Human Oncology, University of Wisconsin, Madison
| | - M N Sharifi
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA
| | - J M Sperger
- Department of Medicine, University of Wisconsin, Madison, USA
| | - Y Shi
- Department of Human Oncology, University of Wisconsin, Madison
| | - M Annala
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada; Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - M L Bootsma
- Department of Human Oncology, University of Wisconsin, Madison
| | - S R Reese
- Department of Human Oncology, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA
| | - A Taylor
- Department of Medicine, University of Wisconsin, Madison, USA
| | - K R Kaufmann
- Department of Medicine, University of Wisconsin, Madison, USA
| | - H K Krause
- Department of Medicine, University of Wisconsin, Madison, USA
| | - J L Schehr
- Carbone Cancer Center, University of Wisconsin, Madison
| | - N Sethakorn
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA
| | - D Kosoff
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA
| | - C Kyriakopoulos
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA
| | - M E Burkard
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA
| | - N R Rydzewski
- Department of Human Oncology, University of Wisconsin, Madison
| | - M Yu
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison
| | - P M Harari
- Department of Human Oncology, University of Wisconsin, Madison; Carbone Cancer Center, University of Wisconsin, Madison
| | - M Bassetti
- Department of Human Oncology, University of Wisconsin, Madison; Carbone Cancer Center, University of Wisconsin, Madison
| | - G Blitzer
- Department of Human Oncology, University of Wisconsin, Madison; Carbone Cancer Center, University of Wisconsin, Madison
| | - J Floberg
- Department of Human Oncology, University of Wisconsin, Madison; Carbone Cancer Center, University of Wisconsin, Madison
| | - M Sjöström
- Department of Radiation Oncology, University of California San Francisco, San Francisco; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco
| | - D A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco; Departments of Epidemiology and Biostatistics; Urology, University of California San Francisco, San Francisco
| | - S M Dehm
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis
| | - A J Armstrong
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Department of Medicine, Duke University, Durham
| | - H Beltran
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston
| | - R R McKay
- Moores Cancer Center, University of California San Diego, La Jolla
| | - F Y Feng
- Department of Radiation Oncology, University of California San Francisco, San Francisco; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco; Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis; Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco
| | - R O'Regan
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA; Department of Medicine, University of Rochester, Rochester, USA
| | - K B Wisinski
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA
| | - H Emamekhoo
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA
| | - A W Wyatt
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada; Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - J M Lang
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA
| | - S G Zhao
- Department of Human Oncology, University of Wisconsin, Madison; Carbone Cancer Center, University of Wisconsin, Madison; William S. Middleton Memorial Veterans' Hospital, Madison, USA.
| |
Collapse
|
7
|
Lundberg A, Zhang M, Aggarwal R, Li H, Zhang L, Foye A, Sjöström M, Chou J, Chang K, Moreno-Rodriguez T, Shrestha R, Baskin A, Zhu X, Weinstein AS, Younger N, Alumkal JJ, Beer TM, Chi KN, Evans CP, Gleave M, Lara PN, Reiter RE, Rettig MB, Witte ON, Wyatt AW, Feng FY, Small EJ, Quigley DA. The Genomic and Epigenomic Landscape of Double-Negative Metastatic Prostate Cancer. Cancer Res 2023; 83:2763-2774. [PMID: 37289025 PMCID: PMC10425725 DOI: 10.1158/0008-5472.can-23-0593] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/20/2023] [Accepted: 06/02/2023] [Indexed: 06/09/2023]
Abstract
Systemic targeted therapy in prostate cancer is primarily focused on ablating androgen signaling. Androgen deprivation therapy and second-generation androgen receptor (AR)-targeted therapy selectively favor the development of treatment-resistant subtypes of metastatic castration-resistant prostate cancer (mCRPC), defined by AR and neuroendocrine (NE) markers. Molecular drivers of double-negative (AR-/NE-) mCRPC are poorly defined. In this study, we comprehensively characterized treatment-emergent mCRPC by integrating matched RNA sequencing, whole-genome sequencing, and whole-genome bisulfite sequencing from 210 tumors. AR-/NE- tumors were clinically and molecularly distinct from other mCRPC subtypes, with the shortest survival, amplification of the chromatin remodeler CHD7, and PTEN loss. Methylation changes in CHD7 candidate enhancers were linked to elevated CHD7 expression in AR-/NE+ tumors. Genome-wide methylation analysis nominated Krüppel-like factor 5 (KLF5) as a driver of the AR-/NE- phenotype, and KLF5 activity was linked to RB1 loss. These observations reveal the aggressiveness of AR-/NE- mCRPC and could facilitate the identification of therapeutic targets in this highly aggressive disease. SIGNIFICANCE Comprehensive characterization of the five subtypes of metastatic castration-resistant prostate cancer identified transcription factors that drive each subtype and showed that the double-negative subtype has the worst prognosis.
Collapse
Affiliation(s)
- Arian Lundberg
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Meng Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Haolong Li
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Li Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Martin Sjöström
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Jonathan Chou
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Kevin Chang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Thaidy Moreno-Rodriguez
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Urology, University of California San Francisco, San Francisco, California
| | - Raunak Shrestha
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Avi Baskin
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Xiaolin Zhu
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Alana S. Weinstein
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Noah Younger
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Joshi J. Alumkal
- Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, Michigan
| | - Tomasz M. Beer
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Kim N. Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher P. Evans
- Comprehensive Cancer Center, University of California Davis, Sacramento, California
- Department of Urologic Surgery, University of California Davis, Sacramento, California
| | - Martin Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Primo N. Lara
- Comprehensive Cancer Center, University of California Davis, Sacramento, California
- Division of Hematology Oncology, Department of Internal Medicine, University of California Davis, Sacramento, California
| | - Rob E. Reiter
- Departments of Medicine, Hematology/Oncology and Urology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, California
| | - Matthew B. Rettig
- Departments of Medicine, Hematology/Oncology and Urology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, California
- VA Greater Los Angeles Healthcare System, Los Angeles, California
| | - Owen N. Witte
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Alexander W. Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Felix Y. Feng
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, California
- Department of Urology, University of California San Francisco, San Francisco, California
| | - Eric J. Small
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - David A. Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Urology, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| |
Collapse
|
8
|
Sjöström M, Fyles A, Liu FF, McCready D, Feng FY, Speers CW, Pierce LJ, Holmberg E, Fernö M, Malmström P, Karlsson P. Reply to V. Nardone et al. J Clin Oncol 2023; 41:3959-3960. [PMID: 37279434 DOI: 10.1200/jco.23.00566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 03/24/2023] [Indexed: 06/08/2023] Open
Affiliation(s)
- Martin Sjöström
- Martin Sjöström, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden; Anthony Fyles, MD; Fei-Fei Liu, MD; and David McCready, MD, Princess Margaret Cancer Centre and University of Toronto, Toronto, Ontario, Canada; Felix Y. Feng, MD, Department of Radiation Oncology, University of California San Francisco, San Francisco, CA; Corey W. Speers, MD, PhD and Lori J. Pierce, MD, Department of Radiation Oncology, University of Michigan, Ann Arbor, MI; Erik Holmberg, PhD, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Mårten Fernö, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden; Per Malmström, MD, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden, Department of Haematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden; and Per Karlsson, MD, PhD, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anthony Fyles
- Martin Sjöström, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden; Anthony Fyles, MD; Fei-Fei Liu, MD; and David McCready, MD, Princess Margaret Cancer Centre and University of Toronto, Toronto, Ontario, Canada; Felix Y. Feng, MD, Department of Radiation Oncology, University of California San Francisco, San Francisco, CA; Corey W. Speers, MD, PhD and Lori J. Pierce, MD, Department of Radiation Oncology, University of Michigan, Ann Arbor, MI; Erik Holmberg, PhD, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Mårten Fernö, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden; Per Malmström, MD, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden, Department of Haematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden; and Per Karlsson, MD, PhD, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Fei-Fei Liu
- Martin Sjöström, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden; Anthony Fyles, MD; Fei-Fei Liu, MD; and David McCready, MD, Princess Margaret Cancer Centre and University of Toronto, Toronto, Ontario, Canada; Felix Y. Feng, MD, Department of Radiation Oncology, University of California San Francisco, San Francisco, CA; Corey W. Speers, MD, PhD and Lori J. Pierce, MD, Department of Radiation Oncology, University of Michigan, Ann Arbor, MI; Erik Holmberg, PhD, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Mårten Fernö, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden; Per Malmström, MD, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden, Department of Haematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden; and Per Karlsson, MD, PhD, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - David McCready
- Martin Sjöström, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden; Anthony Fyles, MD; Fei-Fei Liu, MD; and David McCready, MD, Princess Margaret Cancer Centre and University of Toronto, Toronto, Ontario, Canada; Felix Y. Feng, MD, Department of Radiation Oncology, University of California San Francisco, San Francisco, CA; Corey W. Speers, MD, PhD and Lori J. Pierce, MD, Department of Radiation Oncology, University of Michigan, Ann Arbor, MI; Erik Holmberg, PhD, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Mårten Fernö, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden; Per Malmström, MD, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden, Department of Haematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden; and Per Karlsson, MD, PhD, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Felix Y Feng
- Martin Sjöström, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden; Anthony Fyles, MD; Fei-Fei Liu, MD; and David McCready, MD, Princess Margaret Cancer Centre and University of Toronto, Toronto, Ontario, Canada; Felix Y. Feng, MD, Department of Radiation Oncology, University of California San Francisco, San Francisco, CA; Corey W. Speers, MD, PhD and Lori J. Pierce, MD, Department of Radiation Oncology, University of Michigan, Ann Arbor, MI; Erik Holmberg, PhD, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Mårten Fernö, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden; Per Malmström, MD, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden, Department of Haematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden; and Per Karlsson, MD, PhD, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Corey W Speers
- Martin Sjöström, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden; Anthony Fyles, MD; Fei-Fei Liu, MD; and David McCready, MD, Princess Margaret Cancer Centre and University of Toronto, Toronto, Ontario, Canada; Felix Y. Feng, MD, Department of Radiation Oncology, University of California San Francisco, San Francisco, CA; Corey W. Speers, MD, PhD and Lori J. Pierce, MD, Department of Radiation Oncology, University of Michigan, Ann Arbor, MI; Erik Holmberg, PhD, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Mårten Fernö, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden; Per Malmström, MD, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden, Department of Haematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden; and Per Karlsson, MD, PhD, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lori J Pierce
- Martin Sjöström, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden; Anthony Fyles, MD; Fei-Fei Liu, MD; and David McCready, MD, Princess Margaret Cancer Centre and University of Toronto, Toronto, Ontario, Canada; Felix Y. Feng, MD, Department of Radiation Oncology, University of California San Francisco, San Francisco, CA; Corey W. Speers, MD, PhD and Lori J. Pierce, MD, Department of Radiation Oncology, University of Michigan, Ann Arbor, MI; Erik Holmberg, PhD, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Mårten Fernö, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden; Per Malmström, MD, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden, Department of Haematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden; and Per Karlsson, MD, PhD, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Erik Holmberg
- Martin Sjöström, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden; Anthony Fyles, MD; Fei-Fei Liu, MD; and David McCready, MD, Princess Margaret Cancer Centre and University of Toronto, Toronto, Ontario, Canada; Felix Y. Feng, MD, Department of Radiation Oncology, University of California San Francisco, San Francisco, CA; Corey W. Speers, MD, PhD and Lori J. Pierce, MD, Department of Radiation Oncology, University of Michigan, Ann Arbor, MI; Erik Holmberg, PhD, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Mårten Fernö, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden; Per Malmström, MD, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden, Department of Haematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden; and Per Karlsson, MD, PhD, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Mårten Fernö
- Martin Sjöström, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden; Anthony Fyles, MD; Fei-Fei Liu, MD; and David McCready, MD, Princess Margaret Cancer Centre and University of Toronto, Toronto, Ontario, Canada; Felix Y. Feng, MD, Department of Radiation Oncology, University of California San Francisco, San Francisco, CA; Corey W. Speers, MD, PhD and Lori J. Pierce, MD, Department of Radiation Oncology, University of Michigan, Ann Arbor, MI; Erik Holmberg, PhD, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Mårten Fernö, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden; Per Malmström, MD, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden, Department of Haematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden; and Per Karlsson, MD, PhD, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Per Malmström
- Martin Sjöström, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden; Anthony Fyles, MD; Fei-Fei Liu, MD; and David McCready, MD, Princess Margaret Cancer Centre and University of Toronto, Toronto, Ontario, Canada; Felix Y. Feng, MD, Department of Radiation Oncology, University of California San Francisco, San Francisco, CA; Corey W. Speers, MD, PhD and Lori J. Pierce, MD, Department of Radiation Oncology, University of Michigan, Ann Arbor, MI; Erik Holmberg, PhD, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Mårten Fernö, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden; Per Malmström, MD, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden, Department of Haematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden; and Per Karlsson, MD, PhD, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Per Karlsson
- Martin Sjöström, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden; Anthony Fyles, MD; Fei-Fei Liu, MD; and David McCready, MD, Princess Margaret Cancer Centre and University of Toronto, Toronto, Ontario, Canada; Felix Y. Feng, MD, Department of Radiation Oncology, University of California San Francisco, San Francisco, CA; Corey W. Speers, MD, PhD and Lori J. Pierce, MD, Department of Radiation Oncology, University of Michigan, Ann Arbor, MI; Erik Holmberg, PhD, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Mårten Fernö, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden; Per Malmström, MD, PhD, Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden, Department of Haematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden; and Per Karlsson, MD, PhD, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| |
Collapse
|
9
|
Rydzewski NR, Helzer KT, Bootsma M, Shi Y, Bakhtiar H, Sjöström M, Zhao SG. Machine Learning & Molecular Radiation Tumor Biomarkers. Semin Radiat Oncol 2023; 33:243-251. [PMID: 37331779 DOI: 10.1016/j.semradonc.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Developing radiation tumor biomarkers that can guide personalized radiotherapy clinical decision making is a critical goal in the effort towards precision cancer medicine. High-throughput molecular assays paired with modern computational techniques have the potential to identify individual tumor-specific signatures and create tools that can help understand heterogenous patient outcomes in response to radiotherapy, allowing clinicians to fully benefit from the technological advances in molecular profiling and computational biology including machine learning. However, the increasingly complex nature of the data generated from high-throughput and "omics" assays require careful selection of analytical strategies. Furthermore, the power of modern machine learning techniques to detect subtle data patterns comes with special considerations to ensure that the results are generalizable. Herein, we review the computational framework of tumor biomarker development and describe commonly used machine learning approaches and how they are applied for radiation biomarker development using molecular data, as well as challenges and emerging research trends.
Collapse
Affiliation(s)
- Nicholas R Rydzewski
- Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD; Department of Human Oncology, University of Wisconsin, Madison, WI
| | - Kyle T Helzer
- Department of Human Oncology, University of Wisconsin, Madison, WI
| | - Matthew Bootsma
- Department of Human Oncology, University of Wisconsin, Madison, WI
| | - Yue Shi
- Department of Human Oncology, University of Wisconsin, Madison, WI
| | - Hamza Bakhtiar
- Department of Human Oncology, University of Wisconsin, Madison, WI
| | - Martin Sjöström
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA
| | - Shuang G Zhao
- Department of Human Oncology, University of Wisconsin, Madison, WI; Carbone Cancer Center, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital, Madison, WI.
| |
Collapse
|
10
|
Stenmark Tullberg A, Sjöström M, Tran L, Niméus E, Killander F, Kovács A, Lundstedt D, Holmberg E, Karlsson P. Combining histological grade, TILs, and the PD-1/PD-L1 pathway to identify immunogenic tumors and de-escalate radiotherapy in early breast cancer: a secondary analysis of a randomized clinical trial. J Immunother Cancer 2023; 11:e006618. [PMID: 37208129 PMCID: PMC10201214 DOI: 10.1136/jitc-2022-006618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND The implementation of immunological biomarkers for radiotherapy (RT) individualization in breast cancer requires consideration of tumor-intrinsic factors. This study aimed to investigate whether the integration of histological grade, tumor-infiltrating lymphocytes (TILs), programmed cell death protein-1 (PD-1), and programmed death ligand-1 (PD-L1) can identify tumors with aggressive characteristics that can be downgraded regarding the need for RT. METHODS The SweBCG91RT trial included 1178 patients with stage I-IIA breast cancer, randomized to breast-conserving surgery with or without adjuvant RT, and followed for a median time of 15.2 years. Immunohistochemical analyses of TILs, PD-1, and PD-L1 were performed. An activated immune response was defined as stromal TILs ≥10% and PD-1 and/or PD-L1 expression in ≥1% of lymphocytes. Tumors were categorized as high-risk or low-risk using assessments of histological grade and proliferation as measured by gene expression. The risk of ipsilateral breast tumor recurrence (IBTR) and benefit of RT were then analyzed with 10 years follow-up based on the integration of immune activation and tumor-intrinsic risk group. RESULTS Among high-risk tumors, an activated immune infiltrate was associated with a reduced risk of IBTR (HR 0.34, 95% CI 0.16 to 0.73, p=0.006). The incidence of IBTR in this group was 12.1% (5.6-25.0) without RT and 4.4% (1.1-16.3) with RT. In contrast, the incidence of IBTR in the high-risk group without an activated immune infiltrate was 29.6% (21.4-40.2) without RT and 12.8% (6.6-23.9) with RT. Among low-risk tumors, no evidence of a favorable prognostic effect of an activated immune infiltrate was seen (HR 2.0, 95% CI 0.87 to 4.6, p=0.100). CONCLUSIONS Integrating histological grade and immunological biomarkers can identify tumors with aggressive characteristics but a low risk of IBTR despite a lack of RT boost and systemic therapy. Among high-risk tumors, the risk reduction of IBTR conferred by an activated immune infiltrate is comparable to treatment with RT. These findings may apply to cohorts dominated by estrogen receptor-positive tumors.
