Mono-allelic germline pathogenic variants in the Partner And Localizer of BRCA2 (PALB2) gene predispose to a high-risk of breast cancer development, consistent with the role of PALB2 in homologous recombination (HR) DNA repair. Here, we sought to define the repertoire of somatic genetic alterations in PALB2-associated breast cancers (BCs), and whether PALB2-associated BCs display bi-allelic inactivation of PALB2 and/or genomic features of HR-deficiency (HRD). Twenty-four breast cancer patients with pathogenic PALB2 germline mutations were analyzed by whole-exome sequencing (WES, n = 16) or targeted capture massively parallel sequencing (410 cancer genes, n = 8). Somatic genetic alterations, loss of heterozygosity (LOH) of the PALB2 wild-type allele, large-scale state transitions (LSTs) and mutational signatures were defined. PALB2-associated BCs were found to be heterogeneous at the genetic level, with PIK3CA (29%), PALB2 (21%), TP53 (21%), and NOTCH3 (17%) being the genes most frequently affected by somatic mutations. Bi-allelic PALB2 inactivation was found in 16 of the 24 cases (67%), either through LOH (n = 11) or second somatic mutations (n = 5) of the wild-type allele. High LST scores were found in all 12 PALB2-associated BCs with bi-allelic PALB2 inactivation sequenced by WES, of which eight displayed the HRD-related mutational signature 3. In addition, bi-allelic inactivation of PALB2 was significantly associated with high LST scores. Our findings suggest that the identification of bi-allelic PALB2 inactivation in PALB2-associated BCs is required for the personalization of HR-directed therapies, such as platinum salts and/or PARP inhibitors, as the vast majority of PALB2-associated BCs without PALB2 bi-allelic inactivation lack genomic features of HRD.
Three cases of progressive dyspnoea in young female adults due to pulmonary lymphangitic carcinomatosis are reported. The underlying primary neoplasm was gastric carcinoma in all 3 cases. The diagnosis was not suspected in 2 patients because of their young age.
In June 2015, invitations were sent by email to 151 APAME journals to participate in an online survey with an objective of gaining insight into the common publication misconduct encountered by APAME editors. The survey, conducted through SurveyMonkey over a 20-day-period, comprised 10 questions with expansions to allow anecdotes limited to 400 characters, estimated to take less than 10 minutes to complete. Only one invitation was issued per journal, targeting (in order of priority) editors, editorial board members and editorial staff, and limited by email availability. 54 (36%) journals responded. 98% of respondents held Editor or Editorial Board positions. All respondent journals have editorial policies on publication ethics and 96% provide instructions related to ethics. 45% use anti-plagiarism software to screen manuscripts, the most popular being iThenticate, CrossCheck and Turnitin. Up to 50% of journals had encountered studies without IRB approval. Author misconduct encountered were (in rank order): plagiarism (75%), duplicate publication (58%), unjustified authorship (39%), authorship disputes (33%), data falsification (29%), data/image manipulation (27%), conflict of interest (25%), copyright violation (17%) and breach of confidentiality (10%). Reviewer misconduct encountered were: conflict of interest (19%), plagiarism (17%), obstructive behavior (17%), abusive language (13%) and breach of confidentiality (13%). Notwithstanding the limitations of the survey and the response rate, a few insights have been gained: (1) the need for strengthening the ethical culture of researchers/authors and reviewers, (2) anti-plagiarism software can improve plagiarism detection by about 15%, and (3) the need for technical support to detect plagiarism, duplicate publication and image manipulation.
