Combined genetic and nutritional risk models of triple negative breast cancer

Survivors Overcoming and Achieving Resiliency (SOAR): Mindful Eating Practice for Breast Cancer Survivors in a Virtual Teaching Kitchen

The practice of mindful eating brings awareness to food choices, brings attention to the eating experience, and encourages selecting and preparing food that is both satisfying and nourishing. We examined mindful eating in breast cancer survivors following a 9-week, multidisciplinary virtual teaching kitchen intervention called Survivors Overcoming and Achieving Resiliency (SOAR). SOAR engaged participants through weekly cooking classes that also taught multiple domains of mindfulness. Participants (n = 102) were breast cancer survivors and completed the Mindful Eating Questionnaire (MEQ) prior to and after completion of the intervention. Linear regression analyses examined relationships between the aspects of mindful eating and body mass index (BMI). Wilcoxon (paired) rank sum tests evaluated the significance of the change in the MEQ total sum and subscales scores. A total of 102 participants completed both the pre- and post-intervention surveys. The mean change between the pre- and post-SOAR MEQ summary scores was 0.12 (sd = 0.30; Wilcoxon p-value = 0.0003). All MEQ subscale scores significantly increased with the exception of the distraction subscale. The MEQ summary scores increased for participants across both BMI stratifications. The SOAR teaching kitchen represents one of the first interventions that is tailored for breast cancer survivors and combines behavioral strategies from mindful eating training to nutritional knowledge and culinary medicine pedagogy in a virtual teaching kitchen. Further research is needed to examine whether mindful eating practices among cancer survivors result in sustainable healthy eating behaviors and food choices consistent with the cancer risk reduction guidelines.

The Burden of Cancer, Government Strategic Policies, and Challenges in Pakistan: A Comprehensive Review

Cancer is a severe condition characterized by uncontrolled cell division and increasing reported mortality and diagnostic cases. In 2040, an estimated 28.4 million cancer cases are expected to happen globally. In 2020, an estimated 19.3 million new cancer cases (18.1 million excluding non-melanoma skin cancer) had been diagnosed worldwide, with around 10.0 million cancer deaths. Breast cancer cases have increased by 2.26 million, lung cancer by 2.21 million, stomach by 1.089 million, liver by 0.96 million, and colon cancer by 1.93 million. Cancer is becoming more prevalent in Pakistan, with 19 million new cancer cases recorded in 2020. Food adulteration, gutkha, paan, and nutritional deficiencies are major cancer risk factors that interplay with cancer pathogenesis in this country. Government policies and legislation, cancer treatment challenges, and prevention must be revised seriously. This review presents the current cancer epidemiology in Pakistan to better understand cancer basis. It summarizes current cancer risk factors, causes, and the strategies and policies of the country against cancer.

Identification of a Cowden syndrome patient with a novel PTEN mutation and establishment of patient-derived induced pluripotent stem cells

Cowden syndrome (CS) is an autosomal dominant inherited disorder characterized by multiple hamartomas in various organs such as the mucosa, skin, and gastrointestinal tract. Patients with CS are at high risk for breast and thyroid cancers. Phosphatase and tensin homolog deleted on chromosome 10 (PTEN) is a tumor suppressor gene that negatively regulates the AKT pathway, and PTEN mutations are known to be the major causes of this syndrome. However, the pathogenesis of this syndrome has not been clarified. Here, we present a case of a Japanese woman with multiple oral polyps, breast cancer, and thyroid cancer who was clinically diagnosed with CS. We obtained DNA and RNA samples from the patient’s peripheral blood mononuclear cells (PBMCs) and buccal mucosa tumor. Next-generation sequencing revealed novel germline mutations (c.1020delT and c.1026G > A) in exon 8 of PTEN. Sanger sequencing identified no PTEN transcript from the mutant allele. Furthermore, CS-specific induced pluripotent stem cells (CS-iPSCs) were established from PBMCs of the patient under feeder- and serum-free culture. Compared with healthy PBMCs and iPSCs, both of the CS-derived PBMCs and CS-iPSCs exhibited significantly reduced expression of the PTEN transcript. The transcriptional variant, PTENδ, was increased in CS-iPSCs, suggesting that it may be the cause of the disease.