Collapse
Affiliation(s)
- Axel Stenmark Tullberg
- Department of Oncology, University of Gothenburg Institute of Clinical Sciences, Goteborg, Sweden
| | - Martin Sjöström
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
- Department of Clinical Sciences Lund, Oncology/Pathology and Surgery, Lund University, Lund, Sweden
| | - Lena Tran
- Department of Clinical Sciences Lund, Oncology/Pathology and Surgery, Lund University, Lund, Sweden
| | - Emma Niméus
- Department of Clinical Sciences Lund, Oncology/Pathology and Surgery, Lund University, Lund, Sweden
- Department of Surgery, Skåne University Hospital, Lund, Sweden
| | - Fredrika Killander
- Department of Clinical Sciences Lund, Oncology/Pathology and Surgery, Lund University, Lund, Sweden
- Department of Oncology, Skåne University Hospital, Lund, Sweden
| | - Anikó Kovács
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Dan Lundstedt
- Department of Oncology, University of Gothenburg Institute of Clinical Sciences, Goteborg, Sweden
| | - Erik Holmberg
- Department of Oncology, University of Gothenburg Institute of Clinical Sciences, Goteborg, Sweden
| | - Per Karlsson
- Department of Oncology, University of Gothenburg Institute of Clinical Sciences, Goteborg, Sweden
| |
Collapse
|
11
|
Stenmark Tullberg A, Sjöström M, Niméus E, Killander F, Chang SL, Feng FY, Speers CW, Pierce LJ, Kovács A, Lundstedt D, Holmberg E, Karlsson P. Integrating Tumor-Intrinsic and Immunologic Factors to Identify Immunogenic Breast Cancers from a Low-Risk Cohort: Results from the Randomized SweBCG91RT Trial. Clin Cancer Res 2023; 29:1783-1793. [PMID: 37071498 PMCID: PMC10150244 DOI: 10.1158/1078-0432.ccr-22-2746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/18/2022] [Accepted: 01/20/2023] [Indexed: 04/19/2023]
Abstract
PURPOSE The local immune infiltrate's influence on tumor progression may be closely linked to tumor-intrinsic factors. The study aimed to investigate whether integrating immunologic and tumor-intrinsic factors can identify patients from a low-risk cohort who may be candidates for radiotherapy (RT) de-escalation. EXPERIMENTAL DESIGN The SweBCG91RT trial included 1,178 patients with stage I to IIA breast cancer, randomized to breast-conserving surgery with or without adjuvant RT, and followed for a median of 15.2 years. We trained two models designed to capture immunologic activity and immunomodulatory tumor-intrinsic qualities, respectively. We then analyzed if combining these two variables could further stratify tumors, allowing for identifying a subgroup where RT de-escalation is feasible, despite clinical indicators of a high risk of ipsilateral breast tumor recurrence (IBTR). RESULTS The prognostic effect of the immunologic model could be predicted by the tumor-intrinsic model (Pinteraction = 0.01). By integrating measurements of the immunologic- and tumor-intrinsic models, patients who benefited from an active immune infiltrate could be identified. These patients benefited from standard RT (HR, 0.28; 95% CI, 0.09-0.85; P = 0.025) and had a 5.4% 10-year incidence of IBTR after irradiation despite high-risk genomic indicators and a low frequency of systemic therapy. In contrast, high-risk tumors without an immune infiltrate had a high 10-year incidence of IBTR despite RT treatment (19.5%; 95% CI, 12.2-30.3). CONCLUSIONS Integrating tumor-intrinsic and immunologic factors may identify immunogenic tumors in early-stage breast cancer populations dominated by ER-positive tumors. Patients who benefit from an activated immune infiltrate may be candidates for RT de-escalation.
Collapse
Affiliation(s)
- Axel Stenmark Tullberg
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Martin Sjöström
- Department of Clinical Sciences Lund, Oncology/Pathology and Surgery, Lund University, Lund, Sweden
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California
| | - Emma Niméus
- Department of Clinical Sciences Lund, Oncology/Pathology and Surgery, Lund University, Lund, Sweden
- Department of Surgery, Skåne University Hospital, Lund, Sweden
| | - Fredrika Killander
- Department of Clinical Sciences Lund, Oncology/Pathology and Surgery, Lund University, Lund, Sweden
- Department of Oncology, Skåne University Hospital, Lund, Sweden
| | | | - Felix Y. Feng
- University of California San Francisco, San Francisco, California
| | | | - Lori J. Pierce
- University of Michigan Medical School, Ann Arbor, Michigan
| | - Anikó Kovács
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Dan Lundstedt
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Erik Holmberg
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Per Karlsson
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| |
Collapse
|
12
|
de Jong AC, Danyi A, van Riet J, de Wit R, Sjöström M, Feng F, de Ridder J, Lolkema MP. Predicting response to enzalutamide and abiraterone in metastatic prostate cancer using whole-omics machine learning. Nat Commun 2023; 14:1968. [PMID: 37031196 PMCID: PMC10082805 DOI: 10.1038/s41467-023-37647-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 03/22/2023] [Indexed: 04/10/2023] Open
Abstract
Response to androgen receptor signaling inhibitors (ARSI) varies widely in metastatic castration resistant prostate cancer (mCRPC). To improve treatment guidance, biomarkers are needed. We use whole-genomics (WGS; n = 155) with matching whole-transcriptomics (WTS; n = 113) from biopsies of ARSI-treated mCRPC patients for unbiased discovery of biomarkers and development of machine learning-based prediction models. Tumor mutational burden (q < 0.001), structural variants (q < 0.05), tandem duplications (q < 0.05) and deletions (q < 0.05) are enriched in poor responders, coupled with distinct transcriptomic expression profiles. Validating various classification models predicting treatment duration with ARSI on our internal and external mCRPC cohort reveals two best-performing models, based on the combination of prior treatment information with either the four combined enriched genomic markers or with overall transcriptomic profiles. In conclusion, predictive models combining genomic, transcriptomic, and clinical data can predict response to ARSI in mCRPC patients and, with additional optimization and prospective validation, could improve treatment guidance.
Collapse
Affiliation(s)
- Anouk C de Jong
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Alexandra Danyi
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Job van Riet
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Ronald de Wit
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Martin Sjöström
- Department of Radiation Oncology, University of California, San Francisco, CA, USA
| | - Felix Feng
- Department of Radiation Oncology, University of California, San Francisco, CA, USA
| | - Jeroen de Ridder
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Martijn P Lolkema
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
| |
Collapse
|
13
|
Sjöström M, Fyles A, Liu FF, McCready D, Shi W, Rey-McIntyre K, Chang SL, Feng FY, Speers CW, Pierce LJ, Holmberg E, Fernö M, Malmström P, Karlsson P. Development and Validation of a Genomic Profile for the Omission of Local Adjuvant Radiation in Breast Cancer. J Clin Oncol 2023; 41:1533-1540. [PMID: 36599119 PMCID: PMC10022846 DOI: 10.1200/jco.22.00655] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 08/07/2022] [Accepted: 11/18/2022] [Indexed: 01/06/2023] Open
Abstract
PURPOSE Adjuvant radiotherapy (RT) is used for women with early-stage invasive breast cancer treated with breast-conserving surgery. However, some women with low risk of recurrence may safely be spared RT. This study aimed to identify these women using a molecular-based approach. METHODS We analyzed two randomized trials of women with node-negative invasive breast cancer to ± RT following breast-conserving surgery: SweBCG91-RT (stage I-II, no adjuvant systemic therapy) and Princess Margaret (age 50 years or older, T1-T2, adjuvant tamoxifen). Transcriptome-wide profiling was performed (Affymetrix Human Exon 1.0 ST microarray). Patients with estrogen receptor-positive/human epidermal growth factor receptor 2-negative tumors and with gene expression data were included. The SweBCG91-RT cohort was divided into training (N = 243) and validation (N = 354) cohorts. A 16-gene signature named Profile for the Omission of Local Adjuvant Radiation (POLAR) was trained to predict locoregional recurrence (LRR) using elastic net regression. POLAR was then validated in the SweBCG91-RT validation cohort and the Princess Margaret cohort (N = 132). RESULTS Patients categorized as POLAR low-risk without RT had a 10-year LRR of 6% (95% CI, 2 to 16) and 7% (0 to 27) in SweBCG91-RT and Princess Margaret cohorts, respectively. There was no significant benefit from RT in POLAR low-risk patients (hazard ratio [HR], 1.1 [0.39 to 3.4], P = .81, and HR, 1.5 [0.14 to 16], P = .74, respectively). Patients categorized as POLAR high-risk had a significant decreased risk of LRR with RT (HR, 0.43 [0.24 to 0.78], P = .0055, and HR, 0.25 [0.07 to 0.92], P = .038, respectively). An exploratory analysis testing for interaction between RT and POLAR in the combined validation cohort was performed (P = .066). CONCLUSION The novel POLAR genomic signature on the basis of LRR biology may identify patients with a low risk of LRR despite not receiving RT, and thus may be candidates for RT omission.
Collapse
Affiliation(s)
- Martin Sjöström
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA
| | - Anthony Fyles
- Princess Margaret Cancer Centre and University of Toronto, Toronto, ON, Canada
| | - Fei-Fei Liu
- Princess Margaret Cancer Centre and University of Toronto, Toronto, ON, Canada
| | - David McCready
- Princess Margaret Cancer Centre and University of Toronto, Toronto, ON, Canada
| | - Wei Shi
- Princess Margaret Cancer Centre and University of Toronto, Toronto, ON, Canada
| | | | | | - Felix Y. Feng
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA
| | - Corey W. Speers
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI
| | - Lori J. Pierce
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI
| | - Erik Holmberg
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Mårten Fernö
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Per Malmström
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Department of Haematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Per Karlsson
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| |
Collapse
|
14
|
Karlsson P, Fyles A, Chang SL, Arrick B, Baehner F, Malmström P, Fernö M, Holmberg E, Sjöström M, Liu FF, Cameron DA, Williams LJ, Bartlett JMS, Dunlop J, Caldwell J, Loane JF, Mallon E, Piper T, Jack WJ, Kunkler I, Feng FY, Speers CW, Pierce L, Bennett J, Taylor KJ. Abstract GS4-03: Validation of Profile for the Omission of Local Adjuvant Radiotherapy (POLAR) in a meta-analysis of three randomized controlled trials of breast conserving surgery +/- radiotherapy. Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-gs4-03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Abstract
Background: There are currently no commercially available tests to identify early stage breast cancer patients treated with breast conserving surgery (BCS) and systemic therapy at low risk of locoregional recurrence (LRR) for whom postoperative radiotherapy (RT) may be safely omitted. Profile for the Omission of Local Adjuvant Radiotherapy (POLAR) is a 16-gene molecular signature developed to identify invasive breast cancer patients who may be candidates for RT omission after BCS. In this work, we seek to validate POLAR in a meta-analysis of three RCTs of BCS +/- RT: SweBCG91RT, Scottish Conservation Trial (SCT) and Princess Margaret Hospital (PMH).
Methods: A patient-level meta-analysis was performed in 623 node-negative breast cancer patients with ER+/HER2-negative tumors who were enrolled in the three RCTs and for whom primary tumor material was available for analysis. Contributions from each cohort were as follows: SweBCG91RT N=354 (57%), SCT N=137 (22%), and PMH N=132 (21%). Numbers of LRR events in each cohort were as follows: SweBCG91RT N=72 (20%), SCT N=28 (20%), and PMH N=16 (12%). There was a mix of systemic therapy used (no systemic therapy for SweBCG91RT, chemotherapy or adjuvant endocrine therapy, but not both, in SCT, and tamoxifen but no chemotherapy for PMH). Median follow-up time for the patients who did not have LRR was 13.3 years for SweBCG91RT, 21.1 years for SCT, and 8.6 years for PMH. A multivariable Cox proportional hazards model on time to LRR, including the continuous standardized POLAR score, RT, and interaction, stratified by cohort, was used to test the interaction between the continuous POLAR score and RT. Additional Cox models tested the association between treatment arms separately for patients with a low and high POLAR score using a pre-specified cut point. Cumulative incidences were computed, with distant metastasis and death without recurrence considered as competing events.
Results: The test for interaction between RT treatment and POLAR was statistically significant (p = 0.022). Patients with a high POLAR score (N=429 [69%]) had a large benefit from RT (10-year cumulative incidence of LRR: 20% [15%-26%] for those not treated with RT vs 7% [4%-11%] for those treated with RT; hazard ratio for RT vs no RT: 0.37 [0.23-0.60], p < 0.001), whereas there was no evidence of benefit from RT for patients with a low POLAR score (N=194 [31%], 10-year cumulative incidence of LRR: 5% [2%-11%] for those not treated with RT vs 7% [3%-14%] for those treated with RT; hazard ratio for RT vs no RT: 0.92 [0.42-2.02], p = 0.832).
Conclusions: To our knowledge, POLAR is the first genomic classifier that is not only prognostic for LRR but also predictive, showing a significant interaction between RT and the classifier. Patients with a high POLAR score should be recommended radiotherapy while patients with a low score may be candidates for omission of radiotherapy after breast conserving surgery.
Citation Format: Per Karlsson, Anthony Fyles, S. Laura Chang, Bradley Arrick, Frederick Baehner, Per Malmström, Mårten Fernö, Erik Holmberg, Martin Sjöström, Fei-Fei Liu, David A. Cameron, Linda J. Williams, John MS Bartlett, Joanna Dunlop, Jacqueline Caldwell, Joseph F. Loane, Elizabeth Mallon, Tammy Piper, Wilma J. Jack, Ian Kunkler, Felix Y. Feng, Corey W. Speers, Lori Pierce, John Bennett, Karen J. Taylor. Validation of Profile for the Omission of Local Adjuvant Radiotherapy (POLAR) in a meta-analysis of three randomized controlled trials of breast conserving surgery +/- radiotherapy [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr GS4-03.
Collapse
Affiliation(s)
- Per Karlsson
- 1Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anthony Fyles
- 2Princess Margaret Cancer Centre and University of Toronto, Toronto, ON, Canada
| | | | | | | | - Per Malmström
- 6Division of Oncology, Department of Clinical Sciences Lund, Lund University, Sweden; Department of Haematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Mårten Fernö
- 7Division of Oncology, Department of Clinical Sciences Lund,Lund University, Sweden
| | - Erik Holmberg
- 8Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Martin Sjöström
- 9Division of Oncology, Department of Clinical Sciences Lund,Lund University, Sweden; Department of Radiation Oncology, University of California San Francisco, San Francisco, CA
| | - Fei-Fei Liu
- 10Princess Margaret Cancer Centre and University of Toronto, Toronto, ON, Canada
| | - David A. Cameron
- 11The University of Edinburgh, Edinburgh Cancer Research, EDINBURGH, Scotland, United Kingdom
| | - Linda J. Williams
- 12Edinburgh Clinical Trials Unit, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - John MS Bartlett
- 13University of Edinburgh, Scotland, United Kingdom, United Kingdom
| | - Joanna Dunlop
- 14Scottish Clinical Trials Research Unit (SCTRU), Edinburgh, Scotland, United Kingdom
| | | | - Joseph F. Loane
- 16Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | - Elizabeth Mallon
- 17University of Glasgow - Institute of Cancer Sciences, United Kingdom
| | - Tammy Piper
- 18University of Edinburgh, Edinburgh, United Kingdom
| | | | - Ian Kunkler
- 20University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Felix Y. Feng
- 21Department of Radiation Oncology, University of California San Francisco, San Francisco, CA
| | | | | | | | - Karen J. Taylor
- 25University of Edinburgh Cancer Research Centre, Institute of Genetics and Cancer
| |
Collapse
|
15
|
De Marchi T, Pyl PT, Sjöström M, Reinsbach SE, DiLorenzo S, Nystedt B, Tran L, Pekar G, Wärnberg F, Fredriksson I, Malmström P, Fernö M, Malmström L, Malmstöm J, Niméus E. Proteogenomics decodes the evolution of human ipsilateral breast cancer. Commun Biol 2023; 6:139. [PMID: 36732562 PMCID: PMC9894938 DOI: 10.1038/s42003-023-04526-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 01/24/2023] [Indexed: 02/04/2023] Open
Abstract
Ipsilateral breast tumor recurrence (IBTR) is a clinically important event, where an isolated in-breast recurrence is a potentially curable event but associated with an increased risk of distant metastasis and breast cancer death. It remains unclear if IBTRs are associated with molecular changes that can be explored as a resource for precision medicine strategies. Here, we employed proteogenomics to analyze a cohort of 27 primary breast cancers and their matched IBTRs to define proteogenomic determinants of molecular tumor evolution. Our analyses revealed a relationship between hormonal receptors status and proliferation levels resulting in the gain of somatic mutations and copy number. This in turn re-programmed the transcriptome and proteome towards a highly replicating and genomically unstable IBTRs, possibly enhanced by APOBEC3B. In order to investigate the origins of IBTRs, a second analysis that included primaries with no recurrence pinpointed proliferation and immune infiltration as predictive of IBTR. In conclusion, our study shows that breast tumors evolve into different IBTRs depending on hormonal status and proliferation and that immune cell infiltration and Ki-67 are significantly elevated in primary tumors that develop IBTR. These results can serve as a starting point to explore markers to predict IBTR formation and stratify patients for adjuvant therapy.
Collapse
Affiliation(s)
- Tommaso De Marchi
- Department of Clinical Sciences Lund, Division of Oncology, Lund University, Lund, Sweden.
| | - Paul Theodor Pyl
- grid.452834.c0000 0004 5911 2402Department of Laboratory Medicine, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund, Sweden
| | - Martin Sjöström
- grid.4514.40000 0001 0930 2361Department of Clinical Sciences Lund, Division of Oncology, Lund University, Lund, Sweden ,grid.266102.10000 0001 2297 6811Department of Radiation Oncology, University of California San Francisco, San Francisco, USA
| | - Susanne Erika Reinsbach
- grid.5371.00000 0001 0775 6028Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Gothenburg, Sweden
| | - Sebastian DiLorenzo
- grid.8993.b0000 0004 1936 9457National Bioinformatics Infrastructure Sweden, Uppsala University, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala, Sweden
| | - Björn Nystedt
- grid.8993.b0000 0004 1936 9457National Bioinformatics Infrastructure Sweden, Uppsala University, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala, Sweden
| | - Lena Tran
- grid.4514.40000 0001 0930 2361Department of Clinical Sciences Lund, Division of Oncology, Lund University, Lund, Sweden
| | - Gyula Pekar
- grid.411843.b0000 0004 0623 9987Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Skåne University Hospital, Lund, Sweden
| | - Fredrik Wärnberg
- grid.8761.80000 0000 9919 9582Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Irma Fredriksson
- grid.4714.60000 0004 1937 0626Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden ,grid.24381.3c0000 0000 9241 5705Department of Breast, Endocrine Tumors and Sarcoma, Karolinska University Hospital, Stockholm, Sweden
| | - Per Malmström
- grid.4514.40000 0001 0930 2361Department of Clinical Sciences Lund, Division of Oncology, Lund University, Lund, Sweden ,grid.411843.b0000 0004 0623 9987Department of Haematology, Oncology, and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Mårten Fernö
- grid.4514.40000 0001 0930 2361Department of Clinical Sciences Lund, Division of Oncology, Lund University, Lund, Sweden
| | - Lars Malmström
- grid.4514.40000 0001 0930 2361Department of Clinical Sciences Lund, Division of Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Johan Malmstöm
- grid.4514.40000 0001 0930 2361Department of Clinical Sciences Lund, Division of Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Emma Niméus
- Department of Clinical Sciences Lund, Division of Oncology, Lund University, Lund, Sweden. .,Department of Surgery, Skåne University Hospital, Lund, Sweden.
| |
Collapse
|
16
|
Feng E, Rydzewski NR, Zhang M, Lundberg A, Bootsma M, Helzer KT, Lang JM, Aggarwal R, Small EJ, Quigley DA, Sjöström M, Zhao SG. Intrinsic Molecular Subtypes of Metastatic Castration-Resistant Prostate Cancer. Clin Cancer Res 2022; 28:5396-5404. [PMID: 36260524 PMCID: PMC9890931 DOI: 10.1158/1078-0432.ccr-22-2567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/05/2022] [Accepted: 10/17/2022] [Indexed: 02/03/2023]
Abstract
PURPOSE Although numerous biology-driven subtypes have been described previously in metastatic castration-resistant prostate cancer (mCRPC), unsupervised molecular subtyping based on gene expression has been less studied, especially using large cohorts. Thus, we sought to identify the intrinsic molecular subtypes of mCRPC and assess molecular and clinical correlates in the largest combined cohort of mCRPC samples with gene expression data available to date. EXPERIMENTAL DESIGN We combined and batch-effect corrected gene expression data from four mCRPC cohorts from the Fred Hutchinson Cancer Research Center (N = 157), a small-cell neuroendocrine (NE) prostate cancer (SCNC)-enriched cohort from Weill Cornell Medicine (N = 49), and cohorts from the Stand Up 2 Cancer/Prostate Cancer Foundation East Coast Dream Team (N = 266) and the West Coast Dream Team (N = 162). RESULTS Hierarchical clustering of RNA-sequencing data from these 634 mCRPC samples identified two distinct adenocarcinoma subtypes, one of which (adeno-immune) was characterized by higher gene expression of immune pathways, higher CIBERSORTx immune scores, diminished ASI benefit, and non-lymph node metastasis tropism compared with an adeno-classic subtype. We also identified two distinct subtypes with enrichment for an NE phenotype, including an NE-liver subgroup characterized by liver metastasis tropism, PTEN loss, and APC and SPOP mutations compared with an NE-classic subgroup. CONCLUSIONS Our results emphasize the heterogeneity of mCRPC beyond currently accepted molecular phenotypes, and suggest that future studies should consider incorporating transcriptome-wide profiling to better understand how these differences impact treatment responses and outcomes.