A study was initiated to explore possible differences in handling telomere attrition in the most common lignant and benign tumours of the breast in Malaysian women. Infiltrating ductal carcinoma (IDC) and fibroadenoma (FA) represented the malignant and benign prototypes respectively. 29 IDC, 28 FA and 22 benign non-lesional control (BNL) breast tissue samples were analysed for telomerase activation using a Telomerase PCR ELISA kit (Boehringer Mannheim). In addition, 23 IDC, 12 FA and 14 BNL were subjected to telomere length determination with a TeloTAGGG Telomere Length Assay Kit (Roche Diagnostic GmbH, Germany), following digestion of genomic DNA by frequently cutting restriction enzymes RsaI and HinfI. Mean telomerase activity in IDC (A450nm=0.3338), but not FA (A450nm=0.0003) was significantly raised (p<0.05) compared with BNL (A450nm=0.0031). Similarly IDC (1.2 kb), but not FA (2.2 kb), showed significant telomere shortening (p<0.05) relative to BNL (2.9 kb). The findings imply that telomere attrition and telomerase activation differ between malignant and benign tumours of the breast and may be important for targeted therapy.
Western-style medicine was introduced to Malaya by the Portuguese, Dutch and British between the 1500s and 1800s. Although the earliest pathology laboratories were developed within hospitals towards the end of the 19th Century, histopathology emerged much later than the biochemistry and bacteriology services. The University Departments of Pathology were the pioneers of the renal histopathology diagnostic services. The Department of Pathology, University of Malaya (UM) received its first renal biopsy on 19 May 1968. Hospital Universiti Kebangsaan Malaysia (HUKM) and Hospital Universiti Sains Malaysia (HUSM) started their services in 1979 and 1987 respectively. It is notable that the early services in these University centres caterred for both the university hospitals and the Ministry of Health (MOH) until the mid-1990s when MOH began to develop its own services, pivoted on renal pathologists trained through Fellowship programmes. Currently, key centres in the MOH are Kuala Lumpur Hospital, Sultanah Aminah Hospital Johor Bahru and Malacca Hospital. With the inclusion of renal biopsy interpretation in the Master of Pathology programmes, basic renal histopathology services became widely available throughout the country from 2000. This subsequently filtered out to the private sector as more histopathologists embraced private practice. There is now active continuing professional development in renal histopathology through clinicopathological dicussions, seminars and workshops. Renal research on amyloid nephropathy, minimal change disease, IgA nephropathy, fibrillary glomerulonephritis, lupus nephritis and microwave technology have provided an insight into the patterns of renal pathology and changing criteria for biopsy. More recently, there has been increasing involvement of renal teams in clinical trials, particularly for lupus nephritis and renal transplant modulation.
The past century has seen tremendous changes in the scope and practice of pathology laboratories in tandem with the development of the medical services in Malaysia. Major progress was made in the areas of training and specialization of pathologists and laboratory technical staff. Today the pathology laboratory services have entered the International arena, and are propelled along the wave of globalization. Many new challenges have emerged as have new players in the field. Landmark developments over the past decade include the establishment of national quality assurance programmes, the mushrooming of private pathology laboratories, the establishment of a National Accreditation Standard for medical testing laboratories based on ISO 15189, and the passing of the Pathology Laboratory Act in Parliament in mid-2007. The Pathology Laboratory Act 2007 seeks to ensure that the pathology laboratory is accountable to the public, meets required standards of practice, participates in Quality Assurance programmes, is run by qualified staff, complies with safety requirements and is subject to continuous audit. The Act is applicable to all private laboratories (stand alone or hospital) and laboratories in statutory bodies (Universities, foundations). It is not applicable to public laboratories (established and operated by the government) and side-room laboratories established in clinics of registered medical or dental practitioners for their own patients (tests as in the First and Second Schedules respectively). Tests of the Third Schedule (home test blood glucose, urine glucose, urine pregnancy test) are also exempted. The Act has 13 Parts and provides for control of the pathology laboratory through approval (to establish and maintain) and licensing (to operate or provide). The approval or license may only be issued to a sole proprietor, partnership or body corporate, and then only if the entity includes a registered medical practitioner. Details of personnel qualifications and laboratory practices are left to be specified by the Director-General of Health, providing for a formal recognition process and room for revision as pathology practices evolve. Encompassed in the responsibilities of the licensee is the requirement that samples are received and results issued through, and management vested in, a registered medical or dental practitioner. This effectively prohibits "walk-ins" to the laboratory and indiscriminate public screening. The requirement for a person-in-charge in accordance with class and speciality of laboratory ensures that the laboratory is under the charge of the pathology profession. Examined carefully, the requirements of the Act are similar to laboratory accreditation, but are backed by legislation. Many of these details will be spelt out in the Regulations, and these in turn are likely to fall back on National professional guidelines, as accreditation does. Although not at first obvious, enforcement of the Act is based on self-regulation by pathology laboratory professionals. Sincere professional input is thus required to embrace its philosophy, ensure rational and transparent enforcement of legislation, and develop National guidelines for good pathology practices upon which enforcement may be based.
The Nipah virus outbreak in Malaysia (September 1998 to May 1999) resulted in 265 cases of acute encephalitis with 105 deaths, and near collapse of the billion-dollar pig-farming industry. Because it was initially attributed to Japanese encephalitis, early control measures were ineffective, and the outbreak spread to other parts of Malaysia and nearby Singapore. The isolation of the novel aetiological agent, the Nipah virus (NiV), from the cerebrospinal fluid of an outbreak victim was the turning point which led to outbreak control 2 months later. Together with the Hendra virus, NiV is now recognised as a new genus, Henipavirus (Hendra + Nipah), in the Paramyxoviridae family. Efforts of the local and international scientific community have since elucidated the epidemiology, clinico-pathophysiology and pathogenesis of this new disease. Humans contracted the infection from close contact with infected pigs, and formed the basis for pig-culling that eventually stopped the outbreak. NiV targeted medium-sized and small blood vessels resulting in endothelial multinucleated syncytia and fibrinoid necrosis. Autopsies revealed disseminated cerebral microinfarctions resulting from vasculitis-induced thrombosis and direct neuronal involvement. The discovery of NiV in the urine and saliva of Malaysian Island flying foxes (Pteropus hypomelanus and Petropus vampyrus) implicated these as natural reservoir hosts of NiV. It is probable that initial transmission of NiV from bats to pigs occurred in late 1997/early 1998 through contamination of pig swill by bat excretions, as a result of migration of these forest fruitbats to cultivated orchards and pig-farms, driven by fruiting failure of forest trees during the El Nino-related drought and anthropogenic fires in Indonesia in 1997-1998. This outbreak emphasizes the need for sharing information of any unusual illnesses in animals and humans, an open-minded approach and close collaboration and co-ordination between the medical profession, veterinarians and wildlife specialists in the investigation of such illnesses. Environmental mismanagement (such as deforestation and haze) has far-reaching effects, including encroachment of wildlife into human habitats and the introduction of zoonotic infections into domestic animals and humans.
Metastasising ability connotes one of the most important life-threatening properties of malignant neoplasms. Recent studies indicate that CD44 proteins, multifunctional cell adhesion molecules which contribute to "homing" of lymphocytes to lymph nodes as well as cell-cell and cell-matrix interactions, are potential markers of tumour progression. However, whether CD44 expression by human tumours contribute to increased metastatic risk remains controversial. In an attempt to clarify its role in breast cancer, we have investigated the correlation between CD44 expression by breast carcinoma and the presence of axillary lymph node metastases. CD44 expression was detected using a standard immunoperoxidase method on formalin-fixed, paraffin-embedded, primary infiltrating ductal breast carcinoma tissues taken from 60 female patients who underwent mastectomy with axillary node clearance. Tumours were graded according to the modified Bloom and Richardson criteria. 62% of patients had histologically-proven lymph node metastasis. 40% of primary cancers exhibited cytoplasmic membrane immunopositivity for CD44. 46% of primary tumours which have metastasied to axillary lymph nodes were CD44 positive whereas 30% of tumours which have not metastasised expressed CD44. CD44 positivity was expressed by 20% of grade 1, 31% grade 2 and 58% grade 3 tumours. Our results suggest that CD44 may have a role in the progression of breast cancer and emphasise the need to investigate its interaction with other mechanisms of cancer advancement.
The unique ability of tumour cells to proliferate indefinitely is crucial to neoplastic progression as it allows these cells to express the aggressive properties of cancer without the censure of physiological ageing. This is in contrast to normal somatic cells which are subject to a "mitotic clock," a phenomenon that has been linked to telomeric shortening after each round of cell replication, so that eventually the loss of genetic material reaches a critical stage and the cells undergo senescence and cell death. A study was conducted to investigate the role of telomerase, an RNA-containing enzyme that restores the telomere length, in the neoplastic cell immortalization and progression process. Fresh human tissue samples taken from excision specimens received by the Department of Pathology, University of Malaya Medical Centre, were investigated for telomerase activity using a commercial Telomerase PCR-ELISA kit (Boehringer Mannheim). Specimens comprised 33 breast lesions (10 infiltrating breast adenocarcinoma, 13 fibroadenoma and 10 non-neoplastic breast tissue), 27 colonic lesions (17 colonic adenocarcinoma and 10 non-neoplastic colonic mucosa) and 42 cervical lesions (20 cervical carcinoma and 22 non-neoplastic cervical tissues). Telomerase activity was found in 6 (60%) of 10 breast carcinomas, 6 (46%) of 13 fibroadenomas, none of the 10 nonneoplastic breast samples, 3 (17.6%) of 17 colon carcinomas and none of the 10 non-neoplastic colonic mucosal samples, 12 (60%) of 20 cervical carcinoma and 3 (13.6%) of 22 non-neoplastic cervical samples. 5/10 (50%) Stage I, 4/7 (57%) Stage II, 2/2 (100%) Stage III and 1/1 (100%) Stage IV cervical carcinomas showed telomerase activity. These findings support a contributory role for telomerase in tumourigenesis with activation occurring from neoplastic transformation and increasing with tumour progression.
Although microwave irradiation has been used in the histopathology laboratory for several years, there has been minimal published experimental data on its effects on the technical and staining quality of histological sections. Furthermore, it has not been clear whether the advantages gained in reduction of fixation and staining duration has been at the expense of increasing architectural distortion to the tissues. We report here our experience with computerised morphometric analysis to investigate glomerular artifacts caused by microwave-stimulated fixation of renal tissues. 39 rat and 33 human autopsy kidney samples were subjected to (1) fixation in neutral buffered formaldehyde (control), (2) microwave-stimulated fixation followed by neutral buffered formaldehyde, and (3) neutral buffered formaldehyde followed by microwave irradiation. In addition, the effect of post-fixation in 70% ethanol was also investigated. Microwave irradiation was delivered through a dedicated laboratory microwave oven at 80% power and at 55 degrees C for 3 minutes. The different fixation methods were compared with regards to shrinkage (distortion) to glomerular structures (glomeruli and Bowman's spaces) on H and E sections, as determined by morphometric image analysis using a temporary assembled-system consisting of a trinocular microscope, a digital video camera and personal computer. A FlashPoint VGA 3.3 film-grabber card was used to capture images for morphometric analysis by using a Scion Image program. Morphometric analysis of glomerular structures showed that microwaves caused more shrinkage to the area bounded by the Bowman's capsule than the glomerulus proper, but post-fixation with ethanol reduced this shrinkage. These findings have implications on the logistics of tissue preparation of renal biopsies in clinical practice.
The liver biopsy has a unique place in the investigation of liver disease because the concepts and classification of liver disease are rooted in morphology. Today, the use of the liver biopsy has extended beyond that of diagnosis, to the assessment of disease progression, response to therapy and transplant rejection. To get the best out of the liver biopsy, it is necessary to appreciate the usefulness and limitations of the biopsy specimen. Aspects to consider include: (1) minimizing sampling errors, and appreciating that the changes in the biopsy may not be representative of the primary pathology, (2) good laboratory quality practices to avoid processing artifacts, which may render a biopsy undiagnosable, (3) the appropriate use of special stains and other laboratory techniques, (4) adoption of a systematic and algorithmic approach in the microscopic examination of the biopsy, and (5) good clinicopathological correlation.