Genomic Profiling Comparison of Germline BRCA and Non-BRCA Carriers Reveals CCNE1 Amplification as a Risk Factor for Non-BRCA Carriers in Patients With Triple-Negative Breast Cancer

Background: Differences in genomic profiling and immunity-associated parameters between germline BRCA and non-BRCA carriers in TNBC with high tumor burden remain unexplored. This study aimed to compare the differences and explore potential prognostic predictors and therapeutic targets. Methods: The study cohort included 21 consecutive TNBC cases with germline BRCA1/2 mutations and 54 non-BRCA carriers with a tumor size ≥ 2 cm and/or ≥1 affected lymph nodes. Differences in clinicopathological characteristics and genomic profiles were analyzed through next-generation sequencing. Univariate Kaplan-Meier analysis and Cox regression model were applied to survival analysis. Immunohistochemistry was used to confirm the consistency between CCNE1 amplification and cyclin E1 protein overexpression. Results: The cohort included 16 and five patients with germline BRCA1 and BRCA2 mutations, respectively. Patients with germline BRCA1/2 mutations were diagnosed at a significantly younger age and were more likely to have a family history of breast and/or ovarian cancer. Six non-BRCA carriers (11.11%) carried germline mutations in other cancer susceptibility genes, including five mutations in five homologous recombination repair (HRR) pathway genes (9.26%) and one mutation in MSH3 (1.85%). Somatic mutations in HRR pathway genes were found in 22.22 and 14.29% of the non-BRCA and BRCA carriers, respectively. PIK3CA missense mutation (p = 0.046) and CCNE1 amplification (p = 0.2) were found only in the non-BRCA carriers. The median tumor mutation burden (TMB) was 4.1 Muts/Mb, whereas none of the cases had high microsatellite instability (MSI). BRCA status did not affect disease-free survival (DFS, p = 0.15) or overall survival (OS, p = 0.52). CCNE1 amplification was an independent risk factor for DFS in non-BRCA carriers with TNBC (HR 13.07, 95% CI 2.47-69.24, p = 0.003). Consistency between CCNE1 amplification and cyclin E1 protein overexpression was confirmed with an AUC of 0.967 for cyclin E1 signal intensity. Conclusions: We found differences in genetic alterations between germline BRCA and non-BRCA carriers with TNBC and a high tumor burden. TMB and MSI may not be suitable predictors of TNBC for immune checkpoint inhibitors. Notably, CCNE1 amplification is a novel potential prognostic marker and therapeutic target for non-BRCA carriers with TNBC. Cyclin E1 may be used instead of CCNE1 to improve clinical applicability.

DNA Mismatch Repair Gene Variants in Sporadic Solid Cancers

The phenotypic effects of single nucleotide polymorphisms (SNPs) in the development of sporadic solid cancers are still scarce. The aim of this review was to summarise and analyse published data on the associations between SNPs in mismatch repair genes and various cancers. The mismatch repair system plays a unique role in the control of the genetic integrity and it is often inactivated (germline and somatic mutations and hypermethylation) in cancer patients. Here, we focused on germline variants in mismatch repair genes and found the outcomes rather controversial: some SNPs are sometimes ascribed as protective, while other studies reported their pathological effects. Regarding the complexity of cancer as one disease, we attempted to ascertain if particular polymorphisms exert the effect in the same direction in the development and treatment of different malignancies, although it is still not straightforward to conclude whether polymorphisms always play a clear positive role or a negative one. Most recent and robust genome-wide studies suggest that risk of cancer is modulated by variants in mismatch repair genes, for example in colorectal cancer. Our study shows that rs1800734 in MLH1 or rs2303428 in MSH2 may influence the development of different malignancies. The lack of functional studies on many DNA mismatch repair SNPs as well as their interactions are not explored yet. Notably, the concerted action of more variants in one individual may be protective or harmful. Further, complex interactions of DNA mismatch repair variations with both the environment and microenvironment in the cancer pathogenesis will deserve further attention.

A meta-analysis of zinc levels in breast cancer

BACKGROUND

Breast cancer is the most commonly occurring neoplasm in females, comprising 16% of all female cancers worldwide. Various studies indicate some discrepancies regarding zinc (Zn) levels in various samples of breast cancer patients.

OBJECTIVE

The present study evaluated by meta-analysed the published data for Zn levels analyzed in breast tissue, plasma, serum, and hair samples and its relationship with breast cancer.

METHODS

The present meta-analysis included 36 studies, all of which were published in the years between 1984 to 2017 and selected by searching the databases MEDLINE, EMBASE, Cochrane Library, PubMed, Scopus, and the ISI Web of Knowledge. The articles were analyzed, and I² statistics were used to examine heterogeneity. The objective analysis was performed on data from the 36 studies, with total 1699 study subjects and 2009 controls.

RESULTS

Significant statistical differences overall were observed, based on a random effects model (SMD (95 % CI), -0.78[-1.40, -0.16], P = 0.014). Data from 19 of these studies indicated significant statistical differences between cancerous patients and controls with regard to serum and plasma Zn concentration (SMD [(95 %CI): -1.61(-2.43, -0.79)]. There was a significant statistical difference between the breast tissue and hair as regards Zn status (SMD (95%CI): 2.32(1.42, 3.21)) and (SMD (95v%CI): -1.80(-3.41, -0.20), respectively. Zn concentration levels typically decreased in blood and hair samples of patients with breast cancer, whereas it was elevated in tumor tissues.

CONCLUSIONS

There is a significant relationship between lowered serum Zn concentrations and risk of breast cancer onset or recurrences in women, but because of high heterogeneity, we recommend other primary studies.

Genomics and breast cancer screening

Many women fear the risk of developing breast cancer, and some women have increased fear because of their family history. Thankfully, the study of genetics has brought forth tools to better identify women at risk. An understanding of genetics and cancer has led to genetic testing protocols which enable at-risk women to take preventative action through medication, surgery, and intensive screenings. These protocols not only have the potential to prevent cancer but also lead to early detection. Appropriate screening for women at risk for genetic breast cancer is essential for patient care. These screenings include specific risk assessment tests, genetic counseling, and genetic testing. To provide the best possible care for patients, providers must have a basic understanding of cancer, genetics, screening tests, genetic testing, and available prevention measures.

Thyroid Cancer: The Quest for Genetic Susceptibility Involving DNA Repair Genes

The incidence of thyroid cancer (TC), particularly well-differentiated forms (DTC), has been rising and remains the highest among endocrine malignancies. Although ionizing radiation (IR) is well established on DTC aetiology, other environmental and genetic factors may also be involved. DNA repair single nucleotide polymorphisms (SNPs) could be among the former, helping in explaining the high incidence. To further clarify the role of DNA repair SNPs in DTC susceptibility, we analyzed 36 SNPs in 27 DNA repair genes in a population of 106 DTCs and corresponding controls with the aim of interpreting joint data from previously studied isolated SNPs in DNA repair genes. Significant associations with DTC susceptibility were observed for XRCC3 rs861539, XPC rs2228001, CCNH rs2230641, MSH6 rs1042821 and ERCC5 rs2227869 and for a haplotype block on chromosome 5q. From 595 SNP-SNP combinations tested and 114 showing relevance, 15 significant SNP combinations (p < 0.01) were detected on paired SNP analysis, most of which involving CCNH rs2230641 and mismatch repair variants. Overall, a gene-dosage effect between the number of risk genotypes and DTC predisposition was observed. In spite of the volume of data presented, new studies are sought to provide an interpretability of the role of SNPs in DNA repair genes and their combinations in DTC susceptibility.

Serum Trace Elements and Their Associations with Breast Cancer Subgroups in Korean Breast Cancer Patients

The relationships between serum levels of trace elements and breast cancer remain relatively unknown. In this study, we investigate serum levels of seven trace elements in Korean breast cancer patients compared to controls without breast cancer. Serum trace element levels were determined using inductively coupled plasma mass spectrometry in Korean breast cancer patients before initiation of breast cancer treatment. Korean females without breast cancer served as a control group. Trace element levels were measured in the discovery cohort (n = 287) and were validated in an independent cohort (n = 142). We further investigated possible associations between trace element levels and the presence of lymph node metastasis, distant metastasis, or triple-negative breast cancer among breast cancer patients in subgroup analyses. Serum manganese and molybdenum levels were significantly higher (p < 0.05) in breast cancer patients than in controls. Serum copper levels were significantly higher in breast cancer patients with distant metastasis, while selenium levels were significantly lower. Other trace elements were neither significantly different between breast cancer patients and controls nor between subgroups of breast cancer patients. Our study provides insights about the potential roles and impacts of trace elements through an assessment of the associations between trace elements and breast cancer.

Whole exome sequencing of breast cancer (TNBC) cases from India: association of MSH6 and BRIP1 variants with TNBC risk and oxidative DNA damage

Whole exome sequencing in triple negative breast cancer cases (n = 8) and targeted sequencing in healthy controls (n = 48) revealed BRIP1 rs552752779 (MAF: 75% vs. 6.25%, OR 45.00, 95% CI 9.43-243.32), ERBB2 rs527779103 (MAF: 62.5% vs. 7.29%, OR 21.19, 95% CI 5.11-94.32), ERCC2 rs121913016 (MAF: 56.25% vs. 7.29%, OR 16.34, 95% CI 4.02-70.41), MSH6 rs2020912 (MAF: 56.25% vs. 1.04%, OR 122.13, 95% CI 12.29-2985.48) as risk factors for triple negative breast cancer. Construction of classification and regression tree followed by smart pruning identified MSH6 and BRIP1 variants as the major determinants of TNBC (Triple Negative Breast Cancer) risk. Except for ERBB2, all other genes regulate DNA repair and chromosomal integrity. In TNBC cases, two likely pathogenic variations i.e. NCOR1 rs562300336 and PIM1 rs746748226 were observed at frequencies of 18.75% and 12.5%, respectively. Among the 24 variants of unknown significance, MMP9 rs199676062, SYNE1 rs368709678, AURKA rs373550419, ABCC4 rs11568694 have variant allele frequency ≥ 62.5%. These genes regulate metastasis, nuclear modeling, cell cycle and cellular detoxification, respectively. To conclude, aberrations in DNA mismatch repair, nucleotide excision repair or BRCA1 associated genome surveillance mechanism contribute towards triple negative breast cancer.

Risks and protective factors for triple negative breast cancer with a focus on micronutrients and infections

Triple negative breast cancer (TNBC) is an aggressive form of breast cancer (BC) with a poor prognosis. Second, patients cannot benefit from targeted therapy, except for those with BRCA1/2 mutations, for whom poly (ADP-ribose) polymerase (PARP) inhibition therapy using olaparib has recently been approved. As global priorities continue to be epidemiological analysis of BC risk factors and early diagnosis, this review focuses on the risks and protective factors associated with TNBC. A PubMed keyword search for new knowledge on the risks and protective factors for TNBC was carried out. We also found statistical information from current online databases concerning the estimated incidence, prevalence and mortality worldwide of this cancer. Traditional risk factors for BC and TNBC are those related to reproduction such as the age of menarche, age of first birth, parity, breastfeeding and age at menopause. Attention needs to be paid to familial BC, weight control, alcohol consumption and regular physical activity. Epidemiological studies on TNBC provide evidence for protective factors such as regular consumption of soya, seafood, green tea, folic acid and vitamin D. Potential risk factors may include night work and viral infectious agents like human papillomavirus (HPV) and Epstein-Barr virus (EBV). Droplet digital methylation-specific PCR (ddMSP) is a possible new screening method for detection of BC including TNBC. Further research is necessary to validate these new factors.

Mismatch repair single nucleotide polymorphisms and thyroid cancer susceptibility

Thyroid cancer (TC) is the most common endocrine malignancy and its incidence continues to rise worldwide. Ionizing radiation exposure is the best established etiological factor. Heritability is high; however, despite valuable contribution from recent genome-wide association studies, the current understanding of genetic susceptibility to TC remains limited. Several studies suggest that altered function or expression of the DNA mismatch repair (MMR) system may contribute to TC pathogenesis. Therefore, the present study aimed to evaluate the potential role of a panel of MMR single nucleotide polymorphisms (SNPs) on the individual susceptibility to well-differentiated TC (DTC). A case-control study was performed involving 106 DTC patients and 212 age- and gender-matched controls, who were all Caucasian Portuguese. Six SNPs present in distinct MMR genes (MLH1 rs1799977, MSH3 rs26279, MSH4 rs5745325, PMS1 rs5742933, MLH3 rs175080 and MSH6 rs1042821) were genotyped through TaqMan^® assays and genotype-associated risk estimates were calculated. An increased risk was observed in MSH6 rs1042821 variant homozygotes [adjusted odds ratio (OR)=3.42, 95% CI: 1.04-11.24, P=0.04, under the co-dominant model; adjusted OR=3.84, 95% CI: 1.18-12.44, P=0.03, under the recessive model]. The association was especially evident for the follicular histotype and female sex. The association was also apparent when MSH6 was analysed in combination with other MMR SNPs such as MSH3 rs26279. Interestingly, two other SNP combinations, both containing the MSH6 heterozygous genotype, were associated with a risk reduction, suggesting a protective effect for these genotype combinations. These data support the idea that MMR SNPs such as MSH6 rs1042821, alone or in combination, may contribute to DTC susceptibility. This is coherent with the limited evidence available. Nevertheless, further studies are needed to validate these findings and to establish the usefulness of these SNPs as genetic susceptibility biomarkers for DTC so that, in the near future, cancer prevention policies may be optimized under a personalized medicine perspective.

Multi-omic approach decodes paradoxes of the triple-negative breast cancer: lessons for predictive, preventive and personalised medicine

Breast cancer epidemic in the early twenty-first century results in around two million new cases and half-a-million of the disease-related deaths registered annually worldwide. A particularly dramatic situation is attributed to some specific patient subgroups such as the triple-negative breast cancer (TNBC). TNBC is a particularly aggressive type of breast cancer lacking clear diagnostic approach and targeted therapies. Consequently, more than 50% of the TNBC patients die of the metastatic BC within the first 6 months of the diagnosis. In the current study we have hypothesised that multi-omic approach utilising blood samples may lead to discovery of a unique molecular signature of the TNBC subtype. The results achieved demonstrate, indeed, multi-omics as highly promising approach that could be of great clinical utility for development of predictive diagnosis, targeted prevention and treatments tailored to the person-overall advancing the management of the TNBC.

Dietary Patterns for Women With Triple-negative Breast Cancer and Dense Breasts

Triple-negative breast cancer (TNBC) is a common subtype of breast cancer among women with dense breasts and is associated with a poor prognosis. Diet is a modifiable risk factor for breast cancer, but the association between the risk of TNBC and diet has not been studied. The present study investigated the hypothesis that a healthy dietary pattern was negatively associated with risk of TNBC in women with dense breasts (density types 3 and 4). After total mastectomy or breast conserving surgery, patients with TNBC (n = 38) and non-TNBC (n = 178) were recruited. The risk of TNBC was negatively associated with a healthy dietary pattern involving consumption of seafood and vegetables, and positively associated with a dietary pattern of consuming grains, meats, and eggs. Additionally, intake of animal fat, eggs, and meat was positively associated with the risk of TNBC, but intake of vegetable fats, nuts, and vegetables showed a negative association. Patients with TNBC had higher proportion of obesity or abdominal obesity than those with non-TNBC. The present study is the first to show a negative association between risk of TNBC and a healthy dietary pattern in women with dense breasts and suggests the importance of diet in the prevention of TNBC.

Reducing Breast Cancer Recurrence: The Role of Dietary Polyphenolics

Evidence from numerous observational and clinical studies suggest that polyphenolic phytochemicals such as phenolic acids in olive oil, flavonols in tea, chocolate and grapes, and isoflavones in soy products reduce the risk of breast cancer. A dietary food pattern naturally rich in polyphenols is the Mediterranean diet and evidence suggests those of Mediterranean descent have a lower breast cancer incidence. Whilst dietary polyphenols have been the subject of breast cancer risk-reduction, this review will focus on the clinical effects of polyphenols on reducing recurrence. Overall, we recommend breast cancer patients consume a diet naturally high in flavonol polyphenols including tea, vegetables (onion, broccoli), and fruit (apples, citrus). At least five servings of vegetables and fruit daily appear protective. Moderate soy protein consumption (5-10 g daily) and the Mediterranean dietary pattern show the most promise for breast cancer patients. In this review, we present an overview of clinical trials on supplementary polyphenols of dietary patterns rich in polyphenols on breast cancer recurrence, mechanistic data, and novel delivery systems currently being researched.

The Non-Linear Child: Ontogeny, Isoniazid Concentration, and NAT2 Genotype Modulate Enzyme Reaction Kinetics and Metabolism

N-acetyltransferase 2 (NAT2) catalyzes the acetylation of isoniazid to N-acetylisoniazid. NAT2 polymorphism explains 88% of isoniazid clearance variability in adults. We examined the effects of clinical and genetic factors on Michaelis-Menten reaction kinetic constants of maximum velocity (V_max) and affinity (K_m) in children 0–10 years old. We measured the rates of isoniazid elimination and N-acetylisoniazid production in the blood of 30 children. Since maturation effects could be non-linear, we utilized a pharmacometric approach and the artificial intelligence method, multivariate adaptive regression splines (MARS), to identify factors predicting NAT2 V_max and K_m by examining clinical, genetic, and laboratory factors in toto. Isoniazid concentration predicted both V_max and K_m and superseded the contribution of NAT2 genotype. Age non-linearly modified the NAT2 genotype contribution until maturation at ≥ 5.3 years. Thus, enzyme efficiency was constrained by substrate concentration, genes, and age. Since MARS output is in the form of basis functions and equations, it allows multiscale systems modeling from the level of cellular chemical reactions to whole body physiological parameters, by automatic selection of significant predictors by the algorithm.

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We identified the NAT2 K_m and V_max in children treated with isoniazid.

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Artificial intelligence (AI) algorithms were used to find predictors of K_m and V_max.

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Isoniazid concentration affected V_max and K_m, and superseded NAT2 genotype.

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Age non-linearly modified NAT2 genotype contribution until maturation at ≥ 5.3 years.

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AI output is in the form of equations that allow multiscale systems modeling.

The effects of maturation on drug metabolism have not been studied for the type phase II enzymes such as NAT2, which metabolizes the drug isoniazid. Genes have been found to control speed of isoniazid metabolism. Studies to characterize affinity and maximum velocity for isoniazid metabolism in people were last performed in two individuals' livers in the 1960s. We identified NAT2 affinity and maximum velocity in 30 tuberculosis children treated with isoniazid. Artificial intelligence methods found that metabolism was affected by the drug's concentration more than by genes, which were affected by age up to 5.3 years.

Correlation between polymorphisms in DNA mismatch repair genes and the risk of primary hepatocellular carcinoma for the Han population in northern China

PURPOSE

This study investigated correlations between polymorphisms in DNA mismatch repair (MMR) genes and the risk of primary hepatocellular carcinoma (PHC).

METHODS

Single nucleotide polymorphisms (SNPs) in the DNA MMR genes MLH3 (rs175080), PMS1 (rs5742933), PMS2 (rs1059060), MSH3 (rs26279), MSH5 (rs1150793, rs2075789) and MSH6 (rs1042821) were detected using the SNaPshot method in 250 PHC cases and in 308 patients without PHC in the Han population in northern China.

RESULTS

The AA genotype in MLH3 (rs175080) increased the risk of PHC (odds ratio [OR] = 3.424; 95% confidence interval [CI]: 1.097-10.689). The AG and GG genotypes in MSH3 (rs26279) increased the risk of PHC (OR: 1.644 and 3.300; 95% CI: 1.112-2.428 and 1.765-6.168, respectively). The AA genotype in MSH5 (rs2075789) increased the risk of PHC (OR: 9.229; 95% CI: 1.174-72.535). The CT genotype in MSH6 (rs1042821) reduced the risk of PHC (OR: 0.629; 95% CI: 0.428-0.924).

CONCLUSIONS

Our study suggests that polymorphisms in MLH3 (rs175080), MSH3 (rs26279), MSH5 (rs2075789) and MSH6 (rs1042821) may be independent risk factors for PHC.

Nutritional epidemiology--there's life in the old dog yet!

Consideration is given to the idea that the nutritional epidemiology of cancer is dead, as some in the media have claimed. The basis for the claim does not lie in science nor has anyone with relevant knowledge made such a statement-although that, too, has been claimed. Evidence is adduced for the importance of past achievements of nutritional epidemiology. Attention is similarly drawn to recent contributions. In particular, I note the state of play of cancer and plant foods, fat and breast cancer, meat and cancer, vegetarians, intervention studies, migrant studies, and westernization of diet and lifestyle. Some next steps and some currently important questions are outlined.