Collapse
Affiliation(s)
- Eric Feng
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Nicholas R Rydzewski
- Department of Human Oncology, University of Wisconsin, Madison, Wisconsin
- Radiation Oncology Branch, National Cancer Institute, National Institute of Health, Bethesda, Maryland
| | - Meng Zhang
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California
| | - Arian Lundberg
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California
| | - Matthew Bootsma
- Department of Human Oncology, University of Wisconsin, Madison, Wisconsin
| | - Kyle T Helzer
- Department of Human Oncology, University of Wisconsin, Madison, Wisconsin
| | - Joshua M Lang
- Department of Medicine, University of Wisconsin, Madison, Wisconsin
- University of Wisconsin, Carbone Cancer Center, Madison, Wisconsin
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California
- Department of Medicine, University of California San Francisco, San Francisco, California
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California
- Department of Medicine, University of California San Francisco, San Francisco, California
| | - David A Quigley
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California
| | - Martin Sjöström
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California
- Division of Oncology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
| | - Shuang G Zhao
- Department of Human Oncology, University of Wisconsin, Madison, Wisconsin
- University of Wisconsin, Carbone Cancer Center, Madison, Wisconsin
- William S. Middleton Memorial Hospital, Madison, Wisconsin
| |
Collapse
|
17
|
Chou J, Trepka K, Sjöström M, Egusa EA, Chu CE, Zhu J, Chan E, Gibb EA, Badura ML, Contreras-Sanz A, Stohr BA, Meng MV, Pruthi RS, Lotan Y, Black PC, Porten SP, Koshkin VS, Friedlander TW, Feng FY. TROP2 Expression Across Molecular Subtypes of Urothelial Carcinoma and Enfortumab Vedotin-resistant Cells. Eur Urol Oncol 2022; 5:714-718. [PMID: 35216942 PMCID: PMC10262920 DOI: 10.1016/j.euo.2021.11.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/06/2021] [Accepted: 11/17/2021] [Indexed: 02/02/2023]
Abstract
Sacituzumab govitecan (SG) is an antibody-drug conjugate (ADC) targeting TROP2, which has recently been approved for treatment-refractory metastatic urothelial cancer (UC). However, the variability of TROP2 expression across different bladder cancer (BC) subtypes, as well as after enfortumab vedotin (EV) exposure, remains unknown. Using gene expression data from four clinical cohorts with >1400 patient samples of muscle-invasive BC and a BC tissue microarray, we found that TROP2 mRNA and protein are highly expressed across basal, luminal, and stroma-rich subtypes, but depleted in the neuroendocrine subtype. In addition, TROP2 mRNA levels are correlated with NECTIN4 mRNA but are more highly expressed than NECTIN4 mRNA in patient cohorts and BC cell lines. Moreover, CRISPR/Cas9-mediated knockdown of TROP2 demonstrates that its expression is one factor governing SG sensitivity. After prolonged EV exposure, cells can downregulate NECTIN4, leading to EV resistance, but retain TROP2 expression and remain sensitive to SG, suggesting nonoverlapping resistance mechanisms to these ADCs. While our findings warrant further validation, they have significant implications for biomarker development, patient selection, and treatment sequencing in the clinic as well as clinical trial design and stratification for metastatic BC patients. PATIENT SUMMARY: In this report, we investigated the expression levels of the drug target TROP2 across different molecular subtypes of bladder cancer in multiple patient cohorts and cell lines. We found high levels of TROP2 in most subtypes except in the neuroendocrine subtype. Overall, TROP2 gene expression is higher than NECTIN4 gene expression, and cells resistant to enfortumab vedotin (EV), a NECTIN4-targeting antibody-drug conjugate, remain sensitive to sacituzumab govitecan (SG). Our findings suggest that SG may be effective across most bladder cancer subtypes, including the bladder cancers previously treated with EV.
Collapse
Affiliation(s)
- Jonathan Chou
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA, USA; UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA.
| | - Kai Trepka
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA, USA; UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA; Department of Radiation Oncology, University of California, San Francisco, CA, USA; Medical Scientist Training Program, University of California, San Francisco, CA, USA
| | - Martin Sjöström
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA; Department of Radiation Oncology, University of California, San Francisco, CA, USA
| | - Emily A Egusa
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA; Department of Radiation Oncology, University of California, San Francisco, CA, USA
| | - Carissa E Chu
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, CA, USA
| | - Jun Zhu
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA; Department of Radiation Oncology, University of California, San Francisco, CA, USA
| | - Emily Chan
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA; Department of Pathology, University of California, San Francisco, CA, USA
| | - Ewan A Gibb
- Decipher Biosciences, Inc., San Diego, CA, USA
| | - Michelle L Badura
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA; Department of Radiation Oncology, University of California, San Francisco, CA, USA
| | | | - Bradley A Stohr
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA; Department of Pathology, University of California, San Francisco, CA, USA
| | - Maxwell V Meng
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, CA, USA
| | - Raj S Pruthi
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, CA, USA
| | - Yair Lotan
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Peter C Black
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Sima P Porten
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, CA, USA
| | - Vadim S Koshkin
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA, USA; UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Terence W Friedlander
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA, USA; UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Felix Y Feng
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA, USA; UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA; Department of Radiation Oncology, University of California, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, CA, USA.
| |
Collapse
|
18
|
DiNatale A, Worrede A, Iqbal W, Marchioli M, Toth A, Sjöström M, Zhu X, Corey E, Feng FY, Zhou W, Fatatis A. IL-1β expression driven by androgen receptor absence or inactivation promotes prostate cancer bone metastasis. Cancer Res Commun 2022; 2:1545-1557. [PMID: 36561929 PMCID: PMC9770512 DOI: 10.1158/2767-9764.crc-22-0262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We report the inverse association between the expression of androgen receptor (AR) and interleukin-1beta (IL-1β) in a cohort of patients with metastatic castration resistant prostate cancer (mCRPC). We also discovered that AR represses the IL-1β gene by binding an androgen response element (ARE) half-site located within the promoter, which explains the IL-1β expression in AR-negative (ARNEG) cancer cells. Consistently, androgen-depletion or AR-pathway inhibitors (ARIs) de-repressed IL-1β in ARPOS cancer cells, both in vitro and in vivo. The AR transcriptional repression is sustained by histone de-acetylation at the H3K27 mark in the IL-1β promoter. Notably, patients' data suggest that DNA methylation prevents IL-1β expression, even if the AR-signaling axis is inactive. Our previous studies show that secreted IL-1β supports metastatic progression in mice by altering the transcriptome of tumor-associated bone stroma. Thus, in prostate cancer patients harboring ARNEG tumor cells or treated with ADT/ARIs, and with the IL-1β gene unmethylated, IL-1β could condition the metastatic microenvironment to sustain disease progression.
Collapse
Affiliation(s)
- Anthony DiNatale
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA;,Present address: Janssen Oncology, Spring House, PA
| | - Asurayya Worrede
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA;,Present address: AstraZeneca, Baltimore, MD
| | - Waleed Iqbal
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Michael Marchioli
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA
| | - Allison Toth
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA
| | | | - Xiaolin Zhu
- Department of Radiation Oncology, UCSF, San Francisco, CA
| | - Eva Corey
- Department of Urology, University of Washington, WA
| | - Felix Y. Feng
- Department of Radiation Oncology, UCSF, San Francisco, CA
| | - Wanding Zhou
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Alessandro Fatatis
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA;,Program in Translational and Cellular Oncology, Sidney Kimmel Cancer Center at Thomas Jefferson University, Philadelphia, PA
| |
Collapse
|
19
|
Sjöström M, Zhao SG, Levy S, Zhang M, Ning Y, Shrestha R, Lundberg A, Herberts C, Foye A, Aggarwal R, Hua JT, Li H, Bergamaschi A, Maurice-Dror C, Maheshwari A, Chen S, Ng SWS, Ye W, Petricca J, Fraser M, Chesner L, Perry MD, Moreno-Rodriguez T, Chen WS, Alumkal JJ, Chou J, Morgans AK, Beer TM, Thomas GV, Gleave M, Lloyd P, Phillips T, McCarthy E, Haffner MC, Zoubeidi A, Annala M, Reiter RE, Rettig MB, Witte ON, Fong L, Bose R, Huang FW, Luo J, Bjartell A, Lang JM, Mahajan NP, Lara PN, Evans CP, Tran PT, Posadas EM, He C, Cui XL, Huang J, Zwart W, Gilbert LA, Maher CA, Boutros PC, Chi KN, Ashworth A, Small EJ, He HH, Wyatt AW, Quigley DA, Feng FY. The 5-Hydroxymethylcytosine Landscape of Prostate Cancer. Cancer Res 2022; 82:3888-3902. [PMID: 36251389 PMCID: PMC9627125 DOI: 10.1158/0008-5472.can-22-1123] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/13/2022] [Accepted: 07/29/2022] [Indexed: 02/03/2023]
Abstract
Analysis of DNA methylation is a valuable tool to understand disease progression and is increasingly being used to create diagnostic and prognostic clinical biomarkers. While conversion of cytosine to 5-methylcytosine (5mC) commonly results in transcriptional repression, further conversion to 5-hydroxymethylcytosine (5hmC) is associated with transcriptional activation. Here we perform the first study integrating whole-genome 5hmC with DNA, 5mC, and transcriptome sequencing in clinical samples of benign, localized, and advanced prostate cancer. 5hmC is shown to mark activation of cancer drivers and downstream targets. Furthermore, 5hmC sequencing revealed profoundly altered cell states throughout the disease course, characterized by increased proliferation, oncogenic signaling, dedifferentiation, and lineage plasticity to neuroendocrine and gastrointestinal lineages. Finally, 5hmC sequencing of cell-free DNA from patients with metastatic disease proved useful as a prognostic biomarker able to identify an aggressive subtype of prostate cancer using the genes TOP2A and EZH2, previously only detectable by transcriptomic analysis of solid tumor biopsies. Overall, these findings reveal that 5hmC marks epigenomic activation in prostate cancer and identify hallmarks of prostate cancer progression with potential as biomarkers of aggressive disease. SIGNIFICANCE In prostate cancer, 5-hydroxymethylcytosine delineates oncogene activation and stage-specific cell states and can be analyzed in liquid biopsies to detect cancer phenotypes. See related article by Wu and Attard, p. 3880.
Collapse
Affiliation(s)
- Martin Sjöström
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
- Division of Oncology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
| | - Shuang G Zhao
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI
- William S. Middleton Memorial Veterans' Hospital, Madison, WI
| | | | - Meng Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | | | - Raunak Shrestha
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Arian Lundberg
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Cameron Herberts
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Junjie T Hua
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Haolong Li
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | | | - Corinne Maurice-Dror
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- BC Cancer, Vancouver, BC, Canada
| | - Ashutosh Maheshwari
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Sujun Chen
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Sarah W S Ng
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Wenbin Ye
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Automation, Xiamen University, Xiamen, Fujian, China
| | - Jessica Petricca
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Michael Fraser
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Lisa Chesner
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Marc D Perry
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Thaidy Moreno-Rodriguez
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - William S Chen
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Joshi J Alumkal
- Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI
| | - Jonathan Chou
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Alicia K Morgans
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Tomasz M Beer
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
| | - George V Thomas
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
- Department of Pathology, Oregon Health & Science University, Portland, OR
| | - Martin Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | | | | | | | - Michael C Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA
- University of Washington, Seattle, WA
| | - Amina Zoubeidi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Matti Annala
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Robert E Reiter
- Departments of Medicine, Hematology/Oncology and Urology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA
| | - Matthew B Rettig
- Departments of Medicine, Hematology/Oncology and Urology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA
- VA Greater Los Angeles Healthcare System, Los Angeles, CA
| | - Owen N Witte
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Lawrence Fong
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Rohit Bose
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA
| | - Franklin W Huang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Jianhua Luo
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA
| | - Anders Bjartell
- Department of Translational Medicine, Medical Faculty, Lund University, Malmö, Sweden
- Department of Urology, Skåne University Hospital, Malmö, Sweden
| | - Joshua M Lang
- Department of Medicine, University of Wisconsin-Madison, Madison, WI
| | | | - Primo N Lara
- Division of Hematology Oncology, Department of Internal Medicine, University of California Davis, Sacramento, CA
- Comprehensive Cancer Center, University of California Davis, Sacramento, CA
| | - Christopher P Evans
- Comprehensive Cancer Center, University of California Davis, Sacramento, CA
- Department of Urologic Surgery, University of California Davis, Sacramento, CA
| | - Phuoc T Tran
- Department of Radiation Oncology, University of Maryland, College Park, Baltimore, MD
| | - Edwin M Posadas
- Urologic Oncology Program & Uro-Oncology Research Laboratories, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL
| | - Xiao-Long Cui
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL
| | - Jiaoti Huang
- Department of Pathology, Duke University, Durham, NC
| | - Wilbert Zwart
- Netherlands Cancer Institute, Oncode Institute, Amsterdam, the Netherlands
| | - Luke A Gilbert
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
- Arc Institute, Palo Alto, CA
| | - Christopher A Maher
- Siteman Cancer Center, Washington University, St. Louis, MO
- McDonnell Genome Institute, Washington University, St. Louis, MO
- Department of Internal Medicine, Washington University, St. Louis, MO
- Department of Biomedical Engineering, Washington University, St. Louis, MO
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Human Genetics, Institute for Precision Health, UCLA, Los Angeles, CA
- Jonsson Comprehensive Cancer Center, Departments of Human Genetics and Urology, University of California Los Angeles, Los Angeles, CA
| | - Kim N Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Housheng H He
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA
| | - Felix Y Feng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
| |
Collapse
|
20
|
Severson T, Qiu X, Alshalalfa M, Sjöström M, Quigley D, Bergman A, Long H, Feng F, Freedman ML, Zwart W, Pomerantz MM. Androgen receptor reprogramming demarcates prognostic, context-dependent gene sets in primary and metastatic prostate cancer. Clin Epigenetics 2022; 14:60. [PMID: 35509021 PMCID: PMC9069737 DOI: 10.1186/s13148-022-01278-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/19/2022] [Indexed: 11/10/2022] Open
Abstract
The androgen receptor (AR) is a prostate master transcription factor. It binds to genetic enhancers, where it regulates gene activity and plays a fundamental role in prostate pathophysiology. Previous work has demonstrated that AR-DNA binding is systematically and consistently reprogrammed during prostate tumorigenesis and disease progression. We charted these reprogrammed AR sites and identified genes proximal to them. We were able to devise gene lists based on AR status within specific histological contexts: normal prostate epithelium, primary prostate tumor, and metastatic prostate cancer. We evaluated expression of the genes in these gene sets in subjects from two distinct clinical cohorts-men treated with surgery for localized prostate cancer and men with metastatic prostate cancer. Among men with localized prostate cancer, expression of genes proximal to AR sites lost in the transition from normal prostate to prostate tumor was associated with clinical outcome. Among men with metastatic disease, expression of genes proximal to AR sites gained in metastatic tumors was associated with clinical outcome. These results are consistent with the notion that AR is fundamental to both maintaining differentiation in normal prostate tissue and driving de-differentiation in advanced prostate cancer. More broadly, the study demonstrates the power of incorporating context-dependent epigenetic data into genetic analyses.
Collapse
Affiliation(s)
- Tesa Severson
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mohammed Alshalalfa
- Department of Radiation Oncology, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Martin Sjöström
- Department of Radiation Oncology, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA.,Division of Oncology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
| | - David Quigley
- Department of Radiation Oncology, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Andries Bergman
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Henry Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Felix Feng
- Department of Radiation Oncology, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Mark M Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| |
Collapse
|
21
|
Ekersund J, Samuelsson E, Lindholm L, Sjöström M. A mobile app for the treatment of female mixed and urgency incontinence: a cost-effectiveness analysis in Sweden. Int Urogynecol J 2022; 33:1273-1282. [PMID: 35278093 PMCID: PMC9119896 DOI: 10.1007/s00192-022-05137-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 02/09/2022] [Indexed: 11/28/2022]
Abstract
Abstract
Introduction and hypothesis
A previous randomized controlled trial (RCT) demonstrated that the app Tät II, for self-management of mixed urinary incontinence (MUI) and urgency urinary incontinence (UUI), yielded significant, clinically relevant improvements in symptom severity and quality of life (QoL) compared with a control group. We aimed to assess the cost-effectiveness of Tät II.
Methods
A cost–utility analysis with a 1-year societal perspective was carried out, comparing Tät II with an information app. Data were collected alongside an RCT: 122 community-dwelling women aged ≥18 years with MUI or UUI ≥2 times/week were randomized to 3 months of Tät II treatment focused on pelvic floor muscle training (PFMT) and bladder training (BT; n = 60), or to an information app (n = 62). Self-assessed data from validated questionnaires were collected at baseline and at 3-month and 1-year follow-ups. Costs for assessment, treatment delivery, incontinence aids, laundry, and time for PFMT and BT were included. We calculated quality-adjusted life-years (QALYs) using the International Consultation on Incontinence Modular Questionnaire Lower Urinary Tract Symptoms Quality of Life. The incremental cost-effectiveness ratio (ICER) between the groups was our primary outcome. Sensitivity analyses were performed.
Results
The mean age was 58.3 (SD = 9.6) years. Annual overall costs were €738.42 in the treatment group and €605.82 in the control group; annual QALY gains were 0.0152 and 0.0037 respectively. The base case ICER was €11,770.52; ICERs in the sensitivity analyses ranged from €−9,303.78 to €22,307.67.
Conclusions
The app Tät II is a cost-effective treatment method for women with MUI and UUI.
Collapse
Affiliation(s)
- J Ekersund
- Department of Public Health and Clinical Medicine, Umeå University, 905 81, Umeå, Sweden
| | - E Samuelsson
- Department of Public Health and Clinical Medicine, Umeå University, 905 81, Umeå, Sweden
| | - L Lindholm
- Department of Public Health and Clinical Medicine, Umeå University, 905 81, Umeå, Sweden
| | - M Sjöström
- Department of Public Health and Clinical Medicine, Umeå University, 905 81, Umeå, Sweden.
| |
Collapse
|
22
|
Tutzauer J, Sjöström M, Holmberg E, Karlsson P, Killander F, Leeb-Lundberg LMF, Malmström P, Niméus E, Fernö M, Jögi A. Breast cancer hypoxia in relation to prognosis and benefit from radiotherapy after breast-conserving surgery in a large, randomised trial with long-term follow-up. Br J Cancer 2022; 126:1145-1156. [PMID: 35140341 PMCID: PMC9023448 DOI: 10.1038/s41416-021-01630-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 10/17/2021] [Accepted: 11/03/2021] [Indexed: 12/21/2022] Open
Abstract
Background Breast-conserving surgery followed by radiotherapy is part of standard treatment for early-stage breast cancer. Hypoxia is common in cancer and may affect the benefit of radiotherapy. Cells adapt to hypoxic stress largely via the transcriptional activity of hypoxia-inducible factor (HIF)-1α. Here, we aim to determine whether tumour HIF-1α-positivity and hypoxic gene-expression signatures associated with the benefit of radiotherapy, and outcome. Methods Tumour HIF-1α-status and expression of hypoxic gene signatures were retrospectively analysed in a clinical trial where 1178 women with primary T1-2N0M0 breast cancer were randomised to receive postoperative radiotherapy or not and followed 15 years for recurrence and 20 years for breast cancer death. Results The benefit from radiotherapy was similar in patients with HIF-1α-positive and -negative primary tumours. Both ipsilateral and any breast cancer recurrence were more frequent in women with HIF-1α-positive primary tumours (hazard ratio, HR0–5 yrs1.9 [1.3–2.9], p = 0.003 and HR0–5 yrs = 2.0 [1.5–2.8], p < 0.0001). Tumour HIF-1α-positivity is also associated with increased breast cancer death (HR0–10 years 1.9 [1.2–2.9], p = 0.004). Ten of the 11 investigated hypoxic gene signatures correlated positively to HIF-1α-positivity, and 5 to increased rate/risk of recurrence. Conclusions The benefit of postoperative radiotherapy persisted in patients with hypoxic primary tumours. Patients with hypoxic primary breast tumours had an increased risk of recurrence and breast cancer death.
Collapse
Affiliation(s)
- Julia Tutzauer
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Martin Sjöström
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Erik Holmberg
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Per Karlsson
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Fredrika Killander
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.,Department of Haematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | | | - Per Malmström
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.,Department of Haematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Emma Niméus
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.,Division of Surgery, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.,Department of Surgery Malmö, Skåne University Hospital, Malmö, Sweden
| | - Mårten Fernö
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Annika Jögi
- Translational Cancer Research, Department of Laboratory Medicine, Lund University Cancer Center at Medicon Village, Lund University, Lund, Sweden. .,Skåne University Hospital, Malmö, Sweden.
| |
Collapse
|
23
|
Mazzu YZ, Liao Y, Nandakumar S, Sjöström M, Jehane LE, Ghale R, Govindarajan B, Gerke TA, Lee GSM, Luo JH, Chinni SR, Mucci LA, Feng FY, Kantoff PW. Dynamic expression of SNAI2 in prostate cancer predicts tumor progression and drug sensitivity. Mol Oncol 2021; 16:2451-2469. [PMID: 34792282 PMCID: PMC9251866 DOI: 10.1002/1878-0261.13140] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/05/2021] [Accepted: 11/16/2021] [Indexed: 11/13/2022] Open
Abstract
Prostate cancer is a highly heterogeneous disease, understanding the crosstalk between complex genomic and epigenomic alterations will aid in developing targeted therapeutics. We demonstrate that, even though snail family transcriptional repressor 2 (SNAI2) is frequently amplified in prostate cancer, it is epigenetically silenced in this disease, with dynamic changes in SNAI2 levels showing distinct clinical relevance. Integrative clinical data from 18 prostate cancer cohorts and experimental evidence showed that gene fusion between transmembrane serine protease 2 (TMPRSS2) and ETS transcription factor ERG (ERG) (TMPRSS2–ERG fusion) is involved in the silencing of SNAI2. We created a silencer score to evaluate epigenetic repression of SNAI2, which can be reversed by treatment with DNA methyltransferase inhibitors and histone deacetylase inhibitors. Silencing of SNAI2 facilitated tumor cell proliferation and luminal differentiation. Furthermore, SNAI2 has a major influence on the tumor microenvironment by reactivating tumor stroma and creating an immunosuppressive microenvironment in prostate cancer. Importantly, SNAI2 expression levels in part determine sensitivity to the cancer drugs dasatinib and panobinostat. For the first time, we defined the distinct clinical relevance of SNAI2 expression at different disease stages. We elucidated how epigenetic silencing of SNAI2 controls the dynamic changes of SNAI2 expression that are essential for tumor initiation and progression and discovered that restoring SNAI2 expression by treatment with panobinostat enhances dasatinib sensitivity, indicating a new therapeutic strategy for prostate cancer.
Collapse
Affiliation(s)
- Ying Z Mazzu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - YuRou Liao
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Subhiksha Nandakumar
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martin Sjöström
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Lina E Jehane
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Romina Ghale
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Travis A Gerke
- Prostate Cancer Clinical Trials Consortium, New York, NY, USA
| | - Gwo-Shu Mary Lee
- Department of Medicine, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jian-Hua Luo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Lorelei A Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Felix Y Feng
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Philip W Kantoff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| |
Collapse
|
24
|
Aggarwal R, Rydzewski NR, Zhang L, Foye A, Kim W, Helzer KT, Bakhtiar H, Chang SL, Perry MD, Gleave M, Reiter RE, Huang J, Evans CP, Alumkal JJ, Lang JM, Yu M, Quigley DA, Sjöström M, Small EJ, Feng FY, Zhao SG. Prognosis Associated With Luminal and Basal Subtypes of Metastatic Prostate Cancer. JAMA Oncol 2021; 7:1644-1652. [PMID: 34554200 DOI: 10.1001/jamaoncol.2021.3987] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Importance Luminal and basal subtypes of primary prostate cancer have been shown to be molecularly distinct and clinically important in predicting response to therapy. These subtypes have not been described in metastatic prostate cancer. Objectives To identify clinical and molecular correlates of luminal and basal subtypes in metastatic castration-resistant prostate cancer (mCRPC) and investigate differences in survival, particularly after treatment with androgen-signaling inhibitors (ASIs). Design, Setting, and Participants In this cohort study, a retrospective analysis was conducted of 4 cohorts with mCRPC (N = 634) across multiple academic centers. Treatment was at the physicians' discretion. Details of the study cohorts have been published elsewhere between 2016 and 2019. Data were analyzed from March 2018 to February 2021. Main Outcomes and Measures The primary clinical end point was overall survival from the date of tissue biopsy/molecular profiling. Luminal and basal subtypes were also stratified by postbiopsy ASI treatment. The primary molecular analyses included associations with small cell/neuroendocrine prostate cancer (SCNC), molecular pathways, and DNA alterations. Results In the 634 patients, 288 (45%) had tumors classified as luminal, and 346 (55%) had tumors classified as basal. However, 53 of 59 (90%) SCNC tumors were basal (P < .001). Similar to primary prostate cancer, luminal tumors exhibited overexpression of AR pathway genes. In basal tumors, a significantly higher rate of RB1 loss (23% basal vs 4% luminal; P < .001), FOXA1 alterations (36% basal vs 27% luminal; P = .03) and MYC alterations (73% basal vs 56% luminal; P < .001) were identified. Patients with basal tumors had worse overall survival compared with those with luminal tumors only in patients treated with an ASI postbiopsy (East Coast Dream Team: hazard ratio [HR], 0.39; 95% CI, 0.20-0.74; P = .004; West Coast Dream Team: HR, 0.57; 95% CI, 0.33-0.97; P = .04). Among patients with luminal tumors, those treated with an ASI had significantly better survival (HR, 0.27; 95% CI, 0.14-0.53; P < .001), whereas patients with basal tumors did not (HR, 0.62; 95% CI, 0.36-1.04, P = .07). The interaction term between subtype and ASI treatment was statistically significant (HR, 0.42; 95% CI, 0.20-0.89; P = .02). Conclusions and Relevance These findings represent the largest integrated clinical, transcriptomic, and genomic analysis of mCRPC samples to date, and suggest that mCRPC can be classified as luminal and basal tumors. Analogous to primary prostate cancer, these data suggest that the benefit of ASI treatment is more pronounced in luminal tumors and support the use of ASIs in this population. In the basal tumors, a chemotherapeutic approach could be considered in some patients given the similarity to SCNC and the diminished benefit of ASI therapy. Further validation in prospective clinical trials is warranted.
Collapse
Affiliation(s)
- Rahul Aggarwal
- Department of Human Oncology, University of Wisconsin, Madison.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco
| | | | - Li Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco.,Division of Hematology and Oncology, University of California, San Francisco
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco.,Division of Hematology and Oncology, University of California, San Francisco
| | - Won Kim
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco.,Division of Hematology and Oncology, University of California, San Francisco
| | - Kyle T Helzer
- Department of Human Oncology, University of Wisconsin, Madison
| | - Hamza Bakhtiar
- Department of Human Oncology, University of Wisconsin, Madison
| | - S Laura Chang
- Department of Radiation Oncology, University of California, San Francisco
| | - Marc D Perry
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco.,Department of Radiation Oncology, University of California, San Francisco
| | - Martin Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert E Reiter
- Jonsson Comprehensive Cancer Center, Departments of Medicine and Urology, University of California Los Angeles
| | - Jiaoti Huang
- Department of Pathology, Duke University, Durham, North Carolina
| | - Christopher P Evans
- Comprehensive Cancer Center, Department of Urologic Surgery, University of California Davis, Sacramento
| | - Joshi J Alumkal
- Department of Internal Medicine, Rogel Cancer Center, University of Michigan, Ann Arbor
| | - Joshua M Lang
- Department of Medicine, University of Wisconsin, Madison
| | - Menggang Yu
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco.,Department of Epidemiology and Biostatistics, University of California, San Francisco
| | - Martin Sjöström
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco.,Department of Radiation Oncology, University of California, San Francisco
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco.,Division of Hematology and Oncology, University of California, San Francisco
| | - Felix Y Feng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco.,Division of Hematology and Oncology, University of California, San Francisco.,Department of Radiation Oncology, University of California, San Francisco.,Department of Urology, University of California, San Francisco
| | - Shuang G Zhao
- Department of Human Oncology, University of Wisconsin, Madison.,William S. Middleton Memorial Veterans Hospital, Madison
| |
Collapse
|
25
|
Rydzewski NR, Peterson E, Lang JM, Yu M, Laura Chang S, Sjöström M, Bakhtiar H, Song G, Helzer KT, Bootsma ML, Chen WS, Shrestha RM, Zhang M, Quigley DA, Aggarwal R, Small EJ, Wahl DR, Feng FY, Zhao SG. Predicting cancer drug TARGETS - TreAtment Response Generalized Elastic-neT Signatures. NPJ Genom Med 2021; 6:76. [PMID: 34548481 PMCID: PMC8455625 DOI: 10.1038/s41525-021-00239-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 08/23/2021] [Indexed: 12/14/2022] Open
Abstract
We are now in an era of molecular medicine, where specific DNA alterations can be used to identify patients who will respond to specific drugs. However, there are only a handful of clinically used predictive biomarkers in oncology. Herein, we describe an approach utilizing in vitro DNA and RNA sequencing and drug response data to create TreAtment Response Generalized Elastic-neT Signatures (TARGETS). We trained TARGETS drug response models using Elastic-Net regression in the publicly available Genomics of Drug Sensitivity in Cancer (GDSC) database. Models were then validated on additional in-vitro data from the Cancer Cell Line Encyclopedia (CCLE), and on clinical samples from The Cancer Genome Atlas (TCGA) and Stand Up to Cancer/Prostate Cancer Foundation West Coast Prostate Cancer Dream Team (WCDT). First, we demonstrated that all TARGETS models successfully predicted treatment response in the separate in-vitro CCLE treatment response dataset. Next, we evaluated all FDA-approved biomarker-based cancer drug indications in TCGA and demonstrated that TARGETS predictions were concordant with established clinical indications. Finally, we performed independent clinical validation in the WCDT and found that the TARGETS AR signaling inhibitors (ARSI) signature successfully predicted clinical treatment response in metastatic castration-resistant prostate cancer with a statistically significant interaction between the TARGETS score and PSA response (p = 0.0252). TARGETS represents a pan-cancer, platform-independent approach to predict response to oncologic therapies and could be used as a tool to better select patients for existing therapies as well as identify new indications for testing in prospective clinical trials.
Collapse
Affiliation(s)
| | - Erik Peterson
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Joshua M Lang
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Menggang Yu
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
| | - S Laura Chang
- Department of Radiation Oncology, UCSF, San Francisco, CA, USA
| | - Martin Sjöström
- Department of Radiation Oncology, UCSF, San Francisco, CA, USA
| | - Hamza Bakhtiar
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - Gefei Song
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - Kyle T Helzer
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - Matthew L Bootsma
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - William S Chen
- Department of Radiation Oncology, UCSF, San Francisco, CA, USA
| | | | - Meng Zhang
- Department of Radiation Oncology, UCSF, San Francisco, CA, USA
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA, USA
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, CA, USA
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, CA, USA
| | - Daniel R Wahl
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Felix Y Feng
- Department of Radiation Oncology, UCSF, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, CA, USA
- Department of Urology, UCSF, San Francisco, CA, USA
| | - Shuang G Zhao
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA.
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA.
- William S. Middleton Memorial Veterans Hospital, Madison, WI, USA.
| |
Collapse
|
26
|
Chu CE, Sjöström M, Egusa EA, Gibb EA, Badura ML, Zhu J, Koshkin VS, Stohr BA, Meng MV, Pruthi RS, Friedlander TW, Lotan Y, Black PC, Porten SP, Feng FY, Chou J. Heterogeneity in NECTIN4 Expression Across Molecular Subtypes of Urothelial Cancer Mediates Sensitivity to Enfortumab Vedotin. Clin Cancer Res 2021; 27:5123-5130. [PMID: 34108177 PMCID: PMC8634828 DOI: 10.1158/1078-0432.ccr-20-4175] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 02/02/2021] [Accepted: 05/07/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Enfortumab vedotin (EV) is an antibody-drug conjugate (ADC) targeting NECTIN4 (encoded by the PVRL4/NECTIN4 gene) approved for treatment-refractory metastatic urothelial cancer. Factors that mediate sensitivity or resistance to EV are unknown. In this study, we sought to (i) examine heterogeneity of NECTIN4 gene expression across molecular subtypes of bladder cancer and (ii) determine whether NECTIN4 expression mediates EV sensitivity or resistance. EXPERIMENTAL DESIGN Molecular subtyping and NECTIN4 expression data from seven muscle-invasive bladder cancer clinical cohorts (n = 1,915 total specimens) were used to assess NECTIN4 expression across molecular subtypes. The outcome of the transcriptomic analysis was relative NECTIN4 expression in the consensus molecular subtypes of bladder cancer. Expression of NECTIN4 was validated in bladder cancer cell lines. NECTIN4 was stably overexpressed or knocked down in basal and luminal bladder cancer cell lines and EV drug sensitivity assays were performed, as measured by cell proliferation and clonogenic assays. RESULTS NECTIN4 expression is heterogenous across molecular subtypes of bladder cancer and significantly enriched in luminal subtypes. NECTIN4 expression is positively correlated with luminal markers GATA3, FOXA1, and PPARG across all cohorts. NECTIN4 expression is both necessary and sufficient for EV sensitivity in luminal and basal subtypes of urothelial bladder cancer cells. Downregulation of NECTIN4 leads to EV resistance. CONCLUSIONS Sensitivity to EV is mediated by expression of NECTIN4, which is enriched in luminal subtypes of bladder cancer. These findings may have implications for biomarker development, patient selection, and the inclusion of molecular subtyping in ongoing and future EV clinical trials.See related commentary by Teo and Rosenberg, p. 4950.
Collapse
Affiliation(s)
- Carissa E Chu
- Department of Urology, University of California, San Francisco, California
| | - Martin Sjöström
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, California
| | - Emily A Egusa
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, California
| | - Ewan A Gibb
- Decipher Biosciences, Inc., San Diego, California
| | - Michelle L Badura
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, California
| | - Jun Zhu
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, California
| | - Vadim S Koshkin
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, California
| | - Bradley A Stohr
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
- Department of Pathology, University of California, San Francisco, California
| | - Maxwell V Meng
- Department of Urology, University of California, San Francisco, California
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Raj S Pruthi
- Department of Urology, University of California, San Francisco, California
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Terence W Friedlander
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, California
| | - Yair Lotan
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Peter C Black
- Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sima P Porten
- Department of Urology, University of California, San Francisco, California
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Felix Y Feng
- Department of Urology, University of California, San Francisco, California.
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, California
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, California
| | - Jonathan Chou
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California.
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, California
| |
Collapse
|
27
|
Das R, Sjöström M, Shrestha R, Yogodzinski C, Egusa EA, Chesner LN, Chen WS, Chou J, Dang DK, Swinderman JT, Ge A, Hua JT, Kabir S, Quigley DA, Small EJ, Ashworth A, Feng FY, Gilbert LA. An integrated functional and clinical genomics approach reveals genes driving aggressive metastatic prostate cancer. Nat Commun 2021; 12:4601. [PMID: 34326322 PMCID: PMC8322386 DOI: 10.1038/s41467-021-24919-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/15/2021] [Indexed: 02/07/2023] Open
Abstract
Genomic sequencing of thousands of tumors has revealed many genes associated with specific types of cancer. Similarly, large scale CRISPR functional genomics efforts have mapped genes required for cancer cell proliferation or survival in hundreds of cell lines. Despite this, for specific disease subtypes, such as metastatic prostate cancer, there are likely a number of undiscovered tumor specific driver genes that may represent potential drug targets. To identify such genetic dependencies, we performed genome-scale CRISPRi screens in metastatic prostate cancer models. We then created a pipeline in which we integrated pan-cancer functional genomics data with our metastatic prostate cancer functional and clinical genomics data to identify genes that can drive aggressive prostate cancer phenotypes. Our integrative analysis of these data reveals known prostate cancer specific driver genes, such as AR and HOXB13, as well as a number of top hits that are poorly characterized. In this study we highlight the strength of an integrated clinical and functional genomics pipeline and focus on two top hit genes, KIF4A and WDR62. We demonstrate that both KIF4A and WDR62 drive aggressive prostate cancer phenotypes in vitro and in vivo in multiple models, irrespective of AR-status, and are also associated with poor patient outcome.
Collapse
Affiliation(s)
- Rajdeep Das
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Martin Sjöström
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Raunak Shrestha
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher Yogodzinski
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Emily A Egusa
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Lisa N Chesner
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - William S Chen
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan Chou
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Donna K Dang
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Jason T Swinderman
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Alex Ge
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Junjie T Hua
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Shaheen Kabir
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Felix Y Feng
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
| | - Luke A Gilbert
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
| |
Collapse
|
28
|
Lindgren Å, Sjöström M, Hellsten M, Lif A. Modell zur Ermittlung der Waschkraft einiger technischer nichtionischer Tenside / Modelling of detergency performance for some technical nonionic surfactants. TENSIDE SURFACT DET 2021. [DOI: 10.1515/tsd-1995-320404] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
29
|
Sjöström M, Chang SL, Hartman L, Holmberg E, Feng FY, Speers CW, Pierce LJ, Malmström P, Fernö M, Karlsson P. Discovery and validation of a genomic signature to identify women with early-stage invasive breast cancer who may safely omit adjuvant radiotherapy after breast-conserving surgery. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
512 Background: Adjuvant radiotherapy (RT) is currently the standard of care for women with early-stage invasive breast cancer (BC) treated with breast conserving surgery (BCS). However, some women may have very low risk of recurrence and could safely be spared RT. This study aimed to identify these women using a molecularly-based approach. Methods: We performed an analysis of the SweBCG91-RT cohort, a trial randomizing women with node-negative stage I-II invasive BC +/- RT following breast conserving surgery, with sparse use of adjuvant systemic therapy. Only patients with ER+, HER2- tumors, and not treated with adjuvant systemic therapy, were included in this analysis. Transcriptome-wide profiling of tumors was performed using the Affymetrix Human Exon 1.0 ST microarray. The SweBCG91-RT cohort was divided into a training cohort of 243 patients and a validation cohort of 354 patients. Biological gene sets and individual genes related to locoregional recurrence in patients not receiving RT of the training set were identified, and a 16-gene signature was trained using elastic net regression. The signature, named Profile for the Omission of Local Adjuvant Radiation (POLAR), was locked prior to validation. Results: In the validation cohort, POLAR was prognostic for locoregional recurrence (LRR) in patients not treated with RT (multivariable Cox model adjusting for age, grade, tumor size, and luminal A vs luminal B: HR = 1.7 [1.2,2.3], p < 0.001). Patients categorized as POLAR low-risk had a 10-year locoregional recurrence rate of 7% in the absence of RT. Notably, there was no significant benefit from RT for these POLAR low-risk patients (HR = 1.1 [0.38,3.3], p = 0.83), whereas patients categorized as POLAR high-risk had a significant decreased risk of locoregional recurrence when treated with RT (recurrence rate without RT at 10-years 19%, HR = 0.43 [0.24,0.78], p = 0.0053). Conclusions: These data suggest that the novel POLAR genomic signature based on LRR biology can not only identify patients who have a low risk of LRR without adjuvant RT after BCS but who also would not benefit from RT, thus being prime candidates for RT omission.
Collapse
Affiliation(s)
- Martin Sjöström
- University of California, San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | | | - Linda Hartman
- Lund University, Department of Oncology and Pathology, Lund, Sweden
| | | | - Felix Y Feng
- University of California, San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | | | | | - Per Malmström
- Lund University and Skåne University Hospital, Lund, Sweden
| | - Mårten Fernö
- Lund University, Department of Oncology and Pathology, Lund, Sweden
| | - Per Karlsson
- Sahlgrenska Academy, Sahlgrenska University Hospital, Department of Oncology, Gothenburg, Sweden
| |
Collapse
|
30
|
De Marchi T, Pyl PT, Sjöström M, Klasson S, Sartor H, Tran L, Pekar G, Malmström J, Malmström L, Niméus E. Proteogenomic Workflow Reveals Molecular Phenotypes Related to Breast Cancer Mammographic Appearance. J Proteome Res 2021; 20:2983-3001. [PMID: 33855848 PMCID: PMC8155562 DOI: 10.1021/acs.jproteome.1c00243] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Indexed: 12/21/2022]
Abstract
Proteogenomic approaches have enabled the generat̲ion of novel information levels when compared to single omics studies although burdened by extensive experimental efforts. Here, we improved a data-independent acquisition mass spectrometry proteogenomic workflow to reveal distinct molecular features related to mammographic appearances in breast cancer. Our results reveal splicing processes detectable at the protein level and highlight quantitation and pathway complementarity between RNA and protein data. Furthermore, we confirm previously detected enrichments of molecular pathways associated with estrogen receptor-dependent activity and provide novel evidence of epithelial-to-mesenchymal activity in mammography-detected spiculated tumors. Several transcript-protein pairs displayed radically different abundances depending on the overall clinical properties of the tumor. These results demonstrate that there are differentially regulated protein networks in clinically relevant tumor subgroups, which in turn alter both cancer biology and the abundance of biomarker candidates and drug targets.
Collapse
Affiliation(s)
- Tommaso De Marchi
- Division
of Surgery, Oncology, and Pathology, Department of Clinical Sciences, Lund University, Solvegatan 19, Lund SE-223 62, Sweden
| | - Paul Theodor Pyl
- Division
of Surgery, Oncology, and Pathology, Department of Clinical Sciences, Lund University, Solvegatan 19, Lund SE-223 62, Sweden
| | - Martin Sjöström
- Division
of Surgery, Oncology, and Pathology, Department of Clinical Sciences, Lund University, Solvegatan 19, Lund SE-223 62, Sweden
| | - Stina Klasson
- Department
Plastic and Reconstructive Surgery, Skåne
University Hospital, Inga Marie Nilssons gata 47, Malmö SE-20502, Sweden
| | - Hanna Sartor
- Division
of Diagnostic Radiology, Department of Translational Medicine, Skåne University Hospital, Entrégatan 7, Lund SE-22185, Sweden
| | - Lena Tran
- Division
of Surgery, Oncology, and Pathology, Department of Clinical Sciences, Lund University, Solvegatan 19, Lund SE-223 62, Sweden
| | - Gyula Pekar
- Division
of Oncology and Pathology, Department of Clinical Sciences, Lund University, Skåne University Hospital, Lund SE-22185, Sweden
| | - Johan Malmström
- Division
of Infection Medicine, Department of Clinical Sciences Lund, Faculty
of Medicine, Lund University, Klinikgatan 32, Lund SE-22184, Sweden
| | - Lars Malmström
- S3IT, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
- Institute
for Computational Science, University of
Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Emma Niméus
- Division
of Surgery, Oncology, and Pathology, Department of Clinical Sciences, Lund University, Solvegatan 19, Lund SE-223 62, Sweden
- Department
of Surgery, Skåne University Hospital, Lund 222 42, Sweden
| |
Collapse
|
31
|
Chu CE, Alshalalfa M, Sjöström M, Zhao SG, Liu Y, Chou J, Herlemann A, Mahal B, Kishan AU, Spratt DE, Cooperberg M, Small E, Wong A, Porten S, Hope TA, Ross AE, Davicioni E, Nguyen P, Karnes RJ, Carroll PR, Schaeffer E, Feng FY. Prostate-specific Membrane Antigen and Fluciclovine Transporter Genes are Associated with Variable Clinical Features and Molecular Subtypes of Primary Prostate Cancer. Eur Urol 2021; 79:717-721. [PMID: 33840559 DOI: 10.1016/j.eururo.2021.03.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 03/16/2021] [Indexed: 12/21/2022]
Abstract
18F-Fluciclovine-based positron emission tomography (PET) imaging is recommended in the USA for biochemical recurrence (BCR) after prostate cancer treatment. However, prostate-specific membrane antigen (PSMA)-based PET imaging is more common worldwide, supported by international guidelines, and is now approved by the Food and Drug Administration in the USA for initial staging of primary prostate cancer. Little is known about the molecular profiles of lesions detected by PSMA-targeted PET/computed tomography (CT) versus 18F-fluciclovine PET/CT. We examined the expression of PSMA (FOLH1) and the fluciclovine transporter genes LAT1-4 and ASCT1/2 in a combined cohort of more than 18 000 radical prostatectomy specimens and their associations with clinical outcomes. Expression of PSMA and all but one fluciclovine transporter gene was higher in prostate cancer than in benign tissue. PSMA expression was associated with Gleason score (GS) ≥8 and lymph node involvement (LNI), and had a positive linear correlation with Decipher risk score. By contrast, expression of the fluciclovine transporters LAT2, LAT3, and ASCT2 was negatively associated with GS ≥ 8, LNI, and high Decipher score. The top decile of PSMA expression was associated with poorest metastasis-free survival (MFS), while the bottom deciles of LAT3 and ASCT2 expression were associated with poorest MFS. PATIENT SUMMARY: We measured the expression of genes that encode the targets for two different radiotracers in PET (positron emission tomography) scans of the prostate. We found that PSMA gene expression (PSMA-based tracer) is associated with worse clinical outcomes, while expression of ASCT2, LAT2, and LAT3 genes (fluciclovine tracer) is associated with better outcomes.
Collapse
Affiliation(s)
- Carissa E Chu
- Department of Urology, University of California-San Francisco, San Francisco, CA, USA
| | - Mohammed Alshalalfa
- Department of Radiation Oncology, University of California-San Francisco, San Francisco, CA, USA
| | - Martin Sjöström
- Department of Radiation Oncology, University of California-San Francisco, San Francisco, CA, USA; UCSF Helen Diller Comprehensive Cancer Center, San Francisco, CA, USA
| | - Shuang G Zhao
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Yang Liu
- Decipher Biosciences, La Jolla, CA, USA
| | - Jonathan Chou
- UCSF Helen Diller Comprehensive Cancer Center, San Francisco, CA, USA; Division of Hematology/Oncology, Department of Medicine, University of California-San Francisco, San Francisco, CA, USA
| | - Annika Herlemann
- Department of Urology, Ludwig-Maximilians University, Munich, Germany
| | - Brandon Mahal
- Department of Radiation Oncology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Amar U Kishan
- Department of Radiation Oncology, University of California-Los Angeles, Los Angeles, CA, USA
| | - Daniel E Spratt
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Matthew Cooperberg
- Department of Urology, University of California-San Francisco, San Francisco, CA, USA; Department of Radiation Oncology, University of California-San Francisco, San Francisco, CA, USA
| | - Eric Small
- UCSF Helen Diller Comprehensive Cancer Center, San Francisco, CA, USA; Decipher Biosciences, La Jolla, CA, USA
| | - Anthony Wong
- Department of Radiation Oncology, University of California-San Francisco, San Francisco, CA, USA
| | - Sima Porten
- Department of Urology, University of California-San Francisco, San Francisco, CA, USA; UCSF Helen Diller Comprehensive Cancer Center, San Francisco, CA, USA
| | - Thomas A Hope
- Department of Urology, University of California-San Francisco, San Francisco, CA, USA; UCSF Helen Diller Comprehensive Cancer Center, San Francisco, CA, USA; Department of Radiology and Biomedical Imaging, University of California-San Francisco, San Francisco, CA, USA
| | - Ashley E Ross
- Department of Urology, Northwestern University, Chicago, IL, USA
| | | | - Paul Nguyen
- Department of Radiation Oncology, Dana Farber Cancer Institute, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Peter R Carroll
- Department of Urology, University of California-San Francisco, San Francisco, CA, USA; UCSF Helen Diller Comprehensive Cancer Center, San Francisco, CA, USA
| | - Edward Schaeffer
- Department of Urology, Northwestern University, Chicago, IL, USA.
| | - Felix Y Feng
- Department of Urology, University of California-San Francisco, San Francisco, CA, USA; Department of Radiation Oncology, University of California-San Francisco, San Francisco, CA, USA; UCSF Helen Diller Comprehensive Cancer Center, San Francisco, CA, USA.
| |
Collapse
|
32
|
Sjöström M, Zhao S, Small EJ, Ning Y, Maurice-Dror C, Foye A, Hua JJT, Li H, Beer TM, Evans CP, Rettig M, Chi KN, Alumkal JJ, Aggarwal RR, Ashworth A, Levy S, He HH, Wyatt AW, Quigley DA, Feng FY. 5-hydroxymethylcytosine as a liquid biopsy biomarker in mCRPC. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.6_suppl.148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
148 Background: 5-hydroxymethylcytosine (5hmC) is an epigenetic modification which regulates gene expression and is associated with active transcription. The optimization of 5hmC sequencing in cell-free DNA (cfDNA) could therefore enable assessment of gene activity through a liquid biopsy. We aimed to investigate the 5hmC landscape of metastatic castration-resistant prostate cancer (mCRPC) and to evaluate the potential of 5hmC modifications in cfDNA as biomarkers of outcome in mCRPC patients. Methods: Genome-wide 5hmC modifications were analyzed with a low-input whole-genome 5hmC sequencing method based on selective chemical labeling in DNA from 93 mCRPC tissue biopsies previously profiled with whole-genome sequencing (WGS), RNA-sequencing and whole-genome bisulfite sequencing (WGBS). In addition, we analyzed 64 cell-free DNA (cfDNA) samples, from men with mCRPC before first-line abiraterone or enzalutamide, with both 5hmC sequencing and a conventional targeted ctDNA panel assessing common genomic alterations. Results: In mCRPC tissue samples, 5hmC enrichment was more strongly associated with gene expression than promoter methylation or copy number. Among cancer hallmark pathways, the androgen response genes had the strongest association between 5hmC and gene expression, suggesting a disease specific marking of gene activation. 5hmC patterns in cfDNA could be used to estimate the circulating tumor DNA fraction (ct-fraction), which was prognostic for overall survival (tertiles of ct-fraction, HR = 1.6 95%CI 1.1-2.3, p = 0.007). Further, 5hmC levels were indicative of gain of oncogene activity (such as AR, MYC, and PIK3CA) and loss of tumor suppressor gene activity (such as RB1, TP53 and BRCA2). The number of alterations, by 5hmC levels, of common drivers of mCRPC was prognostic for overall survival, also after adjusting for ct-fraction (adjusted p = 0.00001), and the prognostic value of common alterations detected by 5hmC sequencing versus conventional targeted ctDNA sequencing was similar. Finally, 5hmC levels in cfDNA of genes not significantly altered by copy number gain or loss (and thus not routinely included in targeted ctDNA sequencing assays), such as TOP2A and EZH2, identified a high-risk subgroup of mCRPC, which was highly prognostic for overall survival independent of ct-fraction (adjusted HR = 1.8 95%CI 1.2-2.8, p = 0.007). Conclusions: 5hmC in mCRPC tissue demonstrated an association with gene expression that was highest for prostate cancer driver genes, highlighting the ability to track disease-specific biology. 5hmC in cfDNA from men with mCRPC can be used to estimate the ct-fraction of the sample, infer activity gain and loss of common drivers of mCRPC, and identify high-risk groups of mCRPC based on alterations not commonly detected with conventional ctDNA sequencing, showing its potential as a liquid biomarker. Further studies are aimed at optimizing and validating 5hmC-based biomarkers in larger cohorts.
Collapse
Affiliation(s)
- Martin Sjöström
- University of California, San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Shuang Zhao
- University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Eric Jay Small
- University of California, San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | | | | | - Adam Foye
- University of California, San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Jun Jie T. Hua
- University of California, San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Haolong Li
- University of California, San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Tomasz M. Beer
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | | | - Matthew Rettig
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, and VA Greater Los Angeles Healthcare System, Los Angeles, CA
| | - Kim N. Chi
- University of British Columbia, BC Cancer-Vancouver Center, Vancouver, BC, Canada
| | | | - Rahul Raj Aggarwal
- University of California, San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Alan Ashworth
- University of California, San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | | | - Housheng H. He
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Alexander W. Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - David A. Quigley
- University of California, San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Felix Y Feng
- University of California, San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| |
Collapse
|
33
|
Chu C, Sjöström M, Egusa EA, Gibb E, Badura ML, Koshkin VS, Stohr BA, Meng M, Pruthi R, Friedlander TW, Lotan Y, Black PC, Porten SP, Feng FY, Chou J. Heterogeneity in Nectin-4 expression across molecular subtypes of urothelial cancer mediates sensitivity to enfortumab vedotin. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.6_suppl.463] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
463 Background: Enfortumab vedotin (EV) is an antibody-drug conjugate (ADC) targeting Nectin-4 (encoded by the PVRL4/NECTIN4 gene ) approved for treatment-refractory metastatic urothelial cancer. Factors that mediate sensitivity or resistance to EV are unknown. In the present study, we sought to 1) examine heterogeneity of NECTIN4 gene expression across molecular subtypes of bladder cancer and 2) determine if Nectin-4 expression mediates EV sensitivity or resistance. Methods: NECTIN4 expression data from seven muscle-invasive bladder cancer clinical cohorts (n = 1912 total patients) were used to compare relative NECTIN4 expression across molecular subtypes. The outcome of the gene expression analysis was relative NECTIN4 expression in the consensus molecular subtypes of bladder cancer. Expression of NECTIN4 was validated in multiple bladder cancer cell lines. NECTIN4 was stably over-expressed or knocked down in basal (TCCSUP and UMUC-3) and luminal (HT-1376, HT-1197 and UMUC-9) bladder cancer cell lines, respectively, and EV dose-response assays were performed, as measured by cell proliferation and clonogenic assays. Results: NECTIN4 expression is heterogenous across molecular subtypes of bladder cancer and significantly enriched in luminal subtypes (p < 0.001). NECTIN4 expression is positively correlated with the luminal markers GATA3, FOXA1, and PPARG across cohorts (Spearman’s rank correlation r = 0.57, p < 0.0001 for GATA3, r = 0.37, p < 0.0001 for FOXA1, and r = 0.56, p < 0.0001 for PPARG). NECTIN4 expression is both necessary and sufficient for EV sensitivity in luminal and basal subtypes of urothelial bladder cancer cells. Downregulation of NECTIN4 led to EV resistance, and EV-resistant cell lines expressed decreased levels of Nectin-4. Conclusions: Results of this pre-clinical study suggest that sensitivity to EV is mediated by expression of NECTIN4, which is significantly enriched in luminal subtypes of bladder cancer. Downregulation of NECTIN4 leads to resistance to EV. These findings have implications for biomarker development, patient selection and the inclusion of molecular subtyping in ongoing and future EV clinical trials. Further investigation into Nectin-4 loss as a mechanism of resistance in patients treated on EV is warranted.
Collapse
Affiliation(s)
| | - Martin Sjöström
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | | | - Ewan Gibb
- GenomeDx Biosciences Inc., Vancouver, BC, Canada
| | | | - Vadim S Koshkin
- Division of Hematology/Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA
| | - Bradley A. Stohr
- Department of Pathology, University of California, San Francisco, San Francisco, CA
| | - Maxwell Meng
- Department of Urology, University of California San Francisco, San Francisco, CA
| | - Raj Pruthi
- University of California San Francisco, San Francisco, CA
| | - Terence W. Friedlander
- University of California San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Yair Lotan
- The University of Texas Southwestern Medical Center, Dallas, TX
| | - Peter C. Black
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Sima P. Porten
- University of California San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Felix Y Feng
- University of California, San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Jonathan Chou
- University of California San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| |
Collapse
|
34
|
Chen WS, Haynes WA, Waitz R, Kamath K, Vega-Crespo A, Shrestha R, Zhang M, Foye A, Baselga Carretero I, Perez Garcilazo I, Zhang M, Zhao SG, Sjöström M, Quigley DA, Chou J, Beer TM, Rettig M, Gleave M, Evans CP, Lara P, Chi KN, Reiter RE, Alumkal JJ, Ashworth A, Aggarwal R, Small EJ, Daugherty PS, Ribas A, Oh DY, Shon JC, Feng FY. Autoantibody Landscape in Patients with Advanced Prostate Cancer. Clin Cancer Res 2020; 26:6204-6214. [PMID: 32967941 PMCID: PMC7710628 DOI: 10.1158/1078-0432.ccr-20-1966] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/03/2020] [Accepted: 09/16/2020] [Indexed: 12/16/2022]
Abstract
PURPOSE Autoantibody responses in cancer are of great interest, as they may be concordant with T-cell responses to cancer antigens or predictive of response to cancer immunotherapies. Thus, we sought to characterize the antibody landscape of metastatic castration-resistant prostate cancer (mCRPC). EXPERIMENTAL DESIGN Serum antibody epitope repertoire analysis (SERA) was performed on patient serum to identify tumor-specific neoepitopes. Somatic mutation-specific neoepitopes were investigated by associating serum epitope enrichment scores with whole-genome sequencing results from paired solid tumor metastasis biopsies and germline blood samples. A protein-based immunome-wide association study (PIWAS) was performed to identify significantly enriched epitopes, and candidate serum antibodies enriched in select patients were validated by ELISA profiling. A distinct cohort of patients with melanoma was evaluated to validate the top cancer-specific epitopes. RESULTS SERA was performed on 1,229 serum samples obtained from 72 men with mCRPC and 1,157 healthy control patients. Twenty-nine of 6,636 somatic mutations (0.44%) were associated with an antibody response specific to the mutated peptide. PIWAS analyses identified motifs in 11 proteins, including NY-ESO-1 and HERVK-113, as immunogenic in mCRPC, and ELISA confirmed serum antibody enrichment in candidate patients. Confirmatory PIWAS, Identifying Motifs Using Next-generation sequencing Experiments (IMUNE), and ELISA analyses performed on serum samples from 106 patients with melanoma similarly revealed enriched cancer-specific antibody responses to NY-ESO-1. CONCLUSIONS We present the first large-scale profiling of autoantibodies in advanced prostate cancer, utilizing a new antibody profiling approach to reveal novel cancer-specific antigens and epitopes. Our study recovers antigens of known importance and identifies novel tumor-specific epitopes of translational interest.
Collapse
Affiliation(s)
- William S Chen
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | | | | | | | - Agustin Vega-Crespo
- Division of Hematology and Oncology, University of California Los Angeles, Los Angeles, California
| | - Raunak Shrestha
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | | | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Medicine, University of California San Francisco, San Francisco, California
| | | | - Ivan Perez Garcilazo
- Division of Hematology and Oncology, University of California Los Angeles, Los Angeles, California
| | - Meng Zhang
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Shuang G Zhao
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Martin Sjöström
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Urology, University of California San Francisco, San Francisco, California
| | - Jonathan Chou
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Medicine, University of California San Francisco, San Francisco, California
| | - Tomasz M Beer
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Matthew Rettig
- Division of Hematology and Oncology, University of California Los Angeles, Los Angeles, California
- VA Greater Los Angeles Healthcare System, Los Angeles, California
| | - Martin Gleave
- University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Primo Lara
- University of California Davis, Davis, California
| | - Kim N Chi
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert E Reiter
- Department of Urology, University of California Los Angeles, Los Angeles, California
| | - Joshi J Alumkal
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Department of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Division of Hematology and Oncology, University of California Los Angeles, Los Angeles, California
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Medicine, University of California San Francisco, San Francisco, California
| | | | - Antoni Ribas
- Division of Hematology and Oncology, University of California Los Angeles, Los Angeles, California
| | - David Y Oh
- Department of Medicine, University of California San Francisco, San Francisco, California
| | | | - Felix Y Feng
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California.
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Urology, University of California San Francisco, San Francisco, California
| |
Collapse
|
35
|
Stenmark Tullberg A, Puttonen HAJ, Sjöström M, Holmberg E, Chang SL, Feng FY, Speers C, Pierce LJ, Lundstedt D, Killander F, Niméus E, Kovács A, Karlsson P. Immune Infiltrate in the Primary Tumor Predicts Effect of Adjuvant Radiotherapy in Breast Cancer; Results from the Randomized SweBCG91RT Trial. Clin Cancer Res 2020; 27:749-758. [PMID: 33148672 DOI: 10.1158/1078-0432.ccr-20-3299] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/01/2020] [Accepted: 10/30/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Tumor-infiltrating immune cells play a key role in tumor progression. The purpose of this study was to analyze whether the immune infiltrate predicts benefit from postoperative radiotherapy in a large randomized breast cancer radiotherapy trial. EXPERIMENTAL DESIGN In the SweBCG91RT trial, patients with stage I and II breast cancer were randomized to breast-conserving surgery (BCS) and postoperative radiotherapy or to BCS only and followed for a median time of 15.2 years. The primary tumor immune infiltrate was quantified through two independent methods: IHC and gene expression profiling. For IHC analyses, the absolute stromal area occupied by CD8+ T cells and FOXP3+ T cells, respectively, was used to define the immune infiltrate. For gene expression analyses, immune cells found to be prognostic in independent datasets were pooled into two groups consisting of antitumoral and protumoral immune cells, respectively. RESULTS An antitumoral immune response in the primary tumor was associated with a reduced risk of breast cancer recurrence and predicted less benefit from adjuvant radiotherapy. The interaction between radiotherapy and immune phenotype was significant for any recurrence in both the IHC and gene expression analyses (P = 0.039 and P = 0.035) and was also significant for ipsilateral breast tumor recurrence in the gene expression analyses (P = 0.025). CONCLUSIONS Patients with an antitumoral immune infiltrate in the primary tumor have a reduced risk of any recurrence and may derive less benefit from adjuvant radiotherapy. These results may impact decisions regarding postoperative radiotherapy in early breast cancer.
Collapse
Affiliation(s)
- Axel Stenmark Tullberg
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Henri A J Puttonen
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Martin Sjöström
- Department of Clinical Sciences Lund, Oncology/Pathology and Surgery, Lund University, Lund, Sweden
| | - Erik Holmberg
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | - Felix Y Feng
- University of California San Francisco, San Francisco, California
| | - Corey Speers
- Department of Radiation Oncology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Lori J Pierce
- Department of Radiation Oncology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Dan Lundstedt
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Fredrika Killander
- Department of Clinical Sciences Lund, Oncology/Pathology and Surgery, Lund University, Lund, Sweden
- Department of Oncology, Skåne University Hospital, Lund, Sweden
| | - Emma Niméus
- Department of Clinical Sciences Lund, Oncology/Pathology and Surgery, Lund University, Lund, Sweden
- Department of Surgery, Skåne University Hospital, Lund, Sweden
| | - Anikó Kovács
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Per Karlsson
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden.
| |
Collapse
|
36
|
Sjöström M, Veenstra C, Holmberg E, Karlsson P, Killander F, Malmström P, Niméus E, Fernö M, Stål O. Expression of HGF, pMet, and pAkt is related to benefit of radiotherapy after breast-conserving surgery: a long-term follow-up of the SweBCG91-RT randomised trial. Mol Oncol 2020; 14:2713-2726. [PMID: 32946618 PMCID: PMC7607179 DOI: 10.1002/1878-0261.12803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/19/2020] [Accepted: 09/11/2020] [Indexed: 01/15/2023] Open
Abstract
Experimental studies suggest that hepatocyte growth factor (HGF) and its transmembrane tyrosine kinase receptor, Met, in part also relying on Akt kinase activity, mediate radioresistance. We investigated the importance of these biomarkers for the risk of ipsilateral breast tumour recurrence (IBTR) after adjuvant radiotherapy (RT) in primary breast cancer. HGF, phosphorylated Met (pMet) and phosphorylated Akt (pAkt) were evaluated immunohistochemically on tissue microarrays from 1004 patients in the SweBCG91‐RT trial, which randomly assigned patients to breast‐conserving therapy, with or without adjuvant RT. HGF was evaluated in the stroma (HGFstr); pMet in the membrane (pMetmem); HGF, pMet and pAkt in the cytoplasm (HGFcyt, pMetcyt, pAktcyt); and pAkt in the nucleus (pAktnuc). The prognostic and treatment predictive effects were evaluated to primary endpoint IBTR as first event during the first 5 years. Patients with tumours expressing low levels of HGFcyt and pMetcyt and high levels of pAktnuc derived a larger benefit from RT [hazard ratio (HR): 0.11 (0.037–0.30), 0.066 (0.016–0.28) and 0.094 (0.028–0.31), respectively] compared to patients with high expression of HGFcyt and pMetcyt, and low pAktnuc [HR: 0.36 (0.19–0.67), 0.35 (0.20–0.64) and 0.47 (0.32–0.71), respectively; interaction analyses: P = 0.052, 0.035 and 0.013, respectively]. These differences remained in multivariable analysis when adjusting for patient age, tumour size, histological grade, St Gallen subtype and systemic treatment (interaction analysis, P‐values: 0.085, 0.027, and 0.023, respectively). This study suggests that patients with immunohistochemically low HGFcyt, low pMetcyt and high pAktnuc may derive an increased benefit from RT after breast‐conserving surgery concerning the risk of developing IBTR.
Collapse
Affiliation(s)
- Martin Sjöström
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
| | - Cynthia Veenstra
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.,Department of Oncology, Linköping University, Linköping, Sweden
| | - Erik Holmberg
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, Sahlgrenska University Hospital, University of Gothenburg, Gothenburg, Sweden
| | - Per Karlsson
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, Sahlgrenska University Hospital, University of Gothenburg, Gothenburg, Sweden
| | - Fredrika Killander
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden.,Department of Haematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Per Malmström
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden.,Department of Haematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Emma Niméus
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden.,Division of Surgery, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden.,Department of Surgery, Skåne University Hospital, Lund, Sweden
| | - Mårten Fernö
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
| | - Olle Stål
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.,Department of Oncology, Linköping University, Linköping, Sweden
| |
Collapse
|
37
|
Zhao SG, Chen WS, Li H, Foye A, Zhang M, Sjöström M, Aggarwal R, Playdle D, Liao A, Alumkal JJ, Das R, Chou J, Hua JT, Barnard TJ, Bailey AM, Chow ED, Perry MD, Dang HX, Yang R, Moussavi-Baygi R, Zhang L, Alshalalfa M, Laura Chang S, Houlahan KE, Shiah YJ, Beer TM, Thomas G, Chi KN, Gleave M, Zoubeidi A, Reiter RE, Rettig MB, Witte O, Yvonne Kim M, Fong L, Spratt DE, Morgan TM, Bose R, Huang FW, Li H, Chesner L, Shenoy T, Goodarzi H, Asangani IA, Sandhu S, Lang JM, Mahajan NP, Lara PN, Evans CP, Febbo P, Batzoglou S, Knudsen KE, He HH, Huang J, Zwart W, Costello JF, Luo J, Tomlins SA, Wyatt AW, Dehm SM, Ashworth A, Gilbert LA, Boutros PC, Farh K, Chinnaiyan AM, Maher CA, Small EJ, Quigley DA, Feng FY. The DNA methylation landscape of advanced prostate cancer. Nat Genet 2020; 52:778-789. [PMID: 32661416 PMCID: PMC7454228 DOI: 10.1038/s41588-020-0648-8] [Citation(s) in RCA: 171] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 05/20/2020] [Indexed: 02/08/2023]
Abstract
Although DNA methylation is a key regulator of gene expression, the comprehensive methylation landscape of metastatic cancer has never been defined. Through whole-genome bisulfite sequencing paired with deep whole-genome and transcriptome sequencing of 100 castration-resistant prostate metastases, we discovered alterations affecting driver genes only detectable with integrated whole-genome approaches. Notably, we observed that 22% of tumors exhibited a novel epigenomic subtype associated with hyper-methylation and somatic mutations in TET2, DNMT3B, IDH1, and BRAF. We also identified intergenic regions where methylation is associated with RNA expression of the oncogenic driver genes AR, MYC and ERG. Finally, we showed that differential methylation during progression preferentially occurs at somatic mutational hotspots and putative regulatory regions. This study is a large integrated study of whole-genome, whole-methylome and whole-transcriptome sequencing in metastatic cancer and provides a comprehensive overview of the important regulatory role of methylation in metastatic castration-resistant prostate cancer.
Collapse
Affiliation(s)
- Shuang G Zhao
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - William S Chen
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Yale School of Medicine, New Haven, CT, USA
| | - Haolong Li
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Meng Zhang
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Martin Sjöström
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Denise Playdle
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Joshi J Alumkal
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Rajdeep Das
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Jonathan Chou
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Junjie T Hua
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Travis J Barnard
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Adina M Bailey
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Eric D Chow
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.,Center for Advanced Technology, University of California San Francisco, San Francisco, CA, USA
| | - Marc D Perry
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Ha X Dang
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA.,Department of Internal Medicine, Washington University, St. Louis, MO, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, USA
| | - Rendong Yang
- The Hormel Institute, University of Minnesota, Austin, MN, USA
| | - Ruhollah Moussavi-Baygi
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Li Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Mohammed Alshalalfa
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - S Laura Chang
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Kathleen E Houlahan
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Human Genetics, Institute for Precision Health, UCLA, Los Angeles, CA, USA
| | - Yu-Jia Shiah
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Tomasz M Beer
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Division of Hematology/Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - George Thomas
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Department of Pathology, Oregon Health & Science University, Portland, OR, USA
| | - Kim N Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,British Columbia Cancer Agency, Vancouver Centre, Vancouver, British Columbia, Canada
| | - Martin Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amina Zoubeidi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert E Reiter
- Jonsson Comprehensive Cancer Center, Departments of Medicine and Urology, University of California Los Angeles, Los Angeles, CA, USA
| | - Matthew B Rettig
- Jonsson Comprehensive Cancer Center, Departments of Medicine and Urology, University of California Los Angeles, Los Angeles, CA, USA.,Department of Medicine, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Owen Witte
- Department of Microbiology, Immunology, and Molecular Genetics at the David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - M Yvonne Kim
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Lawrence Fong
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Daniel E Spratt
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Todd M Morgan
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Urology, University of Michigan, Ann Arbor, MI, USA
| | - Rohit Bose
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA.,Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Franklin W Huang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Hui Li
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Lisa Chesner
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Tanushree Shenoy
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Irfan A Asangani
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Shahneen Sandhu
- Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
| | - Joshua M Lang
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Nupam P Mahajan
- Siteman Cancer Center, Washington University, St. Louis, MO, USA.,Department of Surgery, Washington University, St. Louis, MO, USA
| | - Primo N Lara
- Division of Hematology Oncology, Department of Internal Medicine, University of California Davis, Sacramento, CA, USA.,Comprehensive Cancer Center, University of California Davis, Sacramento, CA, USA
| | - Christopher P Evans
- Comprehensive Cancer Center, University of California Davis, Sacramento, CA, USA.,Department of Urologic Surgery, University of California Davis, Sacramento, CA, USA
| | | | | | - Karen E Knudsen
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Housheng H He
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jiaoti Huang
- Department of Pathology, Duke University, Durham, NC, USA
| | - Wilbert Zwart
- Netherlands Cancer Institute, Oncode Institute, Amsterdam, the Netherlands
| | - Joseph F Costello
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Jianhua Luo
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Scott A Tomlins
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Scott M Dehm
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Luke A Gilbert
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Human Genetics, Institute for Precision Health, UCLA, Los Angeles, CA, USA.,Jonsson Comprehensive Cancer Center, Departments of Medicine and Urology, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Arul M Chinnaiyan
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Urology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.,Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Christopher A Maher
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA.,Department of Internal Medicine, Washington University, St. Louis, MO, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, USA.,Department of Biomedical Engineering, Washington University, St. Louis, MO, USA
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Felix Y Feng
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA. .,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA. .,Department of Urology, University of California San Francisco, San Francisco, CA, USA.
| |
Collapse
|
38
|
Stenmark Tullberg A, Nimeus-Malmström E, Killander F, Sjöström M, Puttonen HA, Feng FY, Kovacs A, Lundstedt D, Holmberg E, Karlsson P. Tumor-infiltrating lymphocytes in ipsilateral breast tumor recurrences predict prognosis. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
546 Background: The antitumoral immune response is dynamic and changes with tumor progression. Previous studies show that immunohistochemical (IHC) assessment of TILs in local recurrences can predict prognosis. It is not clear how adjuvant radiotherapy (RT) can alter the local immune response or if gene expression analyses of TILs in recurrences can provide prognostic information. Methods: Matched biopsies from primary tumors and ipsilateral breast tumor recurrences (IBTRs) from the randomized SweBCG91RT trial were assessed for TILs. Analyses were performed using gene expression (86 matched pairs) and IHC assessment (126 matched pairs). Results: The median time to IBTR was 8.0 years among irradiated patients and 3.6 years among unirradiated patients. In the gene expression analyses, higher absolute values of CD8+ T cells, CD4+ effector memory and CD8+ effector memory T cells in the recurrence could significantly predict a decreased risk of subsequent distant metastasis. In addition, a net increase of these cells in the IBTR compared to the primary tumor was associated with a significantly lower risk of metastasis. TILs did not change significantly between the matched tumors for the whole group or among irradiated patients versus unirradiated patients in the gene expression or IHC analyses. Surprisingly, the group with unchanged TILs levels as measured by IHC had the lowest risk of metastasis while an increase or a decrease in TILs was significantly associated with an increased risk. Conclusions: Cytotoxic and memory T cells in the recurrence protect against subsequent distant metastasis although IHC measurement of TILs could not confirm these results. No significant differences in TILs infiltration between irradiated versus unirradiated patients could be determined in the recurrences. Further analyses including changes of subtypes between the primary tumor and the recurrence will be presented.
Collapse
Affiliation(s)
| | - Emma Nimeus-Malmström
- Department of Clinical Sciences, Oncology/ Pathology and Surgery, Lund University, Lund, Sweden
| | | | - Martin Sjöström
- Lund University, Department of Oncology and Pathology, Lund, Sweden
| | | | - Felix Y Feng
- Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Aniko Kovacs
- Sahlgrenska University Hospital, Department of Clinical Pathology, Gothenburg, Sweden
| | - Dan Lundstedt
- Department of Oncology, Sahlgrenska University Hospital, Göteborg, Sweden
| | | | - Per Karlsson
- Sahlgrenska Academy, Sahlgrenska University Hospital, Department of Oncology, Gothenburg, Sweden
| |
Collapse
|
39
|
Small EJ, Zhao S, Chen WS, Li H, Foye A, Sjöström M, Hua JJ, Aggarwal RR, Alumkal JJ, Beer TM, Gleave M, Rettig M, Witte O, Lara P, Chinnaiyan A, Maher C, Quigley DA, Feng FY. The comprehensive methylation landscape of metastatic castration-resistant prostate cancer (mCRPC) identifies new phenotypic subtypes: Results from the West Coast Prostate Cancer Dream Team (WCDT). J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.5507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
5507 Background: While recent studies have delineated the genomic landscape of mCRPC, its epigenomic landscape has not been as well characterized. The goal of this study was to define the comprehensive methylation landscape of mCRPC. Methods: mCRPC patients (pts) underwent a metastasis biopsy as part of a multi-institutional study (NCT02432001). Deep whole-genome bisulfite sequencing (mean depth 46x) was performed on fresh frozen tissue from 100 mCRPC patients; data was paired with deep whole-genome and transcriptome sequencing from the same samples. Unbiased hierarchical clustering of the mCRPC methylome was undertaken, and the survival of patients in each cluster was calculated using the Kaplan Meier method. Results: Unbiased hierarchical clustering revealed several distinct subtypes. 22% of mCRPC samples exhibited a novel epigenomic subtype associated with hyper-methylation. This hypermethylated (HM) cluster was significantly associated with somatic mutations in genes known to be involved in methylation, eg TET2 and DNMT3B, as well as in genes in which mutations have been associated with hyper-methylation in other cancer types ( IDH1 in glioblastoma and BRAF in colon cancer). mCRPC survival was 56.1 mos in pts with HM cancers compared to 35.6 mos in non-HM (p = .055). Methylome clustering also identified a unique cluster comprised of all patients with treatment-induced small cell/neuroendocrine cancer, a subtype previously associated with poor survival. Conclusions: This integrated study of whole-genome, whole methylome and whole-transcriptome sequencing provides the first comprehensive overview of the important regulatory role of methylation in metastatic castration-resistant prostate cancer, and has identified at least two distinct subtypes. The clinical and therapeutic implications of methylation subtypes should be explored in future studies. Clinical trial information: NCT02432001 .
Collapse
Affiliation(s)
- Eric Jay Small
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Shuang Zhao
- Univerisity of Michigan, Baltimore, MI, Cayman Islands
| | - William S. Chen
- UC San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | | | - Adam Foye
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Martin Sjöström
- Lund University, Department of Oncology and Pathology, Lund, Sweden
| | | | | | | | - Tomasz M. Beer
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Martin Gleave
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Matthew Rettig
- UCLA's Jonsson Comprehensive Cancer Center, West Los Angeles VA Medical Center, Los Angeles, CA
| | | | - Primo Lara
- University of California, Sacramento, CA
| | | | - Chris Maher
- Washington University School of Medicine in St. Louis, St. Louis, MO
| | - David A. Quigley
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Felix Y Feng
- Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| |
Collapse
|
40
|
Tutzauer J, Sjöström M, Bendahl PO, Rydén L, Fernö M, Leeb-Lundberg LMF, Alkner S. Plasma membrane expression of G protein-coupled estrogen receptor (GPER)/G protein-coupled receptor 30 (GPR30) is associated with worse outcome in metachronous contralateral breast cancer. PLoS One 2020; 15:e0231786. [PMID: 32302351 PMCID: PMC7164601 DOI: 10.1371/journal.pone.0231786] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/31/2020] [Indexed: 01/13/2023] Open
Abstract
Background G protein-coupled estrogen receptor (GPER), or G protein-coupled receptor 30 (GPR30), is reported to mediate non-genomic estrogen signaling. GPR30 associates with breast cancer (BC) outcome and may contribute to tamoxifen resistance. We investigated the expression and prognostic significance of GPR30 in metachronous contralateral breast cancer (CBC) as a model of tamoxifen resistance. Methods Total GPR30 expression (GPR30TOT) and plasma membrane-localized GPR30 expression (GPR30PM) were analyzed by immunohistochemistry in primary (BC1; nBC1 = 559) and contralateral BC (BC2; nBC2 = 595), and in lymph node metastases (LGL; nLGL1 = 213; nLGL2 = 196). Death from BC (BCD), including BC death or death after documented distant metastasis, was used as primary end-point. Results GPR30PM in BC2 and LGL2 were associated with increased risk of BCD (HRBC2 = 1.7, p = 0.03; HRLGL2 = 2.0; p = 0.02). In BC1 and BC2, GPR30PM associated with estrogen receptor (ER)-negativity (pBC1<0.0001; pBC2<0.0001) and progesterone receptor (PR)-negativity (pBC1 = 0.0007; pBC2<0.0001). The highest GPR30TOT and GPR30PM were observed in triple-negative BC. GPR30PM associated with high Ki67 staining in BC1 (p<0.0001) and BC2 (p<0.0001). GPR30TOT in BC2 did not associate with tamoxifen treatment for BC1. However, BC2 that were diagnosed during tamoxifen treatment were more likely to express GPR30PM than BC2 diagnosed after treatment completion (p = 0.01). Furthermore, a trend was observed that patients with GPR30PM in an ER-positive BC2 had greater benefit from tamoxifen treatment. Conclusion PM-localized GPR30 staining is associated with increased risk of BC death when expressed in BC2 and LGL2. Additionally, PM-localized GPR30 correlates with prognostic markers of worse outcome, such as high Ki67 and a triple-negative subtype. Therefore, PM-localized GPR30 may be an interesting new target for therapeutic exploitation. We found no clear evidence that total GPR30 expression is affected by tamoxifen exposure during development of metachronous CBC, or that GPR30 contributes to tamoxifen resistance.
Collapse
Affiliation(s)
- Julia Tutzauer
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Martin Sjöström
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Pär-Ola Bendahl
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Lisa Rydén
- Department of Clinical Sciences Lund, Division of Surgery, Lund University, Lund, Sweden
- Department of Surgery, Skåne University Hospital, Lund, Sweden
| | - Mårten Fernö
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | | | - Sara Alkner
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
- Department of Oncology, Skåne University Hospital, Lund, Sweden
| |
Collapse
|
41
|
Zhao SG, Lehrer J, Chang SL, Das R, Erho N, Liu Y, Sjöström M, Den RB, Freedland SJ, Klein EA, Karnes RJ, Schaeffer EM, Xu M, Speers C, Nguyen PL, Ross AE, Chan JM, Cooperberg MR, Carroll PR, Davicioni E, Fong L, Spratt DE, Feng FY. The Immune Landscape of Prostate Cancer and Nomination of PD-L2 as a Potential Therapeutic Target. J Natl Cancer Inst 2020; 111:301-310. [PMID: 30321406 DOI: 10.1093/jnci/djy141] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 04/02/2018] [Accepted: 07/17/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Immunotherapy has been less successful in treating prostate cancer than other solid tumors. We sought to better understand the immune landscape in prostate cancer and identify immune-related biomarkers and potential therapeutic targets. METHODS We analyzed gene expression data from 7826 prospectively collected prostatectomy samples (2013-2016), and 1567 retrospective samples with long-term clinical outcomes, for a total of 9393 samples, all profiled on the same commercial clinical platform in a CLIA-certified lab. The primary outcome was distant metastasis-free survival (DMFS). Secondary outcomes included biochemical recurrence-free survival (bRFS), prostate cancer-specific survival (PCSS), and overall survival (OS). All statistical tests were two-sided. RESULTS Unsupervised hierarchical clustering of hallmark pathways demonstrated an immune-related tumor cluster. Increased estimated immune content scores based on immune-specific genes from the literature were associated with worse bRFS (hazard ratio [HR] = 1.26 [95% confidence interval [CI] = 1.12 to 1.42]; P < .001), DMFS (HR = 1.34 [95% CI = 1.13 to 1.58]; P < .001), PCSS (HR = 1.53 [95% CI = 1.21 to 1.92]; P < .001), and OS (HR = 1.27 [95% CI = 1.07 to 1.50]; P = .006). Deconvolution using Cibersort revealed that mast cells, natural killer cells, and dendritic cells conferred improved DMFS, whereas macrophages and T-cells conferred worse DMFS. Interestingly, while PD-L1 was not prognostic, consistent with its low expression in prostate cancer, PD-L2 was expressed at statistically significantly higher levels (P < .001) and was associated with worse bRFS (HR = 1.17 [95% CI = 1.03 to 1.33]; P = .01), DMFS (HR = 1.25 [95% CI = 1.05 to 1.49]; P = .01), and PCSS (HR = 1.45 [95% CI = 1.13 to 1.86]; P = .003). PD-L2 was strongly associated with immune-related pathways on gene set enrichment analysis suggesting that it is playing an important role in immune modulation in clinical prostate cancer samples. Furthermore, PD-L2 was correlated with radiation response pathways, and also predicted response to postoperative radiation therapy (PORT) on multivariable interaction analysis (P = .03). CONCLUSION In the largest study of its kind to date, these results illustrate the complex relationship between the tumor-immune interaction, prognosis, and response to radiotherapy, and nominate PD-L2 as a potential novel therapeutic target in prostate cancer, potentially in combination with radiotherapy.
Collapse
Affiliation(s)
- Shuang G Zhao
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI
| | | | - S Laura Chang
- Department of Radiation Oncology, Helen Diller Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA
| | - Rajdeep Das
- Department of Radiation Oncology, Helen Diller Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA
| | | | - Yang Liu
- GenomeDx Biosciences Inc., Vancouver, BC, Canada
| | - Martin Sjöström
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
| | - Robert B Den
- Department of Radiation Oncology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA
| | - Stephen J Freedland
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Eric A Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH
| | | | | | - Melody Xu
- Department of Radiation Oncology, Helen Diller Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA
| | - Corey Speers
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI
| | - Paul L Nguyen
- Dana-Farber/Brigham and Women's Cancer Center, Department of Radiation Oncology, Harvard Medical School, Boston, MA
| | - Ashley E Ross
- James Buchanan Brady Urological Institute, Johns Hopkins Medical Institutions, Baltimore, MD
| | - June M Chan
- Department of Urology, Helen Diller Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA.,Department of Epidemiology & Biostatistics, Helen Diller Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA
| | - Matthew R Cooperberg
- Department of Urology, Helen Diller Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA
| | - Peter R Carroll
- Department of Urology, Helen Diller Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA
| | | | - Lawrence Fong
- Department of Medicine, Helen Diller Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA
| | - Daniel E Spratt
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI
| | - Felix Y Feng
- Department of Radiation Oncology, Helen Diller Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA.,Department of Medicine, Helen Diller Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA.,Department of Urology, Helen Diller Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA
| |
Collapse
|
42
|
Chu C, Alshalalfa M, Sjöström M, Zhao S, Herlemann A, Chou J, Baskin AL, Mahal BAV, Spratt DE, Cooperberg MR, Small EJ, Aggarwal RR, Wong AC, Porten SP, Hope T, Nguyen PL, Schaeffer EM, Carroll P, Feng FY. Differential expression of PSMA and 18F-fluciclovine transporter genes in metastatic castrate-resistant and treatment-emergent small cell/neuroendocrine prostate cancer. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.6_suppl.24] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
24 Background: 18F-fluciclovine (Axumin) PET/CT imaging is recommended by the NCCN in the setting of biochemical recurrence, while prostate-specific membrane antigen (PSMA) PET/CT is preferred by the EAU. The utility of these methods in the post-androgen deprivation therapy (ADT) setting however, is less defined. Our objective was to compare relative gene expression of the molecular targets of these imaging modalities— fluciclovine transporter genes (LAT1-4, ASCT1-2) and PSMA—in metastatic castrate resistant prostate cancer (mCRPC) and treatment-emergent small cell/neuroendocrine prostate cancer (t-SCNC). Methods: Genome-wide expression profiles of five mCRPC cohorts (Aggarwal, Grasso, Kumar, Beltran, Robinson, et al) were used to characterize relative expression of fluciclovine transporter (LAT1-4, ASC1-2) and PSMA (FOLH1) genes. 3 cohorts (Kumar, Beltran, Aggarwal) were enriched with t-SCNC tumors. The GSE35988 cohort included primary tumors and mCRPC. RNA expression profiling methods were consistent within cohorts. Results: 518 mCRPC specimens were included. In the GSE35988 cohort, PSMA expression was downregulated in mCRPC when compared to primary localized tumors (p=0.01). PSMA expression was further depressed in t-SCNC when compared with mCRPC (p<0.001). Of the fluciclovine transporter genes, LAT1 and LAT4 were overexpressed in mCRPC when compared to primary tumors, while ASC2 was less expressed (p<0.001). LAT1 was further overexpressed in t-SCNC when compared to mCRPC, while LAT2 was less expressed (p<0.001). PSMA expression was negatively correlated with LAT1 (p<0.001) but positively correlated with LAT2 (p=0.006). Other fluciclovine transporters were not correlated. Conclusions: Expression of PSMA and a subset of fluciclovine transporter genes are inversely correlated in mCRPC and t-SCNC. These findings suggest that fluciclovine-based imaging may play a role in castrate resistant states. Clinical comparison between PSMA- and fluciclovine-based imaging modalities in mCRPC and t-SCNC is warranted.
Collapse
Affiliation(s)
- Carissa Chu
- University of California, San Francisco, San Francisco, CA
| | | | - Martin Sjöström
- Lund University, Department of Oncology and Pathology, Lund, Sweden
| | | | | | - Jonathan Chou
- University of California San Francisco, San Francisco, CA
| | | | | | | | | | - Eric Jay Small
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | | | - Anthony C. Wong
- Dept. of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Sima P. Porten
- University of California, San Francisco, San Francisco, CA
| | - Thomas Hope
- University of California, San Francisco, San Francisco, CA
| | - Paul L. Nguyen
- Dana-Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | | | - Peter Carroll
- University of California-San Francisco, San Francisco, CA
| | - Felix Y Feng
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| |
Collapse
|
43
|
Chu C, Alshalalfa M, Sjöström M, Zhao S, Herlemann A, Chou J, Mahal BAV, Kishan AU, Spratt DE, Karnes J, Small EJ, Wong AC, Porten SP, Hope T, Davicioni E, Nguyen PL, Carroll P, Schaeffer EM, Feng FY, Cooperberg MR. Characterization of PSMA and 18F-fluciclovine transporter gene expression in localized prostate cancer. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.6_suppl.295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
295 Background: While 18F-fluciclovine PET/CT is approved in the US and recommended by the NCCN, prostate-specific membrane antigen (PSMA) PET/CT is more common in Europe/Australia and recommended by the EAU. Less is known about the biology of lesions detected by either modality. 18F-fluciclovine PET relies on radiotracer uptake by amino acid transporters LAT1-4 and ASCT1-2. PSMA PET is dependent on surface expression of PSMA. We compared relative expression of PSMA and fluciclovine transporter genes in radical prostatectomy (RP) samples to determine their distribution across subtypes and correlation with outcomes. Methods: Gene expression data of 19,102 RP samples were analyzed using the Affymetrix Human Exon 1.0 ST microarray. 1,135 patients had long term follow up. Associations between expression of PSMA and fluciclovine transporter genes (LAT1-4 and ASCT1-2) and pathologic variables, molecular subtypes, and clinical outcomes were conducted. Results: All fluciclovine transporter genes (LAT 1-4, ASCT1-2) were expressed at lower levels than PSMA (p <0.0001). PSMA expression was positively correlated with genomic risk score and pathologic Gleason score (p<0.0001), but LAT2-3 and ASCT2 were inversely correlated with genomic risk in primary tumors (p<0.0001) and less expressed in GS 9-10 tumors (p<0.0001). PSMA expression was associated with worse metastasis-free survival (MFS) (HR 1.45, p=0.001) and lymph node involvement (HR 2.14, p<0.0001). Expression of LAT2, LAT3, ASCT2 expression was associated with better MFS (HR 0.85, 0.63, 0.74, p<0.0001-0.04). After multivariable adjustment, PSMA expression remained independently prognostic of poorer MFS (HR 1.3, p=0.028). Luminal B subtype was notable for PSMA overexpression; Luminal A was enriched in ASCT2 and LAT2 (p<0.0001). PSMA expression did not correlate with ERG fusion prostate cancers, but LAT2, ASCT1, and ASCT2 were overexpressed in ERG fusion negative tumors (p<0.0001). Conclusions: PSMA expression is associated with more aggressive disease and poorer clinical outcomes than fluciclovine transporter genes in localized prostate cancer. Molecular subtypes of prostate cancer vary in PSMA and fluciclovine transporter gene expression.
Collapse
Affiliation(s)
- Carissa Chu
- University of California, San Francisco, San Francisco, CA
| | | | - Martin Sjöström
- Lund University, Department of Oncology and Pathology, Lund, Sweden
| | | | | | - Jonathan Chou
- University of California San Francisco, San Francisco, CA
| | | | | | | | | | - Eric Jay Small
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Anthony C. Wong
- Dept. of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Sima P. Porten
- University of California, San Francisco, San Francisco, CA
| | - Thomas Hope
- University of California, San Francisco, San Francisco, CA
| | | | - Paul L. Nguyen
- Dana-Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Peter Carroll
- University of California-San Francisco, San Francisco, CA
| | | | - Felix Y Feng
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | | |
Collapse
|
44
|
Tutzauer J, Sjöström M, Bendahl PO, Rydén L, Fernö M, Leeb-Lundberg F, Alkner S. Abstract P6-05-09: G protein-coupled estrogen receptor expressed in the plasma membrane is associated with worse breast cancer outcome, but does not contribute to tamoxifen resistance. Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-p6-05-09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction - G protein-coupled estrogen receptor (GPER), or GPR30, is a membrane receptor reported to mediate rapid, non-genomic estrogen responses. Multiple studies suggest that GPR30 expression associates with breast cancer outcome, although the clinical implications appear to depend on receptor subcellular localization and level of expression. Specifically, high plasma membrane localization of GPR30 has been reported to associate with a worse prognosis. Furthermore, in vitro studies show that tamoxifen up-regulates GPR30 in breast cancer cells, suggesting that GPR30 acts as a mediator of tamoxifen resistance. To further clarify the prognostic and treatment resistance role of GPR30 in vivo, we studied the receptor in patients developing contralateral breast cancer with or without tamoxifen treatment for the first primary tumor, serving as an in vivo model of tamoxifen resistance.
Patients and methods - In a cohort of 688 patients with metachronous contralateral breast cancer, total and plasma membrane specific GPR30 expression were evaluated by immunohistochemistry. Total GPR30 was evaluated in five levels (0-4) and plasma membrane staining as positive or negative. Evaluation was successful for 559 first primary tumors and 595 contralateral tumors. In addition, matched lymph node and distant metastases were evaluated (lymph node matched to first primary tumor, n=213, matched to contralateral tumor, n=196, and distant metastasis, n=197). The relationship between GPR30 and breast cancer mortality was assessed by the Cox proportional hazards model, and illustrated by curves of cumulative incidence. The association between GPR30 and breast cancer outcome in relation to tamoxifen was assessed by comparing groups either untreated or treated with tamoxifen after the first primary tumor.
Results - GPR30 expression in the plasma membrane associated with increased risk of breast cancer mortality both when expressed in the contralateral tumor (HR=1.7, p=0.03) and matched lymph node (HR=2.0; p=0.02). Additionally, GPR30 plasma membrane expression associated with high Ki67 staining both in the first primary tumor (p<0.0001) and contralateral tumor (p<0.0001). In both the first primary tumor and contralateral tumor, GPR30 plasma membrane expression associated with estrogen receptor α (ER)-negativity (p<0.0001 and p<0.0001, respectively) and progesterone receptor (PR)-negativity (p=0.0007 and p<0.0001, respectively). Furthermore, ER and PR expression associated with total GPR30 expression in a biphasic manner in both the first primary tumor and contralateral tumor, as previously observed in three cohorts of primary breast cancer. The highest total and plasma membrane GPR30 expression was observed in triple-negative breast cancer. Total GPR30 expression of the first primary tumor and contralateral tumor did not correlate, but it was significantly lower in the matched lymph node (first primary tumor p<0.0001, contralateral tumor p<0.0001). No clear evidence was found that tamoxifen treatment during contralateral tumor development correlated with GPR30 expression, or that GPR30 expression correlated with response to tamoxifen treatment.
Conclusion - GPR30 expression in the plasma membrane associates with increased risk of breast cancer death when expressed in the contralateral tumor and match lymph node, and correlates strongly with multiple clinicopathological markers of poor outcome. On the other hand, prior tamoxifen treatment does not appear to affect GPR30 expression, suggesting that GPR30 does not mediate tamoxifen resistance. Future studies should aim to characterize the pathophysiological mechanisms and function of GPR30 when located in the plasma membrane. Here, GPR30 could be an novel target for breast cancer treatments.
Citation Format: Julia Tutzauer, Martin Sjöström, Pär-Ola Bendahl, Lisa Rydén, Mårten Fernö, Fredrik Leeb-Lundberg, Sara Alkner. G protein-coupled estrogen receptor expressed in the plasma membrane is associated with worse breast cancer outcome, but does not contribute to tamoxifen resistance [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-05-09.
Collapse
|
45
|
Sjöström M, Chang SL, Fishbane N, Davicioni E, Zhao SG, Hartman L, Holmberg E, Feng FY, Speers CW, Pierce LJ, Malmström P, Fernö M, Karlsson P. Clinicogenomic Radiotherapy Classifier Predicting the Need for Intensified Locoregional Treatment After Breast-Conserving Surgery for Early-Stage Breast Cancer. J Clin Oncol 2019; 37:3340-3349. [PMID: 31618132 PMCID: PMC6901281 DOI: 10.1200/jco.19.00761] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
PURPOSE Most patients with early-stage breast cancer are treated with adjuvant radiotherapy (RT) after breast-conserving surgery (BCS) to prevent locoregional recurrence (LRR). However, no genomic tools are used currently to select the optimal RT strategy. METHODS We profiled the transcriptome of primary tumors on a clinical grade assay from the SweBCG91-RT trial, in which patients with node-negative breast cancer were randomly assigned to either whole-breast RT after BCS or no RT. We derived a new classifier, Adjuvant Radiotherapy Intensification Classifier (ARTIC), comprising 27 genes and patient age, in three publicly available cohorts, then independently validated ARTIC for LRR in 748 patients in SweBCG91-RT. We also compared previously published genomic signatures for ability to predict benefit from RT in SweBCG91-RT. RESULTS ARTIC was highly prognostic for LRR in patients treated with RT (hazard ratio [HR], 3.4; 95% CI, 2.0 to 5.9; P < .001) and predictive of RT benefit (Pinteraction = .005). Patients with low ARTIC scores had a large benefit from RT (HR, 0.33 [95% CI, 0.21 to 0.52], P < .001; 10-year cumulative incidence of LRR, 6% v 21%), whereas those with high ARTIC scores benefited less from RT (HR, 0.73 [95% CI, 0.44 to 1.2], P = .23; 10-year cumulative incidence of LRR, 25% v 32%). In contrast, none of the eight previously published signatures were predictive of benefit from RT in SweBCG91-RT. CONCLUSION ARTIC identified women with a substantial benefit from RT as well as women with a particularly elevated LRR risk in whom whole-breast RT was not sufficiently effective and, thus, in whom intensified treatment strategies such as tumor-bed boost, and possibly regional nodal RT, should be considered. To our knowledge, ARTIC is the first classifier validated as predictive of benefit from RT in a phase III clinical trial with patients randomly assigned to receive or not receive RT.
Collapse
Affiliation(s)
- Martin Sjöström
- Lund University, Lund, Sweden.,Skåne University Hospital, Lund, Sweden
| | | | | | | | - Shuang G Zhao
- University of Michigan Medical School, Ann Arbor, MI
| | | | - Erik Holmberg
- Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Felix Y Feng
- University of California San Francisco, San Francisco, CA
| | | | - Lori J Pierce
- University of Michigan Medical School, Ann Arbor, MI
| | - Per Malmström
- Lund University, Lund, Sweden.,Skåne University Hospital, Lund, Sweden
| | | | - Per Karlsson
- Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| |
Collapse
|
46
|
Lundberg E, Mihajlovic NS, Sjöström M, Ahlqvist J. The use of panoramic images for identification of edentulous persons. J Forensic Odontostomatol 2019; 37:18-24. [PMID: 31589592 PMCID: PMC6981351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The aim of this study was to determine if edentulous persons could be identified using panoramic images by: I) investigating the possibility of matching two panoramic radiographs of the same person obtained on two different occasions, II) determining what anatomical features are used as the base for matching, III) investigating if oral and maxillofacial radiologists (OMR) and dentists who were not oral and maxillofacial radiologists (NOMR) differed in their ability to match the images, and IV) determining if the time elapsed between the images affected the results or the confidence of the match. Panoramic image pairs from 19 patients obtained on two different occasions were included, plus 10 images from other edentulous patients. The time elapsed between the image pairs varied between 4 months and 6 years. Four OMR and four NOMR were asked to match the image pairs depicting the same patient. The participants marked each match as "certain", "likely", or "possible" and what anatomical structure they used for matching. The OMR group correctly matched 100% of the images and the NOMR group correctly matched 96%. The anatomy of the mandible was most often used for matching. The OMR group was more certain in their decisions than the NOMR group. The time elapsed between the examinations did not affect the result. In conclusion, panoramic images can be used to identify edentulous patients. Both OMR and NOMR could identify edentulous individuals when only panoramic radiographic images were available and the OMR were especially confident in the identification process.
Collapse
Affiliation(s)
- E Lundberg
- Department of Odontology, Umeå University, Sweden
| | | | - M Sjöström
- Department of Odontology, Umeå University, Sweden
| | - J Ahlqvist
- Department of Odontology, Umeå University, Sweden
| |
Collapse
|
47
|
Sjöström M, Chang SL, Fishbane N, Davicioni E, Hartman L, Holmberg E, Feng FY, Speers CW, Pierce LJ, Malmström P, Fernö M, Karlsson P. Comprehensive Transcriptomic Profiling Identifies Breast Cancer Patients Who May Be Spared Adjuvant Systemic Therapy. Clin Cancer Res 2019; 26:171-182. [DOI: 10.1158/1078-0432.ccr-19-1038] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/03/2019] [Accepted: 09/17/2019] [Indexed: 11/16/2022]
|
48
|
Kovács A, Stenmark Tullberg A, Werner Rönnerman E, Holmberg E, Hartman L, Sjöström M, Lundstedt D, Malmström P, Fernö M, Karlsson P. Effect of Radiotherapy After Breast-Conserving Surgery Depending on the Presence of Tumor-Infiltrating Lymphocytes: A Long-Term Follow-Up of the SweBCG91RT Randomized Trial. J Clin Oncol 2019; 37:1179-1187. [DOI: 10.1200/jco.18.02157] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
PURPOSE The effects of radiotherapy (RT) on the basis of the presence of stromal tumor infiltrating lymphocytes (TILs) have not been studied. The purpose of this study was to analyze the association of TILs with the effect of postoperative RT on ipsilateral breast tumor recurrence (IBTR) in a large randomized trial. METHODS In the SweBCT91RT (Swedish Breast Cancer Group 91 Radiotherapy) trial, 1,178 patients with breast cancer stage I and II were randomly assigned to breast-conserving surgery plus postoperative RT or breast-conserving surgery only and followed for a median of 15.2 years. Tumor blocks were retrieved from 1,003 patients. Stromal TILs were assessed on whole-section hematoxylin-eosin–stained slides using a dichotomized cutoff of 10%. Subtypes were scored using immunohistochemistry on tissue microarray. In total, 936 patients were evaluated. RESULTS Altogether, 670 (71%) of patients had TILs less than 10%. In a multivariable regression analysis with IBTR as dependent variable and RT, TILs, subtype, age, and grade as independent variables, RT (hazard ratio [HR], 0.42; 95% CI, 0.29 to 0.61; P < .001), high TILs (HR, 0.61; 95% CI, 0.39 to 0.96, P = .033) grade (3 v 1; HR, 2.17; 95% CI, 1.08 to 4.34; P = .029), and age (≥ 50 v < 50 years; HR, 0.55; 95% CI, 0.38 to 0.80; P = .002) were predictive of IBTR. RT was significantly beneficial in the low TILs group (HR, 0.37; 95% CI, 0.24 to 0.58; P < .001) but not in the high TILs group (HR, 0.58; 95% CI, 0.28 to 1.19; P = .138). The test for interaction between RT and TILs was not statistically significant ( P = .317). CONCLUSION This study shows that high values of TILs in the primary tumor independently seem to reduce the risk for an IBTR. Our findings further suggest that patients with breast cancer with low TILs may derive a larger benefit from RT regarding the risk of IBTR.
Collapse
Affiliation(s)
- Anikó Kovács
- Department of Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Axel Stenmark Tullberg
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | - Erik Holmberg
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | | | - Dan Lundstedt
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Per Malmström
- Lund University, Lund, Sweden
- Skåne University Hospital, Lund, Sweden
| | | | - Per Karlsson
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| |
Collapse
|
49
|
Sjöström M, Chang SL, Fishbane N, Davicioni E, Zhao SG, Hartman L, Holmberg E, Feng FY, Speers CW, Pierce LJ, Malmström P, Fernö M, Karlsson P. Abstract P5-12-01: A novel gene expression signature prognostic for both locoregional and distant failure and predictive for adjuvant radiotherapy. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p5-12-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Most patients with early stage breast cancer (BC) are treated with adjuvant radiotherapy (RT) following breast conserving surgery (BCS) to prevent locoregional recurrences (LRR). No predictive tools are currently available to select patients for RT, resulting in considerable over- and under treatment. We aimed to create and validate a gene expression-based classifier to prognosticate for LRR and to stratify patients for treatment with RT.
Patients and methods: A 27-gene expression signature was developed using three publicly available early stage BC gene expression datasets where patients were treated with RT and had detailed local recurrence information. The largest of the datasets was used to train the signature, and the other two datasets were used for signature refinement. As age was the strongest clinical factor for the endpoint in the training dataset, it was included in the model, resulting in a final clinical-genomic classifier of 27 genes and age. The classifier was locked before external validation in the SweBCG91-RT trial. This phase III clinical trial included primary tumors from 765 patients and for which gene expression data was available. The trial randomized node-negative BC patients to +/- RT following BCS, with sparse use of adjuvant systemic treatment (9%) and a median follow-up of 14.0 years for LRR in patients free from event. The classifier was validated using Cox regression with LRR as the primary endpoint, and hazard ratios (HRs) were calculated using the raw continuous classifier score (range: 0.5 to 2.5).
Results: The novel classifier was highly prognostic for LRR in SweBCG91-RT patients treated with RT (HR=7.5[3.3-16.9], p<0.001), and remained prognostic in multivariate analysis (MVA) that included systemic treatment, subtype and grade (HR=7.2[3.1-16.4], p<0.001). To a lesser extent, the classifier was also prognostic for LRR in patients not treated with RT (HR=1.9[1.0-3.5], p=0.03; MVA HR=1.9[1.0-3.3], p=0.05). Patients at high risk of LRR had a smaller effect of RT, and the treatment predictive potential was confirmed by testing for interaction (pinteraction=0.008). In patients treated with RT, age and the genomic component of the model were both prognostic for LRR (p<0.01) as well as predictive for RT response (pinteraction<0.05) and provided independent information (p<0.01). The combined classifier has increased performance over its individual components (10-year AUC=0.72, 0.67, 0.65 for the classifier, age, and genomic component, respectively). While the novel signature was prognostic for metastasis (HR=4.3[2.3-7.8], p<0.0001), calculated scores from previously published signatures to the metastasis endpoint, including the Oncotype-like score, were not prognostic for LRR.
Conclusions: This novel gene expression signature is highly prognostic for LRR, can identify patients at risk of LRR despite RT, and appears to be treatment predictive for adjuvant RT. Furthermore, the current signature is highly prognostic for metastasis. In contrast, calculated scores of previously published signatures modeled for the metastasis endpoint had inferior performance for LRR. These results underscore both the importance of signatures prognostic for LRR and the similarities in the biology of LRR and distant failure.
Citation Format: Sjöström M, Chang SL, Fishbane N, Davicioni E, Zhao SG, Hartman L, Holmberg E, Feng FY, Speers CW, Pierce LJ, Malmström P, Fernö M, Karlsson P. A novel gene expression signature prognostic for both locoregional and distant failure and predictive for adjuvant radiotherapy [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-12-01.
Collapse
Affiliation(s)
- M Sjöström
- Lund University, Clinical Sciences Lund, Oncology and Pathology, Lund, Sweden; PFS Genomics, Vancouver, Canada; GenomeDx Biosciences, Vancouver, Canada; University of Michigan, Michigan, MI; Gothenburg University, Sahlgrenska Academy, Gothenburg, Sweden; University of California, San Francisco, San Francisco, CA
| | - SL Chang
- Lund University, Clinical Sciences Lund, Oncology and Pathology, Lund, Sweden; PFS Genomics, Vancouver, Canada; GenomeDx Biosciences, Vancouver, Canada; University of Michigan, Michigan, MI; Gothenburg University, Sahlgrenska Academy, Gothenburg, Sweden; University of California, San Francisco, San Francisco, CA
| | - N Fishbane
- Lund University, Clinical Sciences Lund, Oncology and Pathology, Lund, Sweden; PFS Genomics, Vancouver, Canada; GenomeDx Biosciences, Vancouver, Canada; University of Michigan, Michigan, MI; Gothenburg University, Sahlgrenska Academy, Gothenburg, Sweden; University of California, San Francisco, San Francisco, CA
| | - E Davicioni
- Lund University, Clinical Sciences Lund, Oncology and Pathology, Lund, Sweden; PFS Genomics, Vancouver, Canada; GenomeDx Biosciences, Vancouver, Canada; University of Michigan, Michigan, MI; Gothenburg University, Sahlgrenska Academy, Gothenburg, Sweden; University of California, San Francisco, San Francisco, CA
| | - SG Zhao
- Lund University, Clinical Sciences Lund, Oncology and Pathology, Lund, Sweden; PFS Genomics, Vancouver, Canada; GenomeDx Biosciences, Vancouver, Canada; University of Michigan, Michigan, MI; Gothenburg University, Sahlgrenska Academy, Gothenburg, Sweden; University of California, San Francisco, San Francisco, CA
| | - L Hartman
- Lund University, Clinical Sciences Lund, Oncology and Pathology, Lund, Sweden; PFS Genomics, Vancouver, Canada; GenomeDx Biosciences, Vancouver, Canada; University of Michigan, Michigan, MI; Gothenburg University, Sahlgrenska Academy, Gothenburg, Sweden; University of California, San Francisco, San Francisco, CA
| | - E Holmberg
- Lund University, Clinical Sciences Lund, Oncology and Pathology, Lund, Sweden; PFS Genomics, Vancouver, Canada; GenomeDx Biosciences, Vancouver, Canada; University of Michigan, Michigan, MI; Gothenburg University, Sahlgrenska Academy, Gothenburg, Sweden; University of California, San Francisco, San Francisco, CA
| | - FY Feng
- Lund University, Clinical Sciences Lund, Oncology and Pathology, Lund, Sweden; PFS Genomics, Vancouver, Canada; GenomeDx Biosciences, Vancouver, Canada; University of Michigan, Michigan, MI; Gothenburg University, Sahlgrenska Academy, Gothenburg, Sweden; University of California, San Francisco, San Francisco, CA
| | - CW Speers
- Lund University, Clinical Sciences Lund, Oncology and Pathology, Lund, Sweden; PFS Genomics, Vancouver, Canada; GenomeDx Biosciences, Vancouver, Canada; University of Michigan, Michigan, MI; Gothenburg University, Sahlgrenska Academy, Gothenburg, Sweden; University of California, San Francisco, San Francisco, CA
| | - LJ Pierce
- Lund University, Clinical Sciences Lund, Oncology and Pathology, Lund, Sweden; PFS Genomics, Vancouver, Canada; GenomeDx Biosciences, Vancouver, Canada; University of Michigan, Michigan, MI; Gothenburg University, Sahlgrenska Academy, Gothenburg, Sweden; University of California, San Francisco, San Francisco, CA
| | - P Malmström
- Lund University, Clinical Sciences Lund, Oncology and Pathology, Lund, Sweden; PFS Genomics, Vancouver, Canada; GenomeDx Biosciences, Vancouver, Canada; University of Michigan, Michigan, MI; Gothenburg University, Sahlgrenska Academy, Gothenburg, Sweden; University of California, San Francisco, San Francisco, CA
| | - M Fernö
- Lund University, Clinical Sciences Lund, Oncology and Pathology, Lund, Sweden; PFS Genomics, Vancouver, Canada; GenomeDx Biosciences, Vancouver, Canada; University of Michigan, Michigan, MI; Gothenburg University, Sahlgrenska Academy, Gothenburg, Sweden; University of California, San Francisco, San Francisco, CA
| | - P Karlsson
- Lund University, Clinical Sciences Lund, Oncology and Pathology, Lund, Sweden; PFS Genomics, Vancouver, Canada; GenomeDx Biosciences, Vancouver, Canada; University of Michigan, Michigan, MI; Gothenburg University, Sahlgrenska Academy, Gothenburg, Sweden; University of California, San Francisco, San Francisco, CA
| |
Collapse
|
50
|
Danielsson K, Nylander E, Sjöström M, Ebrahimi M. Epstein-Barr virus is not detected in mucosal lichen planus. Med Oral Patol Oral Cir Bucal 2018; 23:e560-e563. [PMID: 30148472 PMCID: PMC6167091 DOI: 10.4317/medoral.22617] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 06/12/2018] [Indexed: 12/23/2022] Open
Abstract
Background Lichen planus (LP) is a chronic inflammatory, immunological, mucocutaneous disease can affect skin, genital and oral mucosa. Oral lichen planus (OLP) is the most common noninfectious, chronic inflammatory oral disease affecting 1-2% of the general adult population. World Health Organization (WHO) classifies OLP as a potentially malignant disorder. Epstein Barr virus or human herpesvirus-4, is a member of the herpes virus family and one of the most ubiquitous viruses known to human, infecting approximately 90% of the world’s adult population. The virus often infects B lymphocytes resulting in a wide spectrum of mucocutaneous and systemic diseases, ranging from mild lesions to aggressive malignancies. The aim of this study was to investigate expression of the EBV encoded RNAs EBER1 and EBER2 in oral and genital lichen planus and compare results with normal tissues in situ hybridization which is considered the golden standard for detection of EBER. Material and Methods A total of 68 biopsies, 25 oral LP, 26 genital LP, 10 oral controls and finally 7 genital controls were analysed using situ hybridization. Results All samples had RNA as shown by the control slide, whereas no case contained neither EBER1 nor EBER2. Conclusions Based on results from our study EBV is not involved in aetiology of lichen planus. Key words:Mucosal lichen planus, Epstein - Barr virus.
Collapse
Affiliation(s)
- K Danielsson
- Department of Odontology, Umeå University, SE - 901 85 Umeå, Sweden,
| | | | | | | |
Collapse
|