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Cheung LS, Chen L, Oke TF, Schaffer TB, Boudadi K, Ngo JT, Gross JM, Kemberling H, Diaz LA, Lipson E, Sidhom JWI, Taube J, Anders R, Pardoll DM, Le DT, Meyer CF, Llosa N. Anti-PD-1 elicits regression of undifferentiated pleomorphic sarcomas with UV-mutation signatures. J Immunother Cancer 2021; 9:e002345. [PMID: 34103354 PMCID: PMC8190056 DOI: 10.1136/jitc-2021-002345] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2021] [Indexed: 01/07/2023] Open
Abstract
Undifferentiated pleomorphic sarcoma (UPS), an aggressive soft-tissue sarcoma of adults, has been characterized by low tumor mutational burden (TMB) and high copy number alterations. Clinical trials of programmed death-1 (PD-1) blockade in UPS have reported widely varying efficacy. We describe two patients with recurrent scalp UPS that experienced clinical benefit from PD-1 blockade. These tumors had high TMB with a UV-induced mutational pattern. Analysis of additional head and neck UPS cases identified five out of seven tumors with high TMB and an ultraviolet (UV) mutational signature. Head and neck UPS tumors also had increased programmed death-ligand 1 (PD-L1) expression and CD8+ T cell infiltration as compared with UPS tumors arising from other sites. In summary, we found that UPS tumors of the head and neck, but not elsewhere, have a PD-L1+, T-cell-inflamed tumor microenvironment and high TMB, suggesting that these tumors represent a distinct genetic subgroup of UPS for which immune checkpoint inhibitor therapy might be effective.
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Affiliation(s)
- Laurene S Cheung
- Johns Hopkins Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
- Department of Oncology, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Lingling Chen
- Johns Hopkins Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
- Department of Oncology, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Teniola F Oke
- Johns Hopkins Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
- Department of Oncology, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | | | - Karim Boudadi
- Department of Oncology, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Jillian T Ngo
- Johns Hopkins Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
| | - John McMahon Gross
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Holly Kemberling
- Department of Oncology, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Luis A Diaz
- Division of Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Evan Lipson
- Johns Hopkins Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
- Department of Oncology, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - John-WIlliam Sidhom
- Johns Hopkins Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
- Department of Oncology, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Janis Taube
- Johns Hopkins Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
- Department of Oncology, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Robert Anders
- Johns Hopkins Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
- Department of Oncology, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Drew M Pardoll
- Johns Hopkins Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
- Department of Oncology, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Dung T Le
- Johns Hopkins Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
- Department of Oncology, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Christian F Meyer
- Department of Oncology, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Nicolas Llosa
- Johns Hopkins Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
- Department of Oncology, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
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Ngo JT, Parkins MD, Gregson DB, Pitout JDD, Ross T, Church DL, Laupland KB. Population-based assessment of the incidence, risk factors, and outcomes of anaerobic bloodstream infections. Infection 2013; 41:41-8. [PMID: 23292663 DOI: 10.1007/s15010-012-0389-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 12/07/2012] [Indexed: 12/17/2022]
Abstract
BACKGROUND Anaerobes are a relatively uncommon but important cause of bloodstream infection. However, their epidemiology has not been well defined in non-selected populations. We sought to describe the incidence of, risk factors for, and outcomes associated with anaerobic bacteremia. METHODS Population-based surveillance for bacteremia with anaerobic microorganisms was conducted in the Calgary area (population 1.2 million) during the period from 2000 to 2008. RESULTS A total of 904 incident cases were identified, for an overall population incidence of 8.7 per 100,000 per year; 231 (26 %) were nosocomial, 300 (33 %) were healthcare-associated community-onset, and 373 (41 %) were community-acquired. Elderly males were at the greatest risk. The most common pathogens identified were: Bacteroides fragilis group (3.6 per 100,000), Clostridium (non-perfringens) spp. (1.1 per 100,000), Peptostreptococcus spp. (0.9 per 100,000), and Clostridium perfringens (0.7 per 100,000). Non-susceptibility to metronidazole was 2 %, to clindamycin 17 %, and to penicillin 42 %. Relative to the general population, risk factors for anaerobic bloodstream infection included: male sex, increasing age, a prior diagnosis of cancer, chronic liver disease, heart disease, diabetes mellitus, stroke, inflammatory bowel disease, human immunodeficiency virus (HIV) infection, chronic obstructive pulmonary disease (COPD), and/or hemodialysis-dependent chronic renal failure (HDCRF). The 30-day mortality was 20 %. Increasing age, nosocomial acquisition, presence of malignancy, and several other co-morbid illnesses were independently associated with an increased risk of death. CONCLUSION Anaerobic bloodstream infection is responsible for a significant burden of disease in general populations. The data herein establish the extent to which anaerobes contribute to morbidity and subsequent mortality. This information is key in developing preventative, empiric treatment and research priorities.
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Affiliation(s)
- J T Ngo
- Department of Medicine, Alberta Health Services, The University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
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Kojis TL, Heinzmann C, Flodman P, Ngo JT, Sparkes RS, Spence MA, Bateman JB, Heckenlively JR. Map refinement of locus RP13 to human chromosome 17p13.3 in a second family with autosomal dominant retinitis pigmentosa. Am J Hum Genet 1996; 58:347-55. [PMID: 8571961 PMCID: PMC1914553] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
In order to elucidate the genetic basis of autosomal dominant retinitis pigmentosa (adRP) in a large eight-generation family (UCLA-RP09) of British descent, we assessed linkage between the UCLA-RP09 adRP gene and numerous genetic loci, including eight adRP candidate genes, five anonymous adRP-linked DNA loci, and 20 phenotypic markers. Linkage to the UCLA-RP09 disease gene was excluded for all eight candidate genes analyzed, including rhodopsin (RP4) and peripherin/RDS (RP7), for the four adRP loci RP1, RP9, RP10 and RP11, as well as for 17 phenotypic markers. The anonymous DNA marker locus D17S938, linked to adRP locus RP13 on chromosome 17p13.1, yielded a suggestive but not statistically significant positive lod score. Linkage was confirmed between the UCLA-RP09 adRP gene and markers distal to D17S938 in the chromosomal region 17p13.3. A reanalysis of the original RP13 data from a South African adRP family of British descent, in conjunction with our UCLA-RP09 data, suggests that only one adRP locus exists on 17p but that it maps to a more telomeric position, at band 17p13.3, than previously reported. Confirmation of the involvement of RP13 in two presumably unrelated adRP families, both of British descent, suggests that this locus is a distinct adRP gene in a proportion of British, and possibly other, adRP families.
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Affiliation(s)
- T L Kojis
- Vision Genetics Center, Jules Stein Eye Institute, UCLA School of Medicine, USA
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Affiliation(s)
- J T Ngo
- Jules Stein Eye Institute, UCLA School of Medicine 90024
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Bateman JB, Kojis TL, Cantor RM, Heinzmann C, Ngo JT, Spence MA, Inana G, Kivlin JD, Curtis D, Sparkes RS. Linkage analysis of Norrie disease with an X-chromosomal ornithine aminotransferase locus. Trans Am Ophthalmol Soc 1993; 91:299-307; discussion 307-8. [PMID: 7908152 PMCID: PMC1298472] [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] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Norrie disease is a rare disease of newborn males caused by prenatal or perinatal retinal detachment, which may be associated with mental retardation, psychosis, and/or hearing loss. DXS7 (L1.28) and MAO A and B loci have been linked to the ND locus on the short arm of the X chromosome. Sequences homologous to OAT also have been mapped to the short arm of the X chromosome. We performed linkage analyses between the ND locus and one of the OAT-like clusters of sequences on the X chromosome (OATL1), using a ScaI RFLP in a ND family, and increased the previously calculated lod score (z) to over 3 (3.38; theta = 0.05). Similarly, we calculated a lod score of 4.06 (theta = 0.01) between the OATL1 and DXS7 loci. Alone, the OATL1 ScaI RFLP system is expected to be informative in 48% of females. If this system were used in combination with the DXS7 TaqI polymorphism, 71% of females would be informative for at least one of the markers and 21% would be informative for both. Because the OATL1 ScaI RFLP is a relatively common polymorphism, this system should be useful for the identification of ND carriers and affected male fetuses and newborns.
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Affiliation(s)
- J B Bateman
- Vision Genetics Center, Jules Stein Eye Institute, UCLA School of Medicine
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Abstract
The computational task of protein structure prediction is believed to require exponential time, but previous arguments as to its intractability have taken into account only the size of a protein's conformational space. Such arguments do not rule out the possible existence of an algorithm, more selective than exhaustive search, that is efficient and exact. (An efficient algorithm is one that is guaranteed, for all possible inputs, to run in time bounded by a function polynomial in the problem size. An intractable problem is one for which no efficient algorithm exists.) Questions regarding the possible intractability of problems are often best answered using the theory of NP-completeness. In this treatment we show the NP-hardness of two typical mathematical statements of empirical potential energy function minimization of macromolecules. Unless all NP-complete problems can be solved efficiently, these results imply that a function minimization algorithm can be efficient for protein structure prediction only if it exploits protein-specific properties that prohibit the simple geometric constructions that we use in our proofs. Analysis of further mathematical statements of molecular structure prediction could constitute a systematic methodology for identifying sources of complexity in protein folding, and for guiding development of predictive algorithms.
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Affiliation(s)
- J T Ngo
- Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138
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Lindsay S, Thiselton DL, Bateman JB, Ngo JT, Sparkes RS, Coleman M, Davies KE, Bhattacharya SS. Localisation of the gene for Norrie disease to between DXS7 and DXS426 on Xp. Hum Genet 1992; 88:349-50. [PMID: 1733838 DOI: 10.1007/bf00197273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [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] [Indexed: 12/28/2022]
Abstract
A highly informative microsatellite marker, DXS426, which maps proximal to DXS7 in the interval Xp11.4-Xp11.23, has been used to refine further the localisation of the gene for Norrie disease (NDP). The results from a multiply informative crossover localize the NDP gene proximal to DXS7. In conjunction with information from 2 NDP patients who have a deletion for DXS7 but not for DSX426, our data indicate that the NDP gene lies between DXS7 and DXS426 on proximal Xp.
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Affiliation(s)
- S Lindsay
- Molecular Genetics Unit, University of Newcastle-upon-Tyne, UK
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Morris PG, McIntyre DJ, Rourke DE, Ngo JT. The design of practical selective pulses for magnetic resonance imaging and spectroscopy using SPINCALC. Magn Reson Med 1991; 17:33-40. [PMID: 2067405 DOI: 10.1002/mrm.1910170108] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Recently, we introduced a new numerical approach to the design and optimization of NMR selective pulses, which we have christened "SPINCALC" (J. T. Ngo and P. G. Morris, Biochem. Soc. Trans. 14, 1271 (1986); J. T. Ngo and P. G. Morris, Magn. Reson. Med. 5, 217 (1987]. The first practical application of pulses generated by SPINCALC is demonstrated on a standard 0.5-T clinical MRI system. Results are shown for single phase pi pulses suitable both for selective inversion and for selective refocusing. The extension of SPINCALC to multidimensional pulses is illustrated by the design of a two-dimensional pi pulse.
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Affiliation(s)
- P G Morris
- Department of Biochemistry, University of Cambridge, United Kingdom
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Abstract
We report the mapping of the gene coding for the S-antigen (48-kDa protein) to human chromosome 2 using somatic cell hybrids. In situ hybridization further confirms this assignment and regionally maps the gene to 2q24-q37.
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Affiliation(s)
- J T Ngo
- Vision Genetics Center, Jules Stein Eye Institute, Los Angeles, CA 90024-7001
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Ngo JT, Bateman JB, Spence MA, Cortessis V, Sparkes RS, Kivlin JD, Mohandas T, Inana G. Ornithine aminotransferase (OAT): recombination between an X-linked OAT sequence (7.5 kb) and the Norrie disease locus. Genomics 1990; 6:123-8. [PMID: 1968041 DOI: 10.1016/0888-7543(90)90456-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [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] [Indexed: 12/29/2022]
Abstract
A human ornithine aminotransferase (OAT) locus has been mapped to the Xp11.2, as has the Norrie disease locus. We used a cDNA probe to investigate a 3-generation UCLA family with Norrie disease; a 4.2-kb RFLP was detected and a maximum lod score of 0.602 at zero recombination fraction was calculated. We used the same probe to study a second multigeneration family with Norrie disease from Utah. A different RFLP of 7.5 kb in size was identified and a recombinational event between the OAT locus represented by this RFLP and the disease loci was observed. Linkage analysis of these two loci in this family revealed a maximum load score of 1.88 at a recombination fraction of 0.10. Although both families have affected members with the same disease, the lod scores are reported separately because the 4.2- and 7.5-kb RFLPs may represent two different loci for the X-linked OAT.
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Affiliation(s)
- J T Ngo
- Vision Genetics Center, Jules Stein Eye Institute, Los Angeles, California 90024
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Abstract
Using a human alpha B-crystallin genomic probe and human-mouse somatic cell hybrids, the human alpha B-gene was assigned to chromosome 11 and further corroborated by in situ hybridization to normal metaphase chromosomes. This assignment confirmed and regionally mapped the locus to q22.3-23.1.
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Affiliation(s)
- J T Ngo
- Vision Genetics Center, Jules Stein Eye Institute, UCLA School of Medicine 90024
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Ngo JT, Bateman JB, Cortessis V, Sparkes RS, Mohandas T, Inana G, Spence MA. Norrie disease: linkage analysis using a 4.2-kb RFLP detected by a human ornithine aminotransferase cDNA probe. Genomics 1989; 4:539-45. [PMID: 2568328 DOI: 10.1016/0888-7543(89)90277-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [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] [Indexed: 01/01/2023]
Abstract
Previous study has shown that the usual DNA marker for Norrie disease, the L1.28 probe which identifies the DXS7 locus, can recombine with the disease locus. In this study, we used a human ornithine aminotransferase (OAT) cDNA which detects OAT-related DNA sequences mapped to the same region on the X chromosome as that of the L1.28 probe to investigate the family with Norrie disease who exhibited the recombinational event. When genomic DNA from this family was digested with the PvuII restriction endonuclease, we found a restriction fragment length polymorphism (RFLP) of 4.2 kb in size. This fragment was absent in the affected males and cosegregated with the disease locus; we calculated a lod score of 0.602, at theta = 0.00. No deletion could be detected by chromosomal analysis or on Southern blots with other enzymes. These results suggest that one of the OAT-related sequences on the X chromosome may be in close proximity to the Norrie disease locus and represent the first report which indicates that the OAT cDNA may be useful for the identification of carrier status and/or prenatal diagnosis.
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Affiliation(s)
- J T Ngo
- Jules Stein Eye Institute, UCLA School of Medicine 90024
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Abstract
We have identified a family affected with X-linked recessive Norrie disease, in which a recombinational event occurred between the disease locus and the DXS7 locus identified by the probe L1.28. The addition of our family brings the total of published informative families to seven, with a maximum lod score of 7.58 at a recombination frequency of 0.038 +/- 0.036. This finding indicates that the L1.28 probe is useful but may not be completely reliable for prenatal diagnosis and that the gene for Norrie disease is not within the DNA sequence identified by the L1.28 probe.
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Affiliation(s)
- J T Ngo
- Jules Stein Eye Institute, Department of Ophthalmology, UCLA School of Medicine
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Abstract
The design of an NMR excitation scheme, whether selective or nonselective, is essentially the simultaneous inversion of an array of Bloch equations driven by magnetic fields which differ according to well-defined constraints. We find that if relaxation effects are negligible, nearly exact inversion of the Bloch equations is straightforward when performed in a special time-varying frame of reference. Repeated inversions of the Bloch equations for small perturbations provide the basis for arbitrarily large, optimal adjustments of the magnetization response to an applied time-varying magnetic field. Choice of the target response to be sought at each iteration is not trivial if overall adjustments of more than one-half rotation are required. We present the analysis both formally and in geometric terms and show how it leads to a general algorithm for the optimization of NMR excitation schemes. The unprecedented efficiency of the algorithm and its ability to generate novel pulses from distant starting approximations are demonstrated in the optimization of slice-selective pi pulses for inversion and refocusing, and a prefocused slice-selective pi/2 pulse. Other applications are discussed, including use of the algorithm to compensate for instrumental imperfections such as radiofrequency inhomogeneity.
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Affiliation(s)
- J T Ngo
- Department of Biochemistry, University of Cambridge, United Kingdom